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Installation Guide for Schrödinger Software Release

1. file hostsfile The hosts file to use Default is to use the hosts file that would normally be used for jobs as defined in Section 2 3 5 of the Job Control Guide testall Run a test job for all entries in the hosts file This is the default notest namelist Comma separated list of host names on which test jobs should nor be launched The list must be composed of values for the name entry in the hosts file Jobs are launched for all entries in the hosts file other than those listed with this option test namelist Comma separated list of host names on which to launch test jobs The list must be composed of values for the name entry in the hosts file Default is to launch jobs on all entries in the hosts file Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Table 7 2 Options for the installation check command Continued Option Description nojobs time duration license Do not run any test jobs just report errors in the hosts file Test application testapp job duration in seconds Default is 20 sec Have testapp check out an MMLIBS license This is used to test the license checkout mechanism In addition to output to the terminal the following output is generated a summary jobname summary a directory jobname and a gzipped tar file jobname tarball that contains the contents of the directory and the summary The extension is nonstandard so that this file can be mailed t
2. You should see a single line of output reporting the date on the remote host If you are prompted for a password the setup has not been done correctly You should review the steps above to ensure that you have completed them all especially the permissions 7 2 2 Setting Up Access from a Windows Host to Linux or Mac Hosts On Windows passwordless SSH is handled using plink exe which is provided in the Schr dinger software distribution To set up passwordless SSH you can use the Remote Login Configuration tool to guide you through the process which involves generating and saving keys then configuring your remote hosts This application is available from the Start menu under Schrodinger 2014 2 You can also run the setup process manually see the instructions in Appendix F Before you start you should ensure that your hosts file schrodinger hosts contains settings for all the hosts that you want to use This file is used in the second stage of the setup The schrodinger hosts file used is the first one found in the following locations The startup directory of the configuration tool e USERPROFILE Schrodinger e The installation SSCHRODINGERS If you want to use aschrodinger hosts file from a particular directory right click on the shortcut for the configuration tool and change the Start in directory The first panel is labeled Remote Access Setup A summary of the steps is given in the panel these steps are given in de
3. 7 1 10 The base Setting The base setting can be used to specify settings that are common to a number of entries without having to duplicate them for each entry For example on a queue host you might have several queues with different characteristics but all have the same host name queuing soft ware software installation and scratch directory You could use the base setting as follows Base setting for clusterl name clusterl host clusterl schrodinger clusterl schrodinger schrodinger2014 queue SGE tmpdir var tmp Small queue on clusterl name smalll base clusterl processors 16 Medium queue on clusterl name mediuml base clusterl processors 64 Large queue on clusterl name largel base clusterl processors 256 7 1 11 The securezone Entry To facilitate secure access to a queueing system on a cluster Job Control uses an SSH tunnel by default for information and file transfer between the job submission host and the queue host usually the head node of a cluster If you do not want to use this mechanism you can create secure zones with one or more securezone entries These entries are global and not part of a host entry A securezone entry defines a set of machines that have secure access to each other e g they are all behind a particular firewall Within a secure zone Job Control uses its normal mechanism of opening a port socket connection for file transfer between the submission
4. Indexing these databases causes severe performance issues so you should turn off indexing of this directory before starting the installation 4 Open System Preferences and click on Spotlight 5 In the Privacy tab add the location that you chose for the third party software above Now you can perform the installation 6 In the terminal window run the following commands SCHRODINGER utilities update BLASTDB SCHRODINGER utilities rsync_pdb Due to the size of these databases the commands may take some time to run If you want to use PSIPRED you must compile it in a terminal window using the Linux instructions in Section 3 7 on page 21 To do so you must have XCode installed including the command line tools Preferences gt Downloads gt Command Line Tools in XCode and click Install The command line tools require an Apple Developer account 5 3 Uninstalling Schrodinger Software Schr dinger software comes with an application for uninstalling the software This application performs all the necessary actions to completely remove the software from your Mac You should not use any other method for uninstallation To uninstall Schr dinger software 1 Double click the Uninstall command application This application is in the Schr dingerSuite2014 2 folder in the Applications folder You can also use the copy of this application in the original dmg package that you used to install the software You are prompted to confir
5. SPSP_BLASTDB e SSCHRODINGER_THIRDPARTY database blast e SSCHRODINGER thirdparty database blast Likewise the PDB is installed in the first location found in the following list SSCHRODINGER_ PDB e SSCHRODINGER_THIRDPARTY database pdb e SSCHRODINGER thirdparty database pdb If an environment variable in these lists is not defined the list item is skipped The environ ment variables are described in Section 2 4 on page 11 To compile and install PSIPRED 1 Create a directory in which to download and build PSIPRED This directory will be referred to as the build directory and labeled build dir 2 Download psipred261 tar gz into the build directory from the PSIPRED download site at http bioinfadmin cs ucl ac uk downloads psipred old psipred261 tar gz If this location changes the PSIPRED home page is located at http bioinf cs ucl ac uk psipred and contains information about the program referrals to terms of use and license terms in the README file and a link to download the program The link to download PSIPRED is in the section of the page labeled Software Download You must download version 2 61 to work with Prime 3 6 3 Change to the build directory and unpack the source code cd build dir tar xzvf psipred261 tar gz 4 Compile the code cd src make make install cd Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux 5 Create a directory in SCHRODINGER for
6. 3 7 Installing Prime Third Party Software and Databases from a Download 21 3 8 Installing VMD for DeSMONG cece cece eeeeeeceeeeeeaeeaesaeeeeeeeeaeeaetaeeaeeeteaes 23 3 9 Setting Up Access to PyMOL s ss ssesoswsvsss ssrssonsvossssvsrornsvssspsenssonev nsrsvsrsenessssinsn 25 3 10 Uninstalling the Software 42404nsnnnnnnnennennnnnnnnnnnennnnnennnnnnnnnnnnn 25 Chapter 4 Installing the Products on WiNCIOWS e seememmsmsmssmsmmn 27 4 1 Installing Schr dinger Software smusssssssesessserersssrrrererrrrsrsrrrssssrr senere renarna nro nana 27 411 Prepanng Torn Stall tl l ssni ETR 27 41 2 Installation NOTES isss 28 4 1 3 Installing From the DOS Command Line urrssrssnnsnnnnsnnnnnnnennnnnnnnnnnnnn nen 30 41 4 MOUDIESN OOM F nennen 32 4 2 Installing Prime Third Party Software and Databases 33 4 3 Setting Up Access to PyYMOL sssesusssssussssssusvesersnns ssn sssnssunsoseiesersnns sensrsenensnonnns 35 4 4 Uninstalling Schrodinger Software nnnenennnennennennnnnnnennnnnn 36 Chapter 5 Installing the Products on a Mac 37 5 1 Installing Schr dinger Software smnnnnnnnnnenennennnnnennnnennnnnnnnn 37 5 2 Installing Prime Third Party Databases 4mrnnneenne nennen 37 5 3 Uninstalling Schrodinger Software ennnnennnennnnennnnnnnennnnnn 38 Schr dinger
7. A 2 1 Windows Vista and Windows 7 To open the Environment Variables dialog box 1 Click Start then click Control Panel The Control Panel opens 2 Click User Accounts 3 Click User Accounts again 4 In the Task side pane on the left click Change my environment variables The Environment Variables dialog box opens Installation Guide 97 Appendix A Setting Environment Variables 98 To create a new environment variable 1 In the User variables section click New The New User Variable dialog box opens 2 Enter the name of the variable and its value and click OK The New User Variable dialog box closes and the variable is added to the User variables section of the Environment Variables dialog box 3 Click OK in the Environment Variables dialog box To modify an existing environment variable 4 In the User variables section select the environment variable you want to modify 5 Click Edit The Edit User Variable dialog box opens 6 Change the value of the variable and click OK The Edit User Variable dialog box closes and the variable is updated in the User variables section of the Environment Variables dialog box When you have finished creating or editing environment variables click OK in the Environ ment Variables dialog box to save the values You can then close the Control Panel A 2 2 Windows XP To open the Environment Variables dialog box 1 Right click on My Computer and choose Properties
8. The system must be configured to allow unlimited locked memory You must do at least the following a Add the following lines to etc security limits conf on all nodes soft memlock unlimited hard memlock unlimited b Add the following lines to the appropriate startup scripts csh tesh limit memorylocked unlimited bash ksh ulimit 1 unlimited Installation Guide 9 Chapter 2 Hardware and Software Requirements 10 You should do this in one of the following locations e etc init d sshd e etc profile bash and etc csh cshrc csh tcsh SHOME bashrc bash or HOME cshrc csh tcsh You should also add these lines to the startup scripts for the resource manager dae mons for the Torque PBS LSF queuing systems This is necessary because the limit may be reset to a lower number by some boot procedures or resource managers might not start with unlimited locked memory When you have added these lines you must restart the resource management daemon 2 3 1 2 Graphics Processors GPUs Desmond can be run in parallel on GPGPUs with CUDA See Section 2 1 1 3 on page 6 for the supported graphics cards 2 3 2 Jaguar 8 4 1 GB scratch disk space minimum per process is recommended Large jobs such as frequency and LMP calculations can use several gigabytes of scratch disk space Use local disks for scratch space Performance is significantly reduced if an NFS mounted scratch disk is used Jaguar
9. Card and Monet zus ea 5 2 1 1 3 GPGPU COMPUTING iiss een 6 2 1 1 4 Gl sters 2 2n hend 6 21 2 AAU Hear een 6 2 1153 NVIMEOW SE es ei ee ersehen 7 23A MAG sc ani dar seine sedel le ade nee ne ea ee rer 8 2 1 5 Queleing Systems uassnemneunaniein ana ae 8 2 2 Disk Space for Installation 4n04ennnnnennnnennnnnnenennennnnnnnnnnnennnan 8 2 3 PIOQUEL N T Sr u een aan 9 Oe TDS SiON HE gt 1 ARE ERMREEUE REN a EEE EFEHEFESCERE ONA 9 2 3 1 1 Networks 9 2 3 1 2 Graphics Processors GP US usa HH 10 23 2 Jagar oM ine 10 2 3 3 KNIMEEXtensi ns2 Deere 10 2 3 4 MEPROF 3A Eine ee A 11 2 39 89 mE RE Oase eier 11 2 4 Prime Third Party Software and Databases eennn 11 2 5 Documentation Requirement 44mnrneenen nennen nnnnneenennnnnen nennen nennen 13 Installation Guide Contents Chapter 3 Installing the Products on Linux 15 3 1 ACCESS to the Software 15 3 2 Verifying System Compliance 4nrnnnnnnennnnnnnnnnennnnnennnnnnnnnnnnn 16 3 3 Installing the Software and Documentation nnennn 17 3 4 Setting the Environment Variables 4nnnnennnnennnnennnnnnnnn 19 3 5 Enabling Hardware Stereo Viewing nnnnennnennennennnnnnnnnnnnnn 20 3 6 Installing Script Center SCIIPtS sssssssessssrssossssrsrossrssssersrsorssrsossr renen nonan an 20
10. If a user setting is required the user should copy the hosts file to S HOME schrodinger Linux or Mac or Installation Guide Chapter 7 Preparing for Job Submission 54 SUSERPROFILE Schrodinger Windows on the job submission hosts and add the user settings to this copy 71 3 The tmpdir Setting The tmpdir setting specifies the scratch directory where temporary files can be written Examples are scr or temp The file system on which this directory is mounted should be large enough for the largest temporary files should be mounted locally and should be writable by the user The actual directory created for scratch files the job directory is tmpdir user name uniquename where tmpdir is the directory defined here and username is the user name If you do not specify tmpdir for a host the tmpdir setting from the localhost entry is used if there is one Otherwise the scratch directory is set to SHOME schrodinger tmp on Linux and Mac OS X and to LOCALAPPDATA Schrodinger tmp on Windows The use of the home file system for large temporary files is discouraged in most places so you should always ensure that tmpdir is defined for the hosts you run jobs on if the job requires temporary storage You can override the tmpdir setting in the schrodinger hosts file by setting the SCHRODINGER TMPDIR environment variable or using the TMPDIR command line option see Section 2 3 of the Job Control Guide for more information Fo
11. Schr dinger KNIME Extensions 2 0 SiteMap 3 1 Strike 2 6 and WaterMap 1 7 in addition to Field Based QSAR Induced Fit Docking Ligand amp Structure Based Descriptors Physics Based ADME Tox Quantum Polarized Ligand Docking and Virtual Screening Workflow Schr dinger software is supported on Linux platforms on Mac platforms and on Windows with a few exceptions In this manual the designation UNIX where a broader term is needed includes Linux If you have difficulty with the installation please contact your system manager or Schr dinger by phone at 503 299 1150 or by e mail at help schrodinger com 1 1 Linux Installation Process Summary This is a summary of the installation process For detailed instructions see the page number provided in each step 1 Check this guide for e System requirements page 5 e Disk space requirements page 8 e Product specific installation information page 9 2 Mount the DVD page 15 or download the software from the Schr dinger Support Cen ter If you download the software extract the downloaded tar file tar xvf Schrodinger Internet _Download tar 3 Run the platform script to verify that your machine meets the system requirements page 16 4 Run the INSTALL script to install the products page 17 5 Setthe SCHRODINGER and DISPLAY environment variables page 19 Installation Guide Chapter 1 Installation Notes 6 Obtain and install a licen
12. Schrodinger on Windows and edit it A user copy is necessary if the user has a different user name on any host on which Schr dinger products will be run You can also copy it to a location of your choice and set the SCHRODINGER_HOSTS environment variable to point to this file The hosts file consists of one or more entries each of which describes a configuration for running jobs on a given host Each entry consists of a number of settings one per line Default values for all hosts are taken from the localhost entry which defines the settings for the current host Settings are described in more detail in the following subsections Note If you are editing this file in your installation directory on Windows you should start the editor with administrator privilege for example by right clicking and choosing Run as Administrator Otherwise you will not be allowed to save the file Installation Guide 49 Chapter 7 Preparing for Job Submission 50 To add entries to the hosts file 1 Open the schrodinger hosts file in a text editor When the software is installed there is a copy of this file in the installation directory 2 Create or modify an entry for each remote host using the keywords in Table 7 1 e The syntax for the settings is keyword value e Keywords are case insensitive e Each entry must begin with a name setting e Comments can be included by beginning a line with a sign e Multiple entries can be included
13. Windows is available for Desmond and WaterMap The following operating systems are supported Both 32 bit and 64 bit Schr dinger executa bles are available e Windows 8 and 8 1 64 bit only classic desktop only e Windows 7 SP1 32 bit and 64 bit e Windows Vista SP2 32 bit and 64 bit e Windows Server 2012 2012 R2 64 bit only classic desktop only e Windows Server 2008 2008 R2 2012 2012 R2 64 bit only e Windows XP Home or Pro version SP3 32 bit only Note This is the last release in which Windows XP is supported Only the classic desktop is supported on Windows 8 x and Windows server 2012 Windows 7 support includes English French German Spanish and Japanese versions In addition the following software is required e Microsoft Visual Visual C 2010 SP1 Redistributable Package for both 32 bit x86 and 64 bit Maestro executables x64 This package is included with the software distribution and can be installed as needed You will be prompted to install it during installation if it is not already installed e The Maestro ActiveX control for PowerPoint requires NET 2 in addition to the Visual C Redistributable Package both for content creation and display NET 2 is provided with the installer for the ActiveX control PDF reader for display of manuals If Adobe Reader is installed a version no earlier than 7 0 5 is recommended Adobe Reader 8 0 is not supported Installation Guide 7 Chapter 2 Hardware
14. software such as the Environment Modules package found at http modules sourceforge net If you expect either long delays when a program tries to obtain a license token or competition between programs for license tokens you can set the time limit for trying to obtain a license token in the SCHRODINGER LICENSE RETRY environment variable This environment vari able can be set to time values such as 300s 10m 2h or to an integer value which is inter preted as a time in seconds The default is 10 minutes To use PYMOL from Maestro or Canvas you need to add the top level PYMOL directory to the PATH and PYMOL4MAESTRO environment variables To check that you have set the SCHRODINGER environment variable correctly start Maestro with the following command SSCHRODINGER maestro amp You can also set environment variables for the running of jobs for each host in the schrodinger hosts file See Section 7 1 on page 49 for more information Environment variables that are set in the hosts file are not used for running Maestro so they must be set in the shell or globally For a list of Schr dinger environment variables see Appendix B of the Job Control Guide 3 5 Enabling Hardware Stereo Viewing To run Maestro in hardware stereo mode you must edit etc X11 xorg conf to set the driver in stereo capable mode For information on the option that is required consult the documenta tion for your graphics card The required options for Nvi
15. 4 Turning On License Checking in Job Control The final step is to instruct Job Control to specify license requirements when submitting jobs to the queue This step must be completed after the steps above otherwise jobs submitted to the queue will fail because the license software will assume that the required licenses are not avail able 1 Open the file SSCHRODINGER queues queueing system config in a text editor where queueing system is SGE PBS or LSF 2 Change the LICENSE CHECKING line to read LICENSE CHECKING yes 3 Save the modified file and close the editor 7 5 Configuring Clusters The configuration of a cluster to run Schr dinger software must take into account the special issues of communication between the compute nodes the manager nodes and the job submis sion host and the impact that this communication might have on performance 7 5 1 Configuration Requirements Like any other host each compute node must have access to a license the software and the job related files The requirements can be stated as follows 1 Schr dinger software installations must be available to all hosts the job submission host the manager node and the compute nodes These installations must contain the same software versions but they could be in separate physical installations To reduce network traffic Schr dinger software should be installed either on each com pute node s local disk or on a file system that is accessible
16. 7 2 2 Setting Up Access from a Windows Host to Linux or Mac Hosts 62 7 2 3 Configuring the Firewall sisinio na EEA ann 63 7 2 3 1 Linuxand Mae Firewallss se ssenn een 63 2 32 Windows Elfewallsn nass Bin Ra NOISE ARA 63 7 3 Preparing for Batch Queue Submission snenennnnennnnnnnnnnn 64 7 3 1 Setting Up the Hosts File for Batch Queues numrsnsnnnesonnnnnnsnnnnnnnnnnnnnnnnn 65 7 3 2 Setting Up Access to a Queueing System pesisiran 66 7 3 3 Configuring Queuing Systems for Open MPI Parallel Execution 67 Installation Guide Contents vi 7 3 3 1 SGE COnmfQuratiOnes c4 cccc sesceteaisesd einen Banana 68 7 3 3 2 PBS Family Configuration eiaensneieigeneaa aan 70 7 3 3 3 LSF configuration 7 3 3 4 SLURM configuration 7 3 4 Configuring Queuing Systems for GPU Use nuunsnsssunssnnnannennnnnnnnnnnnnnnnnnnnn 74 7 4 Setting Up License Checking for Queueing Systems TT 7 4 1 Configuring License Checking for SGE Grid Engine s sssssssrsererrsrrssrrrssssnnn 77 7 4 1 1 Adding License AttribUt S ss 1sssisosssasssnbassovisdossnnsssnissdsesserdenissssessbnnerer 77 7 4 1 2 Configuring the Load Scripts sarisini niiatessa 78 1 4 1 3 InstallngitheiLoad Seript u neh aa 80 7 4 1 4 Turning On License Checking in Job Control uur 222244444nnnnn nennen nenn 81 7 4 2 Contiguring License Checking for LSF nee 81 7 4 2 1
17. Adding License Attributes s s ssssssssessrsss rsbensssrsosenskeber rnesenstenerseresansbesskera 81 7 4 2 2 Configuring the Load Script 82 7 4 2 3 Installngtheload Serpt 5 00 ende 83 7 4 2 4 Turning On License Checking in Job Control uuuessssnsnnensennnnnnnnnnnnnnne nn 84 7 4 3 Configuring License Checking for PBS Pro s sssssssssssss sssssssssssensessadsarssenso sesnsser 84 7 4 3 1 Adding LicenSe AttriBUt S sis 1sisssorisisisniasssnes ssseiersniss ssssinssn bes ssesiessn ds 84 7 4 3 2 Configuring the Load SChiptacci keakk Ree Rea RRS 85 7 4 3 3 Installing the Load Seript nrnna EAEN 86 7 4 3 4 Turning On License Checking in Job Control s ssssssssssrssrsrrsrsssrrsrssrsnrrnnrnnnn na 87 75 Contiguring Cl sters a2 87 7 5 1 Contiguration Requirements nassen ehe 87 7 5 2 Secure Channel Communication and Firewalls 7 5 3 Performance Optimization 7 6 Testing the Installations and Connections u neennn 90 7 6 1 The Diagnostics Pale s sissssssscssissirskisasosississkosssossssose ssssosisetesbiessrnssnisenisssnsine 90 7 0 2 Command Line Tools euere 92 Appendix A Setting Environment Variables ee 97 AST LMUR re ecient ieee br st A 97 A2 La OM Scns ee ii rererett reset reer eer terete errr ee 97 A 2 1 Windows Vista and Windows 7 sssmssesssrsrssrssersssersssrsssrrrssrssrrssrrrre rann rr ns nere arenan 97 Schr dinger Software Release 2014 2 Contents A22 Win
18. Install Available Software panel opens If you already have the Base Chemistry Types and Nodes installed you can skip to Step 2 If you are not sure proceed with the next step to check From the Work with option menu choose the KNIME Update Site The URL for this site should begin with http www knime org There may be a delay while the list of extensions is loaded from the web site and the table shows Pending in the Name column next to the check box When the extensions are loaded they are dis played in the table with a tree structure so you can show and hide the individual extensions To check whether you have the required extensions installed ensure that Hide items that are already installed is selected then click the turner button for the KNIME amp Exten sions and KNIME Labs Extensions items to display the list of extensions Ensure that KNIME amp Extensions and KNIME Labs Extensions are checked Checking these items selects all the extensions for these items which you can verify by expanding the tree These extensions include more than the Base Chemistry Types and Nodes but it can be useful to install them all Click Next The Install Details screen is displayed listing the extensions you selected Click Next License agreements are displayed Accept the license agreements and click Next The extensions are installed This may take some time When the installation finishes a dialog box informs you th
19. Software Release 2014 2 Chapter 2 Hardware and Software Requirements Note On Windows a copy of the entire installation is kept for backup and repair You must therefore have the space locally to store a copy of the entire installation in addition to the space for the installed software on the drive to which you are installing space for the download if relevant and for the unpacked MSI files This may mean you need up to 4 times the disk space listed above to perform the installation 2 3 Product Notes This section contains notes specific to each product These notes give information in addition to the requirements listed above Only external software dependencies are listed below Licenses must be obtained for each installed product 2 3 1 Desmond 3 8 Only 64 bit x86_64 executables are available for Desmond Desmond can be run in parallel using Open MPI The mmshare distribution includes Open MPI 1 6 5 for parallel execution Desmond does not support other MPI implementations such as MPICH Parallel execution is supported on SMP hosts as well as clusters 2 3 1 1 Network A high performance network is highly recommended for parallel execution Desmond supports the use of ethernet and Infiniband networks for parallel execution Use of Infiniband requires a Linux kernel no earlier than 2 6 9 and OFED 1 2 Myrinet is not supported If you are using an Infiniband network the following installation issues must be addressed
20. Software Release 2014 2 Contents Chapter 6 Installing and Updating KNIME Extensions 41 6 1 Installing into an Existing Version Of KNIME s ssnssssrsssssssssssrrsssssresssssnssesnrn en aana 41 6 2 Updating Existing Schr dinger Extensions msmsssesessseserssssereseserrresrrrnsnnnrnn anna 45 6 3 Adding New Schr dinger Extensions nnnnnenennennennnnnnnnnn 46 6 4 Installing Knime Workflows ssssmsnssssrsssersrssesesrssssesrsesssrssssrsrers sn esrer areas aren rn ass aan enn 47 6 5 Installing A Web Service for Node Execution nennennn 48 Chapter 7 Preparing for Job Submission 49 7 1 The H sts File eg 49 7 1 1 The name and host Setlings u 53 7 1 2 Theuser Selling ac 53 7 1 3 The tmpdit Seting 22 Haan 54 7 1 4 The processors and processors per node Settings 24u44s40nnnnnnen nen 54 TADS The parallel Setting ssss4u sms aan 55 7 1 6 TSO OPUS STUNG soi re E S essens ena dosen iron ser 55 7 1 2 Ineschredinger Selling Hasena ee 55 FAB Theienv SOMN Gecis hinisna oasia hoiii 56 TAS Theilnelude Seting erse E regen 7 1 10 The base Setting 7 1 11 The securezone Entry 7 1 12 Customizing the Hosts File 7 2 Setting Up Access to Remote HOStS ssssesesososeroroserssososersserrsesnrrsrsnn erna nen 60 7 2 1 Setting Up Access To and From Linux and Mac Hosts ssssrresssrrorrssssrrsrrsnnn 60
21. The syntax is SSCHRODINGER utilities licutil lsfconf f license file The f license file option is not required if your license file is in the default location SCHRODINGER license or if it is already specified by one of the environment variables SCHROD LICENSE FILE or LM LICENSE FILE If you want to query the server directly you must not use the f option and the environment variable you use must be set to the server location Note If you specify multiple servers only the first is queried Licenses on other servers will therefore not be used The output from licutil should consist of lines like the following Copy the text between the dashed lines below into the Resource section of your lsf shared file Don t however copy the RESOURCENAME line below if there s already such a line there RESOURCENAME TYPE INTERVAL INCREASING DESCRIPTION IMPACT MAIN Numeric 10 N IMPACT MAIN license MMLIBS Numeric 10 N MMLIBS license Copy the text between the dahsed lines below into the Parameters section of your lsf cluster lt your_cluster_name gt file Installation Guide Chapter 7 Preparing for Job Submission 82 Copy the text between the dahsed lines below into the ResourceMap section of your lsf cluster lt your_cluster_name gt file Don t however copy the RESOURCENAME line below if there s already such a line there RESOURCENAME LOCATION IMPACT MAIN all MMLIBS all In the first and third par
22. access to a supported queueing system edit the config file and set the QPATH keyword to the path to the queueing software You should not need to edit any of the other files as they are already tailored to the specific queueing system As an example SCHRODINGER queues PBS config contains the settings QPATH usr local pbs bin QSUB qsub QDEL qdel QSTAT qstat If you need to set up the environment for the queuing system you can set the QPROFILE keyword to the absolute path on the queue host of a configuration file This file will be sourced to set up the environment to use the queue This variable is useful for setting up an environment for the queuing system that does not affect the global environment If you want to set up support for an unsupported queueing system or change the configuration for a supported queueing system you can do so with the instructions in Appendix E 7 3 3 Configuring Queuing Systems for Open MPI Parallel Execution Desmond Impact and Jaguar parallel execution use Open MPI 1 6 5 and can operate with a number of queuing systems Open MPI provides tight integration that is compatible with many queuing systems via the PLS Process Launch Subsystem and RAS Resource Allocation Subsystem components Loose integration in which the queuing system is only responsible for allocating resources and dispatching the jobs is also possible Instructions and requirements for the supported queuing systems are listed in t
23. be config ured so that it can find the license file and the FLEXIm utility that it uses to query the license server It can also be configured to reserve licenses for non queue use 3 This script must be installed in the appropriate queueing system directory 4 The Schr dinger Job Control system must be configured to specify license requirements when launching jobs Each of these steps is described in detail in the sections below for each of the three queueing systems that support license checking 7 4 1 Configuring License Checking for SGE Grid Engine 7 4 1 1 Adding License Attributes A resource attribute representing each license must be defined in the queueing system configu ration The utility licutil can be used to parse your license file or query the license server and generate the configuration text that needs to be added to the queueing system configuration files The syntax is SSCHRODINGER utilities licutil sgeconf f license file The f license file option is not required if your license file is in the default location SCHRODINGER license or if it is already specified by one of the environment variables SCHROD LICENSE FILE or LM LICENSE FILE If you want to query the server directly you must not use the option and the environment variable you use must be set to the server location Note If you specify multiple servers only the first is queried Licenses on other servers will therefore not be used Inst
24. close the editor 6 Verify that the script is configured properly by entering the following command perl SCHRODINGER utilities pbs lic sensor pl MMLIBS The script should print a single number which is the number of available licenses of the type specified as the command line argument You can replace MMLIBS with any other license type If you test the script before and after specifying reserved licenses you should see the number of licenses reported decrease by the specified percentage The log output from the script is sent to the system logging facility syslog so you can examine the syslog to find information about the actions performed by the script More verbose information is sent to the logfile which is set manually and optionally inside the script 7 4 3 3 Installing the Load Script The location of the load sensor script pbs lic_sensor pl is specified in the sched priv sched config file see Section 7 4 3 2 on page 85 The configuration produced by licutil points to the location of this script within the Schr dinger installation Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission SCHRODINGER utilities pbs lic sensor pl If this location is acceptable no further action is necessary If the script needs to be installed elsewhere you must copy it to the required location and edit each line of sched_priv sched_config that refers to the script and replace the path with the new path 7 4 3
25. disabled_lib openmpi To use the Torque queuing system you should copy those components to the standard location cd S SCHRODINGER mmshare vversion 1lib arch openmpi disabled_lib openmpi cp rf mca_plm tm la mca_plm tm so mca ras tm la mca ras tm so SCHRODINGER mmshare vversion 1ib arch openmpi 1lib openmpi Note If you are currently running multiple queuing systems from the same installation you may need to create two installations one with these changes and one without them The bundled Torque components depend on the libtorque so 2 library from Torque 2 2 1 If you do not have a compatible libtorque so 2 library on your system you may also need to copy it cd S SCHRODINGER mmshare vversion lib arch openmpi disabled_lib cp libtorque so 2 SCHRODINGER mmshare vversion lib arch openmpi lib Here are some examples of host file entries Request NPROC processors on a single node Name label Queue Torque Qargs q Torque queue 1 nodes 1 ppn NPROC Host submit node Processors processors in queue Installation Guide 71 Chapter 7 Preparing for Job Submission 72 Request NPROC processors one on each node Name label Queue Torque Qargs q Torque queue 1 nodes NPROC ppn 1 Host submit node Processors processors in queue Request NPROC processors spread across nodes 2 cores per node Name label Queue Torque Qargs q Torque queue 1 nodes NPROC 2 ppn 2 Host submit node Processors
26. editor to edit the file SCHRODINGER utilities flexlm_sensor pl 2 Edit the line beginning my LICENSE so that the full path to the license file is between the quotation marks my SLICENSE full path to license file Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission You can specify the license server instead of the license file as follows my LICENSE license server or my SLICENSE port license server The backslash is necessary as Perl interprets as a special character 3 Edit the line beginning my LMUTIL so that the full path to Imutil is between the quo tation marks my LMUTIL full path to Imutil 4 To reserve licenses for non queue use edit the line beginning my reserved to set the value to the fraction or percentage of licenses to reserve For example either of the fol lowing lines reserves 20 of the licenses for non queue use my reserved 0 2 my Sreserved 20 Il 5 Save the modified script and close the editor Follow the instructions below to verify that the script is configured properly If you test the script before and after specifying reserved licenses you should see the number of licenses reported decrease by the specified percentage 1 Enter the following command perl SCHRODINGER utilities flexlm sensor pl 2 Press the ENTER key You should get a block of output like begin global IMPACT_MAIN 20 global MMLIBS 20 end showing the nu
27. for a given host with different settings e g differ ent scratch directories e Entries for batch queue submission including queues on clusters must specify a temporary directory that is available on all compute nodes and is writable by all valid users This directory can be on a common file system shared by the nodes or it can be identically named local storage space on each node e Individual nodes in a cluster must be included unless they are only used as part of a properly configured batch system e If the host has a batch queueing system you can add settings for the batch queue see Section 7 3 on page 64 for more information 3 Save and close the file You can test the connections to the hosts in the schrodinger hosts file by using the Diag nostics panel described in Section 7 6 1 on page 90 or the installation_check command described in Section 7 6 on page 90 Table 7 1 Keywords for schrodinger hosts file settings Keyword Description base Name of an entry the base entry that is the basis for the current entry All the keywords from the base entry are inherited by the current entry and new keywords may be added in any order A base entry can include another base entry env Environment variables to be set on the host The syntax for the environ ment variables is variable value regardless of the shell used List each environment variable on a separate env line gpgpu Specify a graphics processor GPU t
28. name and host settings to specify a batch queue name and the host on which the batch system is available The name setting must not contain spaces The host name does not need to be the fully qualified domain name it can be any name that can be resolved by the domain name server DNS You will probably need the full name if the host on which you plan to run the execution host is not on the same local network as the host from which you plan to submit jobs the submission or launch host For a hosts file on Windows you must use a name for the host that you used when setting up remote access see Section 7 2 2 The value localhost is a special name setting that means the host from which the job was submitted In addition to this function the settings for the localhost entry are used as the default values for all other entries In the schrodinger hosts file example above the host entries ahost and bhost inherit the schrodinger setting from the localhost entry If you run jobs from the command line the name setting is what you should use with the HOST option to select the hosts to run the job 7 1 2 The user Setting If you have different user names on the submission and execution hosts you can include a user setting for the execution host in the hosts file on the submission host The user setting should never be added to entries in the hosts file in the installation directory because this would prevent other users from using those entries
29. processors in queue Parallel Jaguar Hybrid OpenMPI OpenMP Request NPROC total threads with TPP threads per node Name label Queue Torque Qargs q Torque queue 1 nodes NPROC TPP ppn TPP Host submit node Processors processors in queue 7 3 3 3 LSF configuration Loose integration for LSF should work without change Tight integration is supported by LSF from version 7 0 2 on Some examples are given below To simply select SNPROC processors qargs q queue_name n NPROC To tile the job across several nodes using exactly 8 processors per node gargs q queue name n NPROC R span ptile 8 Here are some examples of host file entries Request NPROC processors with an arbitrary cpu topology Name label Queue LSF Qargs q LSF queue n NPROC Host submit node Processors processors in queue Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Request NPROC processors spread evenly over two nodes Name label Queue LSF Qargs q LSF queue n NPROC R span hosts 2 Host submit node Processors processors in queue Request NPROC processors spread across nodes using 2 cores per node Name label Queue LSF Qargs q LSF queue n NPROC R span ptile 2 Host submit node Processors processors in queue Parallel Jaguar Hybrid OpenMPI OpenMP Request NPROC total threads with STPP threads per node Name label Queu
30. provided that queries the FLEXIm license server and reports the number of tokens available for each license in a format that the queueing software can understand To make sure the 1mutil utility and license file can be found when the script is run by the queueing soft ware you need to add the locations of the program and the license file to the script by editing the configuration section at the top of the script You must have permission to change this file Installation Guide 85 Chapter 7 Preparing for Job Submission 86 1 Use a text editor to edit the file SSCHRODINGER utilities pbs lic sensor pl 2 Edit the line beginning my LICENSE so that the full path to the license is between the quotation marks my SLICENSE full path to license file You can specify the license server instead of the license file as follows my SLICENSE license server or my SLICENSE port license server The backslash is necessary as Perl interprets as a special character 3 Edit the line beginning my LMUTIL so that the full path to Imutil is between the quo tation marks my SLMUTIL full path to lmutil 4 To reserve licenses for non queue use edit the line beginning my reserved to set the value to the fraction or percentage of licenses to reserve For example either of the fol lowing lines reserves 20 of the licenses for non queue use my reserved 0 2 my reserved 20 5 Save the modified script and
31. server_priv resourcedef file IMPACT MAIN type long MMLIBS type long Add the text between the dashed lines below to the value of the resources parameter in your lt PBS HOME gt sched_priv sched_config file E g if the resources line in the file was resources ncpus mem arch and the text between the lines was featurel feature3 feature5 then the new resources line should be resources ncpus mem arch featurel feature3 feature5 Copy the text between the dashed lines below into your lt PBS_HOME gt sched_priv sched_config file server dyn res IMPACT MAIN usr bin schro09 utilities pbs lic sensor pl IMPACT MAIN server dyn res MMLIBS usr bin schro09 utilities pbs lic sensor pl MMLIBS In the first and third parts of this output there should be one line for each license in your license file in the second part one word for each license To add the new license attributes follow the instructions in the output The files that you need to modify are PBS HOME server priv resourcedef and PBS HOME sched_ priv sched config where PBS HOME is the PBS home directory often something like var spool PBS on the head node of your cluster For the changes to take effect you must restart PBS The command for doing this is typically the following etc init d pbs restart Refer to your PBS Administrator Guide for more information about restarting PBS 7 4 3 2 Configuring the Load Script A script is
32. the software if it does not already exist mkdir p SCHRODINGER thirdparty bin Linux x86 64 psipred 6 Copy the bin and data directories from the build directory cp r bin SCHRODINGER thirdparty bin Linux x86 64 psipred cp r data SCHRODINGER thirdparty bin Linux x86 64 psipred 7 Check the final layout ls R SCHRODINGER thirdparty bin Linux x86 64 psipred The layout should look as follows bin data bin pfilt psipass2 psipred seq2mtx data weights dat weights dat3 weights p2 dat weights _s dat2 weights dat2 weights dat4 weights s dat weights s dat3 3 8 Installing VMD for Desmond To download VMD 1 Go to the following web site http www ks uiuc edu Development Download download cgi PackageName VMD 2 In the section Version 1 8 7 2009 08 01 Platforms click on LINUX OpenGL CUDA or on LINUX_64 OpenGL CUDA The choice depends on whether you want to use the 32 bit version or the 64 bit version When you click on the link a login page is displayed If you do not already have an account you can request one from this page and then log in When you have logged in the download starts 3 Choose a location to download the tar file vmd 1 8 7 bin LINUX opengl tar gz To install and configure VMD 1 Change to the location of the tar file and extract it cd location of tar file tar zxv vmd 1 8 7 bin LINUX opengl tar gz Installation Guide 23 Chapter 3 Installing the Products on Linux 2
33. variable such as opt schrodinger2014 You can find out which environment variables have been set with the env command If you are setting the environment variable globally to use with applications use the commands given below The environment variables set by these commands are inherited by any shell or application OSX 10 6 10 7 Enter the following command defaults write MacOSX environment variable value To find out which environment variables have been set enter the following command defaults read MacOSX environment OSX 10 8 Enter the following command launchctl setenv variable value Installation Guide 100 Schr dinger Software Release 2014 2 Appendix B File and Resource Locations on Windows This appendix contains information on where various resources or files are kept on Windows These are relative to the standard application data location SAPPDATA local application data location LOCALAPPDATA and user location SUSERPROFILE whose definitions are listed below SUSERPROFILES is set to C Users username on Windows Vista and Windows 7 and to C Documents and Settings username on Windows XP SAPPDATAS is set to SUSERPROFILE AppData Roaming on Windows Vista and Windows 7 and SUSERPROFILE Application Data on Windows XP SLOCALAPPDATA is set to SUSERPROFILE AppData Local on Windows Vista and Windows 7 but is not set on Windows XP its equivalent is SUSERPROFILE Local Sett
34. web download and are available on the Prime DVD set They are installed by default The Pfam database is also installed by default as well as data required for web based BLAST searches PSIPRED is not included or required but is highly recommended Prime can obtain PDB files and run BLAST searches on the web or on a local database For web based searches the default Prime installation is sufficient For local database access the PDB and BLAST databases must be installed If you already have any of the third party products installed and want to use the existing instal lation rather than installing another copy you can do so by setting the appropriate environment variables which are described in Section 2 4 on page 11 Likewise if you want to install any of these products in a location other than the standard location in SCHRODINGER thirdparty you should use that location in the relevant steps below and set the appropriate environment variables The instructions below assume that you are installing into the standard location It is assumed that you have already installed the Prime software and set the SCHRODINGER environment variable Installation Guide 21 Chapter 3 Installing the Products on Linux To install the PDB and BLAST databases e Run the following scripts SCHRODINGER utilities update BLASTDB SSCHRODINGER utilities rsync_pdb The BLAST databases are installed in the first location found in the following list
35. you decide to use a different directory you will need to create it first The INSTALL script will not create it for you Also make sure each person who wants to run jobs has write access to the scratch directory 4 Confirm the information you provided When you have finished entering the information the INSTALL script summarizes your choices If any of the summary information is incorrect answer n at the prompt to run through the questions again Once you are satisfied with your answers press RETURN to install the software The installation can take some time Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux 5 Record the machid information When the installation is complete the INSTALL script runs the machid program which generates machine specific information about the computer on which it is run You will need this information to request a license for your Schr dinger software See http www schrodinger com licensing for full details on how to request a license 6 Remove temporary installation directories and files If you copied tar files onto a remote machine delete those files now Repeat this procedure for all locations where you want to use the software Once you have installed the software you must obtain a license to run it see http www schrodinger com licensing 3 4 Setting the Environment Variables Before you can launch Schr dinger software you must set
36. 4 2 Change to the VMD directory cd vmd 1 8 7 This directory contains a README file that has installation instructions These instruc tions are included in the following steps 3 Edit the configure file and set the values of the install bin dir and install library dir variables to the locations where you wish to install the VMD binary and its supporting libraries install bin dir is the location where the startup script vmd will be installed It should be set to a location in the path of anyone wanting to run VMD install library dir is the location of all other VMD files including the binaries and helper scripts It should not be in the path 4 Run the configuration script to generate a Makefile configure 5 Install VMD cd src make install 6 Make sure that the directory containing the vmd executable the one that you listed for install_bin dir inside the configure file above is in the path for your shell For instance if that directory was usr local bin vmd 1 8 7 and you are using the bash shell you could use the following command PATH PATH usr local bin vmd 1 8 7 To test VMD type the command vmd Two windows should be opened VMD main and VMD version OpenGL Display Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux 3 9 Setting Up Access to PyMOL Both Maestro and Canvas can open PyMOL directly To do so PYMOL must be installed and the location communicated to th
37. ENt sssssssrsssssserssssorresrres ix D Desmond byte transfer layer setting 0 57 Infiniband network setup 9 installing VMD issssisssasss0sssssnniserssasers vi nsnsti 23 MPI implementations sssssssssssssersssesesrnrnr 9 queue configuration for OpenMPI 67 Diagnostics paniel s ss sssesssdnsisssesiossnisrissrs 91 directory default installation SettiNg 35 installation 18 28 31 37 52 55 installation log files Windows 31 Serate bo ren 18 52 54 DVD Gives nannten 15 E entries hosts file batch queue configuration 65 copying keywords from other entries 50 definition 49 SECUTE ZONE 45445s50150005s80sss0 n sn sssasniranssn 58 entry name schrodinger hosts file st environment for queueing software 67 110 environment variables DISPLAY ne neigen 19 for Prime installation 12 LSF_SERVERDIR eeeeenseneneennen 83 MAESTRO WORKFLOW LOCATION 47 OMP_NUM_ THREADS 57 OMPI MCA DEl anne 57 PATH si vsssasvosedvevies tandaviceessssevesvervesdoseateas 25 39 PSP BLAST DATA 13 PSP BLAST DIR 13 PSP_BLASTDB nn 13 22 PSP HMMER DIR nennen 13 PSP_HMMERDB 4 4stsscssevsssndssesvasspstasiosinssnsnenss 13 PSP PSIPRED DB 13 POP PSTPRED DI Rooies eiretier oris 13 PSP SSPRO DB iassssrsssssssoonererersssssnnnnnnn
38. Installation Guide Schr dinger Software Release 2014 2 O Schr dinger Press Installation Guide Copyright 2014 Schr dinger LLC All rights reserved While care has been taken in the preparation of this publication Schr dinger assumes no responsibility for errors or omissions or for damages resulting from the use of the information contained herein Canvas CombiGlide ConfGen Epik Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime PrimeX QikProp QikFit QikSim QSite SiteMap Strike and WaterMap are trademarks of Schr dinger LLC Schr dinger BioLuminate and MacroModel are registered trademarks of Schr dinger LLC MCPRO is a trademark of William L Jorgensen DESMOND is a trademark of D E Shaw Research LLC Desmond is used with the permission of D E Shaw Research All rights reserved This publication may contain the trademarks of other companies Schr dinger software includes software and libraries provided by third parties For details of the copyrights and terms and conditions associated with such included third party software use your browser to open third party legal html which is in the docs folder of your Schr dinger software installation This publication may refer to other third party software not included in or with Schr dinger software such other third party software and provide links to third party Web sites linked sites References to such other third party softwar
39. MPI parallel jobs thus the main need for this setting is to designate hosts that do not support MPI parallel jobs The setting allows applications to detect a host selection that does not support MPI parallel jobs and post a warning before the job is submitted to the host or queue thereby avoiding job failure The setting is merely a flag there is no checking of the actual host to verify its support of MPI 7 1 6 The gpgpu Setting To make use of GPU cards for Desmond calculations the hosts file must be configured for each host For example on a local workstation you could use an entry like this Local workstation name myhostname host localhost processors 4 tmpdir usr tmp gpgpu 0 GTX 680 This entry indicates that the local workstation has a single GeForce GTX 680 card available at device index 0 For a remote host you could use an entry like this Remote host name otherhostl host remotel mycorp com processors 8 schrodinger path to schrodinger tmpdir usr tmp gpgpu 0 Tesla K20 gpgpu 1 Tesla K20 Here the remote workstation has two Tesla K20 cards residing at device indices 0 and 1 7 1 7 The schrodinger Setting The schrodinger setting specifies the directory in which your Schr dinger software is installed on this host the installation directory This setting is used as a fallback by Job Control to locate compatible software versions on the remote machine The way in which this is done is descri
40. RDPARTY to the chosen location This location should have a database directory in which databases are stored and a bin directory in which executables are stored If you install any of these third party products in a location other than the default loca tion S SCHRODINGER thirdparty you must set environment variables listed in Table 2 2 to identify the location of the products that are in a nondefault location e If you already have copies of the third party products you can provide links to them using the environment variables described in Table 2 2 You do not need to set these envi ronment variables if you are installing Prime from the supplied DVDs On Windows if you are using an installed copy of the PDB to run Structure Prediction jobs you must set the SCHRODINGER_PDB environment variable in Windows or UNC format See Appendix A for information on setting environment variables on Windows You can set the environment variables for remote hosts in the schrodinger hosts file see Section 7 1 on page 49 for more information Schr dinger Software Release 2014 2 Chapter 2 Hardware and Software Requirements Table 2 2 Environment variables defining the nonstandard location of third party software and databases for Prime Environment Variable Description SCHRODINGER_ PDB PSP_BLASTDB PSP BLAST DIR PSP BLAST DATA PSP HMMER DIR PSP HMMERDB PSP PSIPRED DIR PSP PSIPRED DB PSP SSPRO DB PDB dis
41. RPROFILE Local Settings Application Data Schr dinger Software Release 2014 2 Chapter 4 Installing the Products on Windows Table 4 1 Modules to install for each product Product Modules Product Modules BioLuminate BioLuminate LigPrep MacroModel Desmond Epik optional Epik MacroModel MacroModel MacroModel Prime Maestro maestro Canvas Canvas P450 Site of Metab Epik CombiGlide CombiGlide olism Prediction Impact Impact Prime MacroModel QikProp Phase Phase MacroModel ConfGen MacroModel Prime Prime Core Hopping CombiGlide Impact PrimeX Prime MacroModel Impact Phase Epik MacroModel Desmond Desmond QikProp QikProp Epik Epik QM Polarized Impact Glide Impact Ligand Docking Jaguar Impact Impact QSite Impact Jaguar Induced Fit Docking Impact Prime SiteMap Impact Jaguar Jaguar Strike Maestro KNIME Extensions Knime Virtual Screening Impact Workflow Epik Liaison Impact MacroModel Prime Ligand amp Structure Impact QikProp Based Descriptors MacroModel Prime WaterMap WaterMap QikProp Desmond Installation Guide 29 Chapter 4 Installing the Products on Windows e If you want to use Prime or BioLuminate you must have access to the PDB and BLAST databases If you do not have web access you must install them see Section 4 2 on page 33 for instructions e You can choose to create shortcuts for selected Maestro profiles These profiles present Maestro with different customizations for different user bases e T
42. SCHRODINGER text box The default paths are Windows C Program Files Schrodinger 2014 2 or for 32 bit software on a 64 bit OS C Program Files x86 Schrodinger 2014 2 e Mac opt schrodinger suites2014 2 If you want to start PyMol from KNIME enter the path to the PyMol installation in the PYMOL4MAESTRO text box Restart KNIME to start using the Schr dinger nodes If you want to use the 2D renderer you must make settings in your KNIME startup script as the preferences set above do not include this feature The following lines should be added to the startup script Linux export SCHRODINGER schrodinger installation mmshare SCHRODINGER hunt mmshare SCHRODINGER sed e s bin lib gt export LD LIBRARY PATH Smmshare LD_LIBRARY_PATH Schr dinger Software Release 2014 2 Chapter 6 Installing and Updating KNIME Extensions Mac export SCHRODINGER schrodinger installation mmshare SCHRODINGER hunt mmshare SCHRODINGER sed e s bin lib export DYLD LIBRARY PATH S mmshare DYLD LIBRARY PATH Windows set SCHRODINGER schrodinger installation set PATH SCHRODINGERS SCHRODINGER unxutils SCHRODINGER utilities PATH set PATH PATH for F I in SCHRODINGER hunt exe mmshare do set MMSHARE EXEC I set PATH MMSHARE EXEC PATH These lines set the SCHRODINGER environment variable which supersedes the preferences setting You could also set the PYMOL4MAESTRO env
43. TCHID if n PBS NODEFILE then SCHRODINGER_NODEFILE PBS_ NODEFILE export SCHRODINGER NODEFILE fi lt ENVIRONMENT COMMAND The PBS lines are directives that are interpreted by PBS In this case the first directive sets the job name for this job to the Schr dinger job name while the fourth specifies the number of processors to use for the job Most other queueing systems also allow directives to be provided in the initial comment lines of the job submission scripts The words delimited by percent signs are variables which are replaced at job launch time with the actual job name Schr dinger job ID etc for the job you are submitting Variables that you can put in any new template sh file are listed in Table E 1 Table E 1 Batch script variables Variable Variable action ZNAME Schr dinger job name usually derived from your input file name DIR Directory from which the job was submitted SHOSTS Machine from which the job was submitted SUSERS Name of the user who submitted the job lt JOBID Job ID assigned by the Schr dinger job control system SENVIRONMENTS Commands that define the environment variables required for your job to run PRODUCTS Product name NOT the executable SAPP_EXEC VER_ARGS HUNT_PATH JOBDB ZNPROCE The name of the exec variable for the product Version arguments The path to the hunt executable The path to the job database Number of processors that were req
44. To optimize the performance of a cluster for Schr dinger software we suggest that you consider the following options when purchasing upgrading or configuring a cluster Invest in a highly capable file server for the external network Invest in a high performance intra cluster network especially for Desmond Invest in shared storage for the private intra cluster network to reduce traffic to and from the external network Shared storage makes installation and maintenance of the code much simpler and can be used to store large data files temporarily or permanently Divide services among several management nodes For example the queueing system the private network s shared storage and the routing could all be handled by separate management nodes Likewise nodes used as file servers should not run computations Ensure that the management nodes have fast processors large memory and high quality motherboards and network interfaces Run more recent Linux versions which have better facilities for network address transla tion NAT and related functionality than earlier versions Store large databases on high performance network attached storage for efficient genera tion management and screening Run a robust queuing system that is relatively immune to stalling crashing or bringing down its host if it is heavily loaded If you are likely to have more than 250 actively running jobs on the cluster it is important to make som
45. To work around this problem cre ate a registry key under HKEY_LOCAL_MACHINE SOFTWARE Microsoft Windows CurrentVersion Policies System named EnableLinkedConnections and of type DWORD and set its value to 1 4 1 2 Installation Notes The following notes describe choices that must be made or conditions that must be met when you install the software If you are installing the software as administrator and you browse to create a directory and rename it you must press F5 to force the dialog box to update the directory to the new name so that it is no longer shown as New Folder The default installation folder is C Program Files Schrodinger 2014 2 or C Program Files x86 Schrodinger 2014 2 for 32 bit executables on a 64 bit OS If you want to install into another folder it cannot be a drive such as C and it cannot be the same as a previous Schr dinger software installation The installer does not allow you to choose the same directory as a previous release installation e The software distribution includes Schr dinger products or clients for running products remotely in addition to Maestro To install products you must select the corresponding modules in the installer If you want to run jobs either on the local Windows host or on a remote Linux host you must install the product or client on the local Windows host 1 LOCALAPPDATAS is set to SUSERPROFILE AppData Local except on XP where the equivalent location is SUSE
46. Torque queueing system smmmnsnssssssesesrsenennnnnnnen 64 parallel configuration 71 U Ubuntu requirements uppercase file names on DVD user name for remote hosts 0 0 0 0 eee Schr dinger Software Release 2014 2 V version PSIPRED sssoosnrsssssssessressreserrsererresrrerrnnrr rn ren 12 VITUS checker uuucsesa ana 30 Visual C libraries nnnnen 7 VMD Web Site 2asscessovosssersdss ssdenssinessssesneeressersen 23 w Windows setting environment variables supported products sssssrssssssesserrsrsersrsnsr Windows installation AllUsers mode cccccccccccssecesssceesseessseeeees 27 command line cccececcesecesseeeesseessseeeees 30 Hosts file a 0 Bene 30 OnlyForMe mode ensena 27 unregistered software uceeeenenen 32 Windows setup domain name server 60 120 West 45th Street 17th Floor New York NY 10036 155 Gibbs St Suite 430 Rockville MD 20850 0353 Quatro House Frimley Road Camberley GU16 7ER United Kingdom 101 SW Main Street Suite 1300 Portland OR 97204 Dynamostrafe 13 D 68165 Mannheim Germany 8F Pacific Century Place 1 11 1 Marunouchi Chiyoda ku Tokyo 100 6208 Japan 245 First Street Riverview II 18th Floor Cambridge MA 02142 8910 University Center Lane Suite 270 San Diego CA 92122 Zeppelinstra e 73 Potsdamer Platz 11 D 81669 M nchen D 10785 Berlin Germany Germany No 102 Ath Block 3rd Main R
47. allation Guide 77 Chapter 7 Preparing for Job Submission 78 The output from licutil should consist of lines like the following IMPACT MAIN IMPACT MAIN INT lt YES YES 0 0 MMLIBS MMLIBS INT lt YES YES 0 0 There should be one line for each license in your license file To add the new license attributes 1 Copy the existing configuration to a text file qconf sc gt complex txt where qconf is the SGE queue configuration command 2 Append the new configuration lines to complex txt SSCHRODINGER utilities licutil sgeconf gt gt complex txt 3 Load the new configuration qconf Mc complex txt This last command should produce a number of messages like user host added IMPACT MAIN to complex entry list user host added MMLIBS to complex entry list To verify that the attributes have been added display the complex configuration with aconf sc and make sure the new license attributes appear 7 4 1 2 Configuring the Load Scripts A script is provided that queries the FLEXIm license server and reports the number of tokens available for each license in a format that the queueing software can understand To make sure the 1mutil utility and license file can be found when the script is run by the queueing soft ware you need to add the locations of the program and the license file to the script by editing the configuration section at the top of the script You must have permission to change this file 1 Use a text
48. and Jaguar Custom profiles can be installed if they are added to apps customize profiles prior to installation The values are case sensitive By default all profiles are installed includ ing custom profiles Only valid with install Remove products rather than install them Default is to remove all including documentation Repair the existing installation The default is to install Vista only Display output from the installer after it finishes if set to on close console window immediately if set to of Default on For XP the console window remains open after installation Install for all users or for the current user Default is all users Installation Guide 31 Chapter 4 Installing the Products on Windows 4 1 4 Troubleshooting e If the installation fails with the following error message it may be that some of the soft ware required for the installation is not registered on your machine Error 1720 There is a problem with this Windows Installer package A script required for this install to complete could not be run Contact your support personnel or package vendor To provide us with information on your registry you can download RegDll View from http www nirsoft net utils registered_ dll view html run it and send the output to help schrodinger com Ifyou see a warning that there is not enough disk you will have to clean up your primary disk before proceeding even if the disk that you are ins
49. and Software Requirements 2 1 4 Mac Requirements for Mac computers are as follows e Intel processor 64 bit only e Mac OS X 10 7 10 8 or 10 9 e Adobe Reader is required to use the search index for the manuals and for proper func tioning of the facility to open tutorial documentation Preview does not follow links between the distributed documents from Mac OS X 10 7 on All Schr dinger products except MCPRO are supported Quad buffered hardware stereo is not supported interlaced stereo is supported If you need to compile Prime third party programs you must install XCode including the command line tools This requires an Apple Developer account 2 1 5 Queueing Systems The following queueing systems are supported e PBS including PBS Pro e Grid Engine including SGE and GE minimum version 6 2 LSF minimum version 7 0 2 SLURM minimum version 2 1 Torque License checking is available for SGE PBS Pro and LSF see Section 7 4 on page 77 2 2 Disk Space for Installation Disk space requirements for a full installation of Schr dinger software including the docu mentation are given in Table 2 1 These values do not include the PDB or BLAST databases which require 14 GB and 13 GB The Pfam database included requires less than 1 GB Table 2 1 Disk space for a full software installation Platform Disk space Linux x86_64 8 4 GB Windows 5 5 GB Windows x64 6 4 GB Mac OS X 7 5 GB Schr dinger
50. are To install Schr dinger software 1 2 5 2 Click the disk image dmg in your Downloads folder or insert the DVD Double click the installer package pkg The installer starts Follow the prompts in the installer The installation path is opt schrodinger suites2014 2 You can use a different disk by clicking Change Location Enter the required password to install the software The software is installed and a folder named SchrodingerSuites2014 2 is added to the Applications folder This folder contains icons for various Schr dinger applications which you can drag to the dock if you wish Installing Prime Third Party Databases Prime requires access to the PDB and BLAST databases If these databases are not installed locally you can use web access to send queries and retrieve the results If you want to use a local installation instead for security reasons for example use the following instructions 1 2 3 Check that you have at least 20 GB disk space available Open a terminal window Set the SCHRODINGER THIRDPARTY environment variable to a suitable location that is not inside your software distribution e g export SCHRODINGER THIRDPARTY opt schrodinger thirdparty Installation Guide 37 Chapter 5 Installing the Products on a Mac 38 This choice ensures that the database is not installed inside your software installation as it would be removed when you uninstalled the software
51. ases into the Schr dinger software installation Installation Guide 33 Chapter 4 Installing the Products on Windows 34 The databases from the FTP site or DVDs should be updated to obtain the most recent changes using the instructions below Note PSIPRED is not supported on Windows To update or download the BLAST and PDB databases 1 Choose Start gt All Programs gt Schrodinger 2014 2 Schrodinger Command Prompt A DOS command prompt window opens in which you can type the required commands 2 Set the path to the third party databases by typing the following command set SCHRODINGER_THIRDPARTY thirdparty location If you installed the third party databases in the default location or if the SCHRODINGER_THIRDPARTY environment variable is already set skip this step 3 Run the rsync_pdb utility by typing the following command rsync_pdb 4 Run the update _BLASTDB utility by typing the following command update BLASTDB b The download starts and the progress of the process is printed in the shell window When it is finished you can close the command prompt window Alternative To download and install the PDB and BLAST databases and software 1 Go to the following site ftp ftp schrodinger com support hidden prime Windows Suite2014 If you double click on this link it should open up a file explorer that lists all the files available at this location 2 Download the following zip files psp blast thi
52. at you must restart KNIME for the installation to finish and offers several Click Restart KNIME Now KNIME restarts and you can proceed to the installation of the Schr dinger extensions Schr dinger Software Release 2014 2 Chapter 6 Installing and Updating KNIME Extensions To install the Schr dinger extensions 1 2 Start KNIME if it is not already running Choose Help Install New Software The Install Available Software panel opens In the Available Software tab click Add The Add Repository dialog box opens Specify the location of the update site If you are using the web site directly a Enter the following URL in the Location text box https support schrodinger com releases knime extensions You can also enter a name to identify the site b Click OK in the Add Repository dialog box c Enter your user name email address and password for the Schr dinger web site If you downloaded the archived site a Click Archive b Navigate to and select the downloaded zip file c Click OK in the file selector d Click OK in the Add Repository dialog box The available software from this site is listed in the center of the panel Select the newly created tree for the update site Ensure that Show only the latest versions of available software and Hide items that have already been installed are both selected Select the Schr dinger nodes you want to install by clicking the check boxe
53. ation Guide 51 Chapter 7 Preparing for Job Submission 52 Table 7 1 Keywords for schrodinger hosts file settings Continued Keyword Description queue recoverjobs schrodinger tmpdir user Queuing system name PBS SGE LSF and SLURM are the supported systems Must be set to the subdirectory of SCHRODINGER queues that contains the support files for the queuing system Disable recovery of failed jobs if set to no Use this setting only for jobs where job recovery might not be possible such as on the cloud The path to the Schr dinger software installation on the host Base directory for temporary or scratch files also called the scratch directory The file system on which this directory is mounted should be large enough for the largest temporary files should be mounted locally and should be writable by the user Do not use symbolic links as these can cause some programs to fail The actual directory created for scratch files is tmpdir username jobname where tmpdir is the directory defined here and username is the user name Multiple tmpdir settings can be added for a given host and are used by Maestro but the first set ting is used otherwise User name to use on the host This should never be set in the hosts file in the installation directory It is required if the user has a different user name on the defined host than on the host on which the job is launched A sample schrodinger hosts fi
54. bed in Section 2 5 of the Job Control Guide If you want to submit jobs from a Windows host to a Linux host you must add schrodinger settings to ensure that the software is located because the default is to use the path to the local installation and the Windows installation path will never be located on Linux Installation Guide 55 Chapter 7 Preparing for Job Submission 56 Note The schrodinger settings in the hosts file should always point to an installation for the current release You can provide multiple schrodinger settings for a single host entry You may want to do this if you have installations of several versions of Schr dinger software in different directo ries For example suppose your Schr dinger software is installed on a Linux host in the direc tory usr bin schrodinger2014 2 and you have a cluster named mycluster in which the software is installed in storage schrodinger2014 2 If storage is only accessible to the cluster you could set up your hosts file with the following schrodinger settings name localhost schrodinger usr bin schrodinger2014 name clus4hr host mycluster queue PBS qargs 1 walltime 04 00 00 schrodinger storage schrodinger2014 In this example the cluster is running queuing software Another way of making the settings is to include both schrodinger settings for the localhost entry name localhost schrodinger usr bin schrodinger2014 schrodinger storage schroding
55. can be run in parallel with MPI on Linux and Mac OS X By default Jaguar uses Open MPI 1 6 5 which is included in the Schr dinger software distribution Jaguar runs on shared memory architectures in SMP mode or on distributed architectures and clusters Jaguar cannot be run in parallel on Windows Jaguar can also be run in parallel with OpenMP on Linux only not Mac OS or Windows Both OpenMP and Open MPI can be used in the same job To run parallel Jaguar jobs from a batch queue you should ensure that multiple calls to MPI per job are permitted Some queue configuration might also be needed see Section 7 3 3 on page 67 for more information 2 3 3 KNIME Extensions 2 0 The Schr dinger KNIME Extensions for 2014 2 are built on KNIME 2 8 0 This is the required minimum version If you add the Schr dinger KNIME Extensions to an existing KNIME installation you must have this version installed at a minimum Schr dinger Software Release 2014 2 Chapter 2 Hardware and Software Requirements On Linux the 1ibstde so version installed in usr 1ib64 must be no less than 6 0 14 If you cannot upgrade your installation and you are using an external version of KNIME you must set LD LIBRARY PATH to include the following path KNIME installation plugins com schrodinger knime_version lib Linux x86_64 Schr dinger KNIME Extensions require a full installation of Schr dinger software 2 3 4 MCPRO 3 4 MCPRO is only supported on L
56. chr dinger software ensure that all Schr dinger applications and supporting programs are not running this includes utilities Maestro Schrodinger Command Prompt or SchrodingerShell windows and any other Schr dinger applications If remote jobs are running you should wait until they finish before uninstalling Maestro otherwise the results will not be copied back to the working directory or incorporated into the project If you want to kill all Schr dinger applications and supporting programs navigate to the mmshare vversion bin WIN32 x86 folder in your Schr dinger software installation and run SchrodingerProckill You cannot use Add Remove Programs to uninstall the software this has been explicitly disabled because setup exe performs some tasks that are not performed with Add Remove Programs You must therefore use setup exe or its equivalent as explained below For releases prior to Schr dinger Suite 2009 Update 2 you must use the setup exe program to uninstall the software If you no longer have this program for the particular release you can download it again from the Downloads page of the Schr dinger web site From Schr dinger Suite 2009 Update 2 on you can use one of the following methods e Run the uninstaller by going to Start gt All Programs gt Schrodinger year Uninstall e Run the uninstall exe program which is located in the installer folder of your Schr dinger software installation SCHRODINGER installe
57. d to run the subjobs with LOCAL To test the startup use NOLAUNCH which stops short of actually starting the job Table 7 4 Options for the para_testapp command Option Description DIR jobdir Job launch directory The default is chosen automatically j jobname Job name Default dist njob pid n njob Number of subjobs to start Default 1 Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Table 7 4 Options for the para testapp command Option Description NOLAUNCH Stop just before running the job p Request njob processors from the queue parallel mode where njob is specified by n t seconds Duration of each subjob in seconds Default 30 Installation Guide 95 96 Schr dinger Software Release 2014 2 Appendix A Setting Environment Variables This appendix describes how to set an environment variable on the supported platforms A 1 Linux To set an environment variable on Linux enter the following command at a shell prompt csh tcsh setenv variable value bash ksh export variable value where variable is the name of the environment variable such as SCHRODINGER and value is the value you want to assign to the variable such as opt schrodinger2014 A 2 Windows You can create or change environment variables in the Environment Variables dialog box If you are adding to the PATH environment variable you should separate each field with a semi colon
58. date site should be in the folder you extracted the download into with the name SchrodingerKNIMEUpdateSite_ version zip e If you want to update the Schr dinger KNIME Extensions use the update site or a down loaded archive of this site see the previous paragraph See Section 6 2 6 1 Installing into an Existing Version of KNIME If you want to install the Schr dinger extensions into an existing version of KNIME you can do so from the KNIME interface If the version of KNIME does not meet the minimum requirements you must update your version of KNIME first The installation requires access to the Schrodinger KNIME update web site or to a local archived copy of this site You must also install the KNIME Base Chemistry Types and Nodes from the KNIME update site before you install the Schrodinger extensions if you have not done so already To use the Schr dinger KNIME extensions you must identify the Schr dinger installation to KNIME The nodes will not work without access to a Schr dinger installation The installation thus has three stages instructions for which are given below e Installing and updating KNIME itself e Installing the Schr dinger nodes e Identifying the Schr dinger software installation to KNIME Installation Guide 41 Chapter 6 Installing and Updating KNIME Extensions 42 To install the KNIME Base Chemistry Types and Nodes 1 2 Start KNIME Choose Help Install New Software The
59. dia cards are Option Stereo 3 in the Device section and in the Extensions section Option Composite Disable 3 6 Installing Script Center Scripts Scripts that have been downloaded from the Script Center can be installed from the command line or using Maestro see Section 15 1 1 of the Maestro User Manual for details When installing from the command line you can choose whether to install into just your user area or into a common area for all users The default common area is the directory SCHRODINGER mmshare vversion python common but a different common area can be specified by setting Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux the SCHRODINGER SCRIPTS environment variable to the desired directory before proceeding with the installation First extract the tar file containing the scripts with the command tar xvf Schrodinger Scripts Download tar To install into a common area from the command line cd Schrodinger Scripts Download SCHRODINGER run installscripts py c d MaestroPythonScripts SCHRODINGER run installscripts py c d CommandLineScripts To install into your user area from the command line cd Schrodinger Scripts Download SCHRODINGER run installscripts py u d MaestroPythonScripts SCHRODINGER run installscripts py u d CommandLineScripts 3 7 Installing Prime Third Party Software and Databases from a Download Prime third party products are included in the
60. diagnostics in a terminal window Windows Choose Start gt All Programs Schrodinger 2014 2 Diagnostics or enter diagnostics in a Schrodinger Command Prompt window e Mac Double click the Diagnostics icon in the SchrodingerSuite2014 folder of the Appli cations folder or enter SCHRODINGER diagnostics in a terminal window This panel can also be opened from the Help menu in Maestro and Canvas It is opened auto matically if Maestro fails to start After starting the application a set of tests is run to verify that the licenses are correctly installed and the license server is running and to verify that the hosts file is correctly set up Their progress is reported in the Running Tests information box which is displayed along with the Diagnostics panel The results of these tests are then displayed in the panel The host tests that are run when the panel opens do not include test jobs on remote hosts only syntax checking on the hosts file To run a test job on a host select the row for that host in the Hosts table Hosts tab and click Selected Host To run test jobs on all hosts in the hosts file click All Hosts The status of the test is reported in the Result column of the table with messages in the Results area below the table If the result for a queue host is OK SECURE then file transfer to that host is secured by the Secure Channel SSH tunnel mechanism if the result does not include SECURE then the file trans
61. dir should contain a set of Python scripts named workflow py and directories named workflow dir When Maestro is started these workflows should appear on the Workflows menu If you do not want to install the workflows into the installation you can simply place them in a directory and set the MAESTRO WORKFLOW LOCATION environment variable to point to this directory Installation Guide 47 Chapter 6 Installing and Updating KNIME Extensions 48 If you are using an external KNIME installation rather than the one in the Schr dinger installa tion you must make sure that the external installation has the Schr dinger nodes installed and everything under KNIME amp Extensions and KNIME Labs Extensions for the current version of KNIME In addition you must add a knime setting in the hosts file for the hosts on which you plan to run Maestro or to the localhost entry See Section 7 1 on page 49 for information on the hosts file This setting will have to be updated if you update the external KNIME and the path to the KNIME startup script or executable changes Note that this setting is applied if you try to run the Schr dinger KNIME instance via the icon or the startup script the external KNIME will start instead of the Schr dinger KNIME 6 5 Installing A Web Service for Node Execution Some KNIME nodes can be run through a web service The instructions for setting up the web service and the necessary configuration are given b
62. dows AP en 98 BEE ae 99 Appendix B File and Resource Locations on Windows 101 Appendix C Access to the Web via a Proxy 103 Appendix D Global Configuration Flle 105 Appendix E Adding an Unsupported Queueing System 107 EA The submit SONP ssniesiokaniiensnunies aNs 107 E 2 The Cancel Script 82H 108 E 3 The Job Script Template File 2 0 0 cece eeeeeeeceeeeeeeceeeeeesaesaseeseeeateeeaes 108 E 4 The contig File ss seele 110 Appendix F Setting Up Remote Access Manually on Windows 111 MOOK rie E en TR enone Cannon Tae 115 Installation Guide vii viii Schr dinger Software Release 2014 2 Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SSCHRODINGER maestro File names directory names commands envi ronment variables command input and output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys uppercase Links to other locations in the current document or to other PDF documents are colored like this Document Conventions In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets 1 enclose optional items and the bar symbol s
63. e LSF Qargs q LSF queue n NPROC R span ptile STPP Host submit node Processors processors in queue 7 3 3 4 SLURM configuration Below are some examples of SLURM entries in the hosts file Request NPROC processors with an arbitrary cpu topology Name label Queue SLURM2 1 Qargs partition SLURM partition ntasks NPROC Host submit node Processors processors in queue Request NPROC processors one on each node Name label Queue SLURM2 1 Qargs partition SLURM partition nodes 1 ntasks per node NPROC Host submit node Processors processors in queue Installation Guide 73 Chapter 7 Preparing for Job Submission 74 Request NPROC processors spread across nodes 2 cores per node Name label Queue SLURM2 1 Qargs partition SLURM partition nodes NPROC 2 ntasks per node 2 Host submit node Processors processors in queue Parallel Jaguar Hybrid OpenMPI OpenMP Request NPROC total threads with TPP threads per node Name label Queue SLURM2 1 Qargs partition SLURM partition nodes NPROC TPP ntasks per node TPP Host submit node Processors processors in queue Note that the Qargs entry should all be on a single line with no break 7 3 4 Configuring Queuing Systems for GPU Use Queuing systems must assign the appropriate resources to the GPU This can be a bit chal lenging as not all queueing systems fully manage GPU resources Desmo
64. e application The recommended procedure is 1 2 3 Install PyMOL in a location outside SCHRODINGER using setup sh You must use this script to ensure that the PyMOL installation is configured properly Add the PyMOL top level directory to the PATH environment variable Set the PYMOL4MAESTRO environment variable to the PyMOL top level directory Canvas requires that the PyMOL location is in the PATH environment variable Maestro does not use PATH but uses the following sources to find an installation of PyMOL first in the order given 1 The PYMOL4MAESTRO environment variable This environment variable should point to the top directory of the PyMOL installation This is the preferred method of specifying the location of PyMOL APyMOL launch script called pymol4maestro in the Schr dinger software installation This script must run PyMOL APyMOL installation in SCHRODINGER pymol The standard PyMOL environment variable PYMOL_PATH A launch script called SCHRODINGER pymol 3 10 Uninstalling the Software To uninstall the software for a release delete the release directory rm r install directory Installation Guide 25 26 Schr dinger Software Release 2014 2 Chapter 4 Installing the Products on Windows 4 1 Installing Schrodinger Software We recommend that you install Schr dinger software as an administrator and install for all users AllUsers mode However if you do not have administra
65. e channel access 1 Block ports above 1024 in the firewall on the externally facing network 2 Leave ports above 1024 open on the cluster s internal network If you want to leave some ports above 1024 on the externally facing network open for other applications you should do the following 1 Choose a port range that you can block and block these ports Ensure that there are sufficient ports in the range for all users jobs e g a few hundred 2 For each cluster entry in the hosts file add a proxyport entry that specifies this port range If you want to turn off encrypted data transfer you can do so but you should ensure that you trust the network on which the clusters to which you submit jobs are connected For clusters on your trusted network you can create securezone entries in the hosts file see Section 7 1 11 on page 58 for information If all your clusters are on a trusted network you can set the environ ment variable SCHRODINGER_SECURE_TRANSFERS to 0 to disable all secure channel commu nication You can also set this environment variable to 1 to enforce secure channel communication regardless of the securezone settings If you want to enforce this policy globally you can use a site configuration file see Appendix D Note The secure channel mechanism is not available for job submission from Windows Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 7 5 3 Performance Optimization
66. e file SSCHRODINGER utilities elim schrodinger 2 Edit the line beginning my LICENSE so that the full path to the license is between the quotation marks my SLICENSE full path to license file Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission You can specify the license server instead of the license file as follows my LICENSE license server or my SLICENSE port license server The backslash is necessary as Perl interprets as a special character 3 Edit the line beginning my LMUTIL so that the full path to Imutil is between the quo tation marks my LMUTIL full path to Imutil 4 To reserve licenses for non queue use edit the line beginning my reserved to set the value to the fraction or percentage of licenses to reserve For example either of the fol lowing lines reserves 20 of the licenses for non queue use my reserved 0 2 my Sreserved 20 Il 5 Save the modified script and close the editor 6 Verify that the script is configured properly by entering the following command perl SCHRODINGER utilities elim schrodinger The script should print a line like the following every thirty seconds 2 IMPACT_ MAIN 10 MMLIBS 15 The first number is the number of different licenses you have followed by the name and token count for each license Exit the script by typing CTRL C If you test the script before and after specifying reserved licenses you should see the
67. e mechanism for locating the hosts file that is used when you start a job If you have a custom hosts file in your Schr dinger user resources directory it uses that file If you have a custom hosts file in some other location you can test it from the command line by changing to the directory containing that file and running this application The results of the diagnostic tests can be collected so that you can send them to technical support Click Technical Support which collects the results into a file and opens a dialog box that gives the path to the file You can attach this file to your email message 7 6 2 Command Line Tools You can test the connections to remote hosts with the installation_check application This application reads a hosts file and runs a test job using the host entries defined in the file Errors in the hosts file and failures in the test jobs are reported and to the extent possible recommendations are given for fixing the problems that were uncovered It also checks the status of the license server and access to licenses The syntax of the command is as follows installation_check options To run this command on Windows open a Schr dinger Command Prompt window from Start All Programs Schrodinger 2014 2 and enter the command To run this command on Linux or Mac prepend it with SCHRODINGER The options are listed in Table 7 2 Table 7 2 Options for the installation_check command Option Description
68. e or linked sites do not constitute an endorsement by Schr dinger LLC or its affiliates Use of such other third party software and linked sites may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for such other third party software and linked sites or for damage resulting from the use thereof Any warranties that we make regarding Schr dinger products and services do not apply to such other third party software or linked sites or to the interaction between or interoperability of Schr dinger products and services and such other third party software May 2014 Contents Document CONVENtiONS naniaanidunannduieannhiomimnincaniiiinenizimmcennies ix Chapter 1 Installation Notes msunms eeesessss gt sssssssssssssssssssss sssss smsussssssmsssssssss 1 1 1 Linux Installation Process SUMMAIY sssssrerersrsressrsrsesrsrsenssessn annen snara arna anar a nanna ana 1 1 2 Windows Installation Process Summary isssssrersssrsrsssrsrsenssrsesssrsen annen ananas snaran annan 2 1 3 Mac Installation Process Summary sssnssersrsrsrsrsesssrsrsssrsrsensnesan enes en areas ananas asarna ana 2 Chapter 2 Hardware and Software Requirements 5 2 1 General Requirementis 44nsennnnnnennnnenennnnennnnnnennnnnnnnnnnnnnnnnnen 5 2 1 1 HardW te unaseansannieneninnee aha 5 2111 CPU Memory and DISK ar nase ade 5 214122 Graphics
69. e system level adjustments Increase the shell limit on open file handles to 10240 for example This can done on Linux with ulimit n 10240 This setting should be made in the global bashrc and cshrc on each machine in the cluster so that the user environment limits are always set appropriately It might also be necessary to set this limit in the environment of the queueing system since the queueing system s daemons are responsible for starting jobs For SGE you can set the following in the global configuration execd params S_DESCRIPTORS 10240 H_DESCRIPTORS 10240 Increase the backlog of TCP SYN requests echo 10240 gt proc sys net ipv4 tcp max syn backlog Installation Guide 89 Chapter 7 Preparing for Job Submission 90 This setting is not persistent across reboots so you will need ensure this comand is exe cuted at boot time perhaps in an init script 7 6 Testing the Installations and Connections Once you have installed the software and set up the hosts file on the desired hosts you should test the installation To do this you can use the Diagnostics panel or you can run checks from the command line 7 6 1 The Diagnostics Panel The Diagnostics panel runs checks on the license server and the hosts file and can be used to run test applications on hosts to ensure that the connections are working properly To open the Diagnostics panel use one of the following methods Linux Enter SSCHRODINGER
70. ection 7 5 on page 87 3 1 Access to the Software The software can be obtained on a DVD or downloaded from the Schr dinger web site You must ensure that it is accessible from each host on which you want to install it The directory that contains the software for installation will be called the installer directory When you have completed this section the installer directory designated installer dir should be one of the following locations e DVD mount directory e directory on a remote machine containing the copied files e download directory Schrodinger Suite2014_ type If you obtained the software on a DVD The DVD must be mounted Most computers automatically mount the DVD when it is inserted into the DVD drive Note DVDs are only readable by a DVD ROM drive or a DVD R or DVD R Read Write drive DVD R Read Write drives cannot read the DVDs we supply If you want to install the software on multiple hosts you can either copy the files to a place that is accessible to each host as described in Step 3 below or mount the DVD on each host If the DVD is not automatically mounted consult your system administrator If you obtained the software on a DVD and the host you want to install on does not have a DVD drive The software must be copied to the desired host as follows 1 Mount the product DVD on the machine that has a DVD drive 2 Change to the mount directory and display the DVD contents Installation Guide Chapte
71. eeverveeeede 77 license file replacement Of 0 17 license server access from Cluster to 87 Statii 2 250080 ass dan e aae oa 92 STOPPINS een 92 licenses academic Maestro on WindOWS 27 checking access TOn snas 90 obtaining and installing 2 3 testing checkout mechanism 93 time period for obtaining 66 timeout Priod isisisi inisesin 20 79 83 86 1 3 load sensor scripts log output localhost definition locked memory issiria 9 LSF queueing system 64 license checking ss AT parallel configuration 12 M Mac disabling indexing of databases 38 installation directory 37 Index OS X versions supported 8 setting environment variables 99 SLELEO SUPPOIE u uuannsn kun 5 Maestro display problems enenene 6 STANE si sitisesesaieii atau inne 20 Stereo Viewing ccris essen 5 modules to install Windows antenne 29 MPI configuring queueing systems 67 use with unsupported queuing systems 110 Myrinet networks siessen 9 O OPED Version anna een 9 Open MPI configuring queueing system 67 temporary directory 0 eee eens ST VETSION 24 5084050000s0005enss08s00ss sp0 sen tsin e estasia 9 OpenMP multithreaded execution 57 P parallel environment ssssssssessseseseserenesenennnen 68 PBS Pro queu
72. eing system license checking 77 parallel configuration ieee 70 PBS queueing System ieee eeeeeteeeeees 64 parallel configuration eee 70 PDB disabling indexing on Mac e 38 environment variable for location of 13 22 installing on Linux 22 installing on Mac eeenenn 37 installing on Windows 34 WED SiO rer raae einen 13 PDF teade oken E T 13 Patri database sssssssssessscccvsesseussessssnteviserdescesess 11 environment variable for 13 VETSIOM un ie dann 12 WED Siteni ipia riie 13 Platform SCPE sein 17 plink exe use on Windows 62 ports job communication 63 88 PREVI We 2esedi aise acisserstsbenteeenehaciecec teaeee desta 14 Prime environment VariableS sssessssesessesrsren 12 third party software 21 33 processors scheduling for GE eene 69 specifying number available on host 51 54 PSIPRED inst lling ars a 22 LO n E 12 WED SILC iis ises 5048 140000 E EEA RRA REEE ES 13 Q queue NOSE ccscssssssssessssssssisessacescssssssnscsassossoscoste 66 firewall configuration 0 eee eee 88 secure data transfer 88 queueing system adding support for ssssssssssssrrsssrsenrsnnn 66 configuring unsupported for parallel EXECUON 5455551555050555srensosnenssnssnssesenerensenes 110 PBS Pro configuration for OpenMPI 70 setting name in hosts file 52 SGE configuration fo
73. elow To set up the web server 1 Install the Apache Tomcat web server on the machine where the Schr dinger software is installed If you already have the web server on this machine stop the web server 2 Copy the SchrodingerExecCommand war file from your Schr dinger software instal lation into the webapps folder of your Apache Tomcat server location This file is in the knime vversion webservices folder directory of your Schr dinger software installa tion 3 On Linux set the SCHRODINGER and SCHRODINGER_TMPDIR environment variables 4 Start the Apache Tomcat server There are two ways to set up the client You can use Schr dinger Job Control to send the job to the server from your node or you can use a generic web service client node To set up the client using Job Control you must add an entry to the hosts file schrodinger hosts with the following settings name server alias host server host name port server port processors maximum server cores See Section 7 1 on page 49 for more information on the hosts file and its entries Instructions for configuring the nodes are given in Section 4 2 of the KNIME Extensions User Manual Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Schr dinger products use a common Job Control facility which allows the user to submit monitor suspend and terminate jobs The Job Control facility is described in detail in the Job Control Guide To r
74. en tutorial documentation from the Tutorials panel in Maestro Installation Guide 13 Chapter 2 Hardware and Software Requirements 14 e On Windows the default PDF reader is Adobe Reader Adobe Reader 8 0 is not sup ported e On Linux an alternative reader is required to use the documentation index and to follow links between manuals and this must be set as your default PDF reader Adobe Reader is not recommended for display of the manuals from Maestro because links between docu ments work only intermittently You should set the file association for PDF documents to the alternative reader We recommend Okular or Evince 2 0 or later You can also use kpdf e On Mac Adobe Reader is used if it is installed Preview does not support links between the distributed PDF files as of Mac OS X 10 7 so Adobe Reader is recommended If you have Adobe Reader installed we recommend that you use a version no earlier than 7 0 5 and that you ensure that it can be used as a plug in to your browser This is so that you can make full use of the indexing and hyperlink features in the documentation Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux Before installing Schr dinger products and documentation read Chapter 2 for information on hardware and software requirements including product specific requirements These require ments must be met before installation If you are installing on a cluster read S
75. eparates items in a list from which one item must be chosen Lines of command syntax that wrap should be interpreted as a single command File name path and environment variable syntax is generally given with the UNIX conven tions To obtain the Windows conventions replace the forward slash with the backslash in path or directory names and replace the at the beginning of an environment variable with a at each end For example SCHRODINGER maestro becomes SCHRODINGERS maestro Keyboard references are given in the Windows convention by default with Mac equivalents in parentheses for example CTRL H 8H Where Mac equivalents are not given COMMAND should be read in place of CTRL The convention CTRL H is not used In this document to type text means to type the required text in the specified location and to enter text means to type the required text then press the ENTER key References to literature sources are given in square brackets like this 10 Installation Guide x Schr dinger Software Release 2014 2 Chapter 1 Installation Notes This document gives information on the installation of the Schr dinger Suite 2014 2 software which comprises Maestro 9 8 BioLuminate 1 5 Canvas 2 0 CombiGlide 3 3 ConfGen 2 8 Core Hopping 1 7 Desmond 3 8 Epik 2 8 Glide 6 3 Impact 6 3 Jaguar 8 4 Liaison 6 3 LigPrep 3 0 MacroModel 10 4 Materials Science Suite 1 3 MCPRO 2 0 Phase 3 9 Prime 3 6 QikProp 4 0 QSite 6 3
76. equested give me 1 gpus N gpus resources So by setting 1 gpus 1 you are effectively asking for NPROC gpus resources as well Torque name torque gpu host headnode mycluster com queue Torque qargs q myqueue 1 nodes 1 ppn NPROC gpus SNPROC tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 gpgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 LSF name lsf gpu host headnode mycluster com queue LSF gargs q myqueue n NPROC R span hosts 1 rusage gpus NPROC tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 gpgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 7 4 Setting Up License Checking for Queueing Systems On large clusters it is possible for jobs to fail because there are too few licenses for all the jobs to run A mechanism has been provided to ensure that a queued job will not run unless all the licenses it requires are available This facility is available for the SGE 6 0 PBS Pro 10 1 and Platform LSF 6 2 queueing systems The configuration process consists of the following steps 1 A resource representing each license must be defined in the queueing system configura tion 2 The External Load Information Manager ELIM script LSF or load sensor script PBS and SGE which reports how many tokens are available for each license must
77. er2014 name clus4hr host mycluster queue PBS qargs 1 walltime 04 00 00 In this case both schrodinger settings are used in the default search for software on any host not just on mycluster The order in which they are included is only used if more than one installation of a particular software version release is found You can override the schrodinger setting with the VER and REL options if you run a program from the command line See Table 2 4 of the Job Control Guide for details 71 8 The env Setting The env setting specifies an environment variable that is to be set on this host when any job is started The syntax of the setting is variable value regardless of the UNIX shell used where variable is the environment variable and value is its value For example env SCHRODINGER_THIRDPARTY software databases Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission To set multiple environment variables include one env setting for each variable Environment variables set in the hosts file take precedence over any that are set in your UNIX shell either on the local host or the remote host For products that use OpenMP multithreaded execution you should set the environment vari able OMP NUM THREADS to the number of processors or cores on a host that you want to use for multithreaded execution For Desmond it is useful to set the environment variable OMPI MCA btlto self sm tcp if the host d
78. f processors perl version number and relevant libraries glibc for Linux 3 3 Installing the Software and Documentation When you select the locations for installing the software you must ensure that the software is accessible from all hosts that are used either to submit jobs or to run jobs This includes indi vidual nodes on a cluster Note The installation process does not replace the SCHRODINGER schrodinger hosts or SCHRODINGER license files or files in the SCHRODINGER queues directory If you want to install new versions of these files when upgrading your software you must move or remove them first 1 Change to the installer directory 2 Enter the command INSTALL This script accepts a number of options for providing the required information For details enter the command INSTALL h 3 Enter the information requested by the INSTALL script You can accept the default values for each question by pressing RETURN e You can quit the INSTALL script at any time by pressing CTRL C Installation Guide 17 Chapter 3 Installing the Products on Linux e If you realize you have entered incorrect information simply press RETURN at all of the prompts then enter n at the confirmation screen to start the questions again Below are explanations of the questions asked by the script SCHRODINGER directory This is the installation directory where the executables data files and other files related to Schr din
79. fer is not secured by this mechanism Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission BEE SCHRODINGER nfs builds NB suite2012 2012 03 08 License Hosts license software license Defined by SCHRODINGER license Server Status License Test Job Capacity Your license is not server based This usually means that your license provides unlimited use of your purchased products on particular machines specified by hostid or IP address Recheck Stop License server start License Server Tech Support Figure 7 1 The Diagnostics panel To change the reporting level you can start the application from the command line with the 1 option which takes the values critical error warning info debug These values represent different levels of reporting The default level is error or Running Tests Getting diagnostics info License server status Not run License test Completed Job capacities Completed Hosts Running Figure 7 2 The Running Tests dialog box Installation Guide 91 Chapter 7 Preparing for Job Submission 92 If you run this application on the license server host you can use the Stop License Server and Start License Server buttons to stop and start the license server These buttons are not available otherwise The hosts file is identified by the sam
80. from the shortcut menu The System Properties dialog box opens 2 In the Advanced tab click Environment Variables The Environment Variables dialog box opens To create a new environment variable 1 In the User variables section click New The New User Variable dialog box opens 2 Enter the name of the variable and its value and click OK The New User Variable dialog box closes and the variable is added to the User variables section of the Environment Variables dialog box Schr dinger Software Release 2014 2 Appendix A Setting Environment Variables To modify an existing environment variable 1 In the User variables section select the environment variable you want to modify 2 Click Edit The Edit User Variable dialog box opens 3 Change the value of the variable and click OK The Edit User Variable dialog box closes and the variable is updated in the User variables section of the Environment Variables dialog box When you have finished creating or editing environment variables click OK in the Environ ment Variables dialog box and again in the System Properties dialog box A 3 Mac OSX To set an environment variable on Mac OSX first open a terminal window If you are setting the environment variable to run jobs from the command line use the following command export variable value where variable is the name of the environment variable such as SCHRODINGER and value is the value you want to assign to the
81. ge for sge pe documents the output from this command The number of processors to specify is the total number of cores available to the queue It is generally recommended that you use fill up scheduling for the queues The use of round robin scheduling has a larger risk of failure on startup that may be related to an SGE bug http gridengine sunsource net issues show_bug cgi id 2393 You can set the allocation rule to i11_up either in the QMON interface started with the qmon command or by editing the parallel environment with the command qconf mp pe This command opens a text editor in which you can change or add the allocation rule setting Regardless of the allocation rule it is advisable to use a high quality network for Desmond and if possible to separate MPI traffic from other I O traffic Below are some examples of host file entries Request NPROC slots for the job using SGE parallel environment pe Name label Queue SGE Qargs q SGE queue pe pe NPROC Host submit node Processors processors in queue Parallel Jaguar Hybrid OpenMPI OpenMP Request NPROC total threads with TPP threads per node Name label Queue SGE Qargs q SGE queue pe orte rr NPROC TPP 1 dedicated TPP Host submit node Processors processors in queue For the second example some configuration of the queue is required in order to force SGE to distribute the job in a specific cpu topology First make
82. ger products will be installed Depending on the type of license you have we recommend the following installations e Token based or IP based license Use a shared file system so that you only have to install the software once and all client machines with access can use it e Node locked license Use the local file system of the machine for best performance or an NFS mounted file system if local space is limited You must install a new release into a new SCHRODINGER directory When the script has located or created the SCHRODINGER directory it asks you to confirm that the selection is correct Press RETURN to accept Hardware Software platform In this screen the INSTALL script reports the machine type and operating system Press RETURN to continue SCHRODINGER_THIRDPARTY directory This is the directory where third party programs required by Prime are installed By default they are installed in the software installation in the thirdparty subdirectory but you can choose a different location It is recommended that you do not install the PDB or BLAST databases inside the installation Scratch directory This directory is for the large temporary files generated by computa tional programs during calculations We recommend this directory be located on a fast local drive with at least 4 GB of disk space The INSTALL script checks for existing directories named scr scratch or usr tmp and suggests the first of these as the default If
83. he following subsections Note The queues that are set up using the instructions below should only be used for jobs that run under MPI such as Desmond and Jaguar parallel jobs They should not be used for distributed computing jobs such as distributed Glide LigPrep and Prime jobs Open MPI can create large temporary files which are written in the location defined by TMPDIR TEMP TMP with a fallback to tmp To avoid performance problems you should ensure that these files are written to a local file system with sufficient space by setting one of these environment variables in the hosts file For example env TEMP mylocaldisk env SCHRODINGER MPIRUN_OPTIONS x TEMP Installation Guide 67 Chapter 7 Preparing for Job Submission 68 For efficient queuing it may be necessary to specify the number of processors cores per node as well as the total number of processors available As Jaguar can also use OpenMP threads for parallelization in addition to MPI you may also need to specify the maximum number of threads to use per MPI process The Qargs setting in the hosts file can define these values with three basic variables e NPROC the total number of CPU cores requested for the job e TPP the number of threads per process requested by the job PPN the number of CPU cores processors per node The values of NPROC and TPP are obtained from the command used to launch the job whereas PPN is obtained from
84. host and the execution host The syntax of the securezone setting is securezone machine list Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission where the machine list is a list of short or full host names fully qualified domain names or IP addresses You can specify ranges with wild cards e g 1 2 or mycompany com Do not use hosts file entry names the names must be actual machine names or domains resolvable by the domain name server e Do not add 127 0 0 1 localhost or localhost localdomain to a securezone setting as this can result in unsecured file transfer outside the secure zone You can create more than one secure zone with multiple securezone entries Job submission to a cluster queue from one zone to another zone uses the ssh tunnel job submission within the zone uses the normal socket connection The securezone entry is a global setting it is not associated with any host entry We recom mend placing these entries at the beginning or the end of the schrodinger hosts file to separate it from host entries Some examples of securezone settings follow securezone myhost otherhost 123 45 67 89 securezone mydomain com 12 34 The first line places three hosts two defined by their host names and one by IP into the same secure zone The second line places any host in mydomain com as well as any host in the given IP range into the same secure zone With these settings connect
85. hr dinger user resources directory SHOME schrodinger on linux APPDATA Schrodinger on Windows If you want to store the information in Installation Guide 103 Appendix C Access to the Web via a Proxy 104 another location run the script with f ile filename For example if you want to install this file as a global resource for all users use f SCHRODINGER web_proxy json When the application attempts to contact the web it looks for the proxy information in the following locations and uses the first location that it finds e The file specified by the environment variable SCHRODINGER_PROXY_CONFIG e The file web_proxy json file in your user resources directory SHOME schrodinger on Linux APPDATA on Windows e The file web_proxy json in the software installation SCHRODINGER If you do not want to use any of these locations set SCHRODINGER PROXY CONFIG to an empty string The getpdb application requires access to the addresses listed below www tcsb org eutils ncbi nlm nih gov www ncbi nlm nih gov helixweb nih gov www schrodinger com Two other utilities rsync_pdb and update BLASTDB perform updates of databases from the web These utilities use rsync on Linux and wget on Windows To allow access via a proxy on Linux you can set the RSYNC_PROXY environment variable to hostname port where host name is the proxy server name and port is the port used You must use just the host name do not prepe
86. in order to cache the fingerprint for each name 10 If prompted to save the RSA key for that host choose yes This choice ensures that in future the prompt is not displayed The above command should then list the files in your home directory on the remote host For a more detailed explanation go to the following web site http the earth li sgtatham putty 0 58 htmldoc Chapter8 html pubkey Installation Guide 113 114 Schr dinger Software Release 2014 2 Index A Add Remove Programs 36 Adobe Reader ua 614 authorized keysfilen u ccsseseeese 61 B batch ID s ners nens 107 110 batch queues configuring for OpenMPI uneee 67 configuring unsupported eee 66 defining arguments for nneee 51 eNVirONMEeNt sssssssssesrrsserressornresnnn ner nn nn 67 110 hosts file entries script replacement setting name in hosts file supported systems uuenessneseenennenennenennennn BLAST database installing on Linux 22 database installing on Mac waT database installing on Windows 34 database updating 22 34 38 environment variables for location of 13 22 VETSION nn rero EAER R E GEE EEEE 12 WED Sitea E ETER 13 Cc cache Size uis eisen 3 CentOS requirements uusesesnennennenennenennnnnn I clusters hardware recommendations 6 optimizing performance 89 Conventions dOCUM
87. information on configuring queues for MPI applications including Open MPI for Desmond Jaguar and Impact see Section 7 3 3 on page 67 Note You should not add cwd to the Qargs setting for SGE as this causes jobs to fail 7 3 2 Setting Up Access to a Queueing System Support for queueing systems is provided through a set of scripts and a template that contain the specific syntax required to submit jobs to a queue These files are installed in a subdirectory of the SCHRODINGER queues directory that is named after the queue for each of the supported queueing systems The name of this subdirectory is used as the name of the queueing system in the hosts file as described above The Schr dinger software installation must be available to any host on which queue commands can be executed the queue host The files that are installed for any queueing system are e A submit script which is a wrapper for the queueing system s own job submission utility qsub for PBS and SGE e A cancel script which is a wrapper for the queueing system s job removal command adel for PBS and SGE e A template sh file which is a template for the shell script that is actually submitted to the batch queue and used to launch your calculation on the execution host Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission e A config file which contains settings for the keywords QPATH QSUB QDEL QSTAT and OPROFILE To set up
88. ings Application Data Table B 1 Location of files written or used by Schr dinger software Main Location Folder Files APPDATA Schrodinger maestroNN scriptsN M LOCALAPPDATA Schrodinger Installer year Installer tmp jobdb2 appcrash web_proxy json Maestro resource files such as prefer cmd default menu rotamer res and so on Command line scripts Installer log files SCHRODINGER INSTALLER LOGFILE DIR schrodingerRegCure_year log SchrodingerProcKill log Maestro temporary files including scratch projects SCHRODINGER_TEMP PROJECT MAESTRO TEMP LOCATION Job directories SCHRODINGER_TMPDIR Job database Application crash files maestro_error txt maestro EXE dmp Installation Guide 101 Appendix B File and Resource Locations on Windows Table B 1 Location of files written or used by Schr dinger software Main Location Folder Files maestroNN Maestro recent projects list mruprojectlist SUSERPROFILE Schrodinger Customized schrodinger hosts license txt queues Custom queue definition files product Customized data files such as reagentprep ini Com biGlide solvation files etc 102 Schr dinger Software Release 2014 2 Appendix C Access to the Web via a Proxy Some Schr dinger applications can retrieve information from the web If you are using a proxy server for web access you may have to perform some configuration to allow these applications acces
89. internally to all cluster nodes that is one that does not create network traffic through the manager node to the external network 2 The job submission host and the compute nodes must be able to open socket connections to the FlexLM license server The license file can be stored on the external network the internal network or copied to each node Since this file is small the location does not matter Installation Guide 87 Chapter 7 Preparing for Job Submission 88 3 Compute nodes must be able to open socket connections to each other and to the manager node They should also be able to connect to a node or host from which jobs can be sub mitted 4 Passwordless SSH must be enabled a from the job submission host to the manager node b from the compute nodes to the manager node For parallel Jaguar the following are required in addition e The user s home directory has to be mounted on the compute nodes e Passwordless SSH has to be enabled between compute nodes 7 5 2 Secure Channel Communication and Firewalls Job Control uses an SSH tunnel for data transfer between the job submission host and the queue host to ensure secure transfer by default the secure channel This applies to commu nication to and from a cluster Within a cluster Job Control uses ports above 1024 for commu nication between the manager node and the compute nodes using socket connections To configure the manager node for secur
90. inux platforms 2 35 Prime 3 6 Prime requirements cover Prime Induced Fit Docking and Covalent Docking Prime requires the installation of or access to various third party products See Section 2 4 on page 11 for more information 2 4 Prime Third Party Software and Databases To use Prime you must install or have access to the PDB the BLAST program and associated sequence databases and the HMMER program and Pfam database The required third party programs and databases for web based searching are provided in the download and on DVD Use of PSIPRED is also highly recommended for secondary structure predictions and for GPCR modeling PSIPRED is not available on Windows PSIPRED is not distributed as part of the Schr dinger software package see Section 3 7 on page 21 for information on obtaining and installing this program on Linux The databases are available on DVD If you downloaded Prime and do not have the databases instructions for obtaining them are provided in Section 3 7 on page 21 for Linux Section 4 2 on page 33 for Windows and Section 5 2 on page 37 for Mac OS For Induced Fit Docking you do not need to install the third party programs or databases e For Homology Modeling you do not need to install the PDB or BLAST databases if you have access to these databases on the web e If you do not intend to identify families for your query sequence you do not need to install HMMER and Pfam Disk space requirements a
91. ions between somehost mydo main com and 12 34 56 78 will not be secured because they are in the same zone but connec tions between 123 45 67 89 and 12 34 56 78 will be secured because they are in different zones 7 1 12 Customizing the Hosts File You can copy and edit the schrodinger hosts file from the installation directory to customize its settings The edited hosts file should be placed in your Schr dinger user resources directory which is HOME schrodinger on Linux and Mac and SUSERPROFILE Schrodinger on Windows You usually do not need to do this unless you have different user names on different hosts If you have installed Schr dinger products on multiple hosts you may need to edit the schrodinger hosts file on each host to add entries for the other hosts Installation Guide 59 Chapter 7 Preparing for Job Submission 60 7 2 Setting Up Access to Remote Hosts To run jobs on remote hosts you must set up access to these hosts by allowing use of the ssh command without specifying a password If you have a firewall you must allow access across the firewall Setting up access is described in the subsections below Remote jobs can be submitted to Linux and Mac hosts but not to Windows hosts e To be able to run jobs on remote hosts Schr dinger products must be installed on both the local job launch host and the remote hosts or on a file system that is accessible to both e If access has been set up previou
92. ironment variable in the KNIME startup script rather than via Preferences On Linux if you cannot update usr 1ib64 libstdc so 6 to version 6 0 14 you must set LD LIBRARY PATH in the KNIME startup script to include the following location KNIME installation plugins com schrodinger knime_version lib Linux x86_64 6 2 Updating Existing Schrodinger Extensions If you have direct access to the web you can update the existing Schr dinger KNIME exten sions to new versions using the update mechanism in KNIME as follows 1 Start KNIME 2 Choose Help gt Check for Updates The Contacting Software Sites panel opens and checks for updates to the software by contacting the web sites defined in your Available Software Sites preferences see File gt Preferences Install Update You are prompted to log on to the Schr dinger web site 3 Enter your email address and password as you normally do to log on to the Schr dinger web site If there are updates the Available Updates window opens listing the updates that are available This list includes updates to all installed KNIME components 4 Review the list of updates and deselect any items that you do not want to update If you only want to update the Schr dinger extensions deselect all other updates Installation Guide 45 Chapter 6 Installing and Updating KNIME Extensions 46 5 8 Note If you update the KNIME Desktop or Eclipse we do not guarantee tha
93. la mca_ras_tm so If loose integration is used however your parallel jobs will not be the under control of PBS Pro and in the case of a failure the slave processes might not be terminated by MPI Alterna tively you can replace the bundled Open MPI with your own Open MPI installation contact help schrodinger com for more information Here are some examples of host file entries Request NPROC processors on a single node Name label Queue PBS10 4 Qargs q PBS queue 1 select 1 ncpus NPROC mpiprocs NPROC Host submit node Processors processors in queue Request NPROC processors one on each node Name label Queue PBS10 4 Qargs q PBS queue 1 select NPROC ncpus 1 mpiprocs 1 Host submit node Processors processors in queue Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Request SNPROC processors spread across nodes using 2 cores per node Name label Queue PBS10 4 Qargs q PBS queue 1 select NPROC 2 ncpus 2 mpiprocs 2 Host submit node Processors processors in queue Parallel Jaguar Hybrid OpenMPI OpenMP Request NPROC total threads with STPP threads per node Name label Queue PBS10 4 Qargs q PBS queue 1 nodes NPROC TPP ncpus TPP mpiprocs TPP Host submit node Processors processors in queue Torque Due to a naming conflict components for Torque have been placed under SCHRODINGER mmshare vversion lib arch openmpi
94. le is shown below name tmpdir ame ame ame fe Ber ie a Se ame schrodinger tmpdir processors name host queue qargs Schrodinger hosts file schrodinger localhost software schrodinger2014 ser larry curly moe server usr local schrodinger2014 big scr 8 cluster manager PBS lwalltime 1000 00 00 Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission schrodinger sw schrodinger2014 env SCHRODINGER THIRDPARTY fast disk processors 16 tmpdir storage TMPDIR End of Schrodinger hosts file 7 1 1 The name and host Settings The name setting must be the first line for each entry This is the name that is used to select the host or batch queue with the configuration specified in the following settings It is displayed in the list of hosts in the Start dialog box Host menu or table Usually entry label is the name of a host that can be used to run a calculation If it is not you must include a host setting that supplies the host name The host setting is only needed if the name line does not give the host address You might for example want to provide an alias in the name setting and define the host name in a host setting if the host name is long Another use of multiple entries for a single host is to specify different settings on a host such as different scratch directories or different software installations You can also use the
95. m the uninstallation 2 Type yes and press Enter A password prompt is displayed 3 Enter the administrator password The software is removed from disk and the SchrodingerSuites2014 2 folder is removed from the Applications folder Schr dinger Software Release 2014 2 Chapter 5 Installing the Products on a Mac 4 Close the command window for the uninstaller If you do not use the uninstaller and try to install software the applications will not run You must then use the uninstaller to uninstall the software and then reinstall it Installation Guide 39 40 Schr dinger Software Release 2014 2 Chapter 6 Installing and Updating KNIME Extensions The Schr dinger KNIME Extensions are available with the software distribution either on DVD or the software download page or from the Schrodinger KNIME update web site The software distribution includes KNIME itself as well as the extensions e To install KNIME and the Schr dinger extensions from the software distribution select the KNIME Extensions when you install the Schr dinger software Windows only KNIME and the extensions are automatically installed on Linux and Mac e If you already have a compatible version of KNIME installed and want to use this version of KNIME instead you should install from the Schr dinger KNIME update web site using the instructions in Section 6 1 An archived copy of this site is included in your Schr dinger software download The up
96. mary Schr dinger software user e Computer platform type e Operating system with version number Version numbers of products installed e mmshare version number 4 2 Installing Prime Third Party Software and Databases Prime allows you to do both web based searches of the BLAST and PDB databases and searches of a local copy of these databases The required Prime third party software is included in the Prime installer and is installed into the thirdparty folder of the installation by default The databases needed for web based searches are also included in the Prime installer and are installed by default When you do a default installation of Prime you need not do anything more to enable web based searches for finding homologs secondary structure prediction and alignments If you have a web proxy server you may have to configure it see Appendix C If you want to use local databases you must install the databases and set the appropriate envi ronment variables The required Prime third party databases can be installed directly from the web They are also available from the Schr dinger FTP site as a set of zip files or on DVDs When you install the databases you should consider installing them to a network mounted disk because of the space required and so that they can be used by multiple users If you do so you must set envi ronment variables to identify these databases see Table 2 2 on page 13 You should not install the datab
97. mber of tokens available for each license Exit the script by typing CTRL D The log output from the script is sent to the system logging facility syslog so you can examine the syslog to find information about the actions performed by the script More verbose information is sent to the logfile which is set manually and optionally inside the script Installation Guide 79 Chapter 7 Preparing for Job Submission 80 7 4 1 3 Installing the Load Script To install lexlm_sensor pl you need to add a load_sensor attribute to the host configu ration of one of the hosts managed by SGE The load sensor is executed periodically on that host and feeds information about license availability back into the queueing system You can get a list of the execution hosts using the command aconf sel To add the load sensor to the host configuration for the chosen host 1 Enter the command qconf mconf hostname 2 In the resulting edit window add the line load_sensor installation utilities flexlm_sensor pl where installation is the installation directory SCHRODINGER You must specify the path explicitly you cannot use environment variables in the SGE configuration files If there is already a load_sensor line replace it with the above line 3 Save the modified file and close the editor 4 Verify that your changes were accepted by displaying the host configuration with the command qconf sconf hostname SGE starts the load sen
98. nan ea a a sterne 13 host list for MPI parallel jobs 110 host name schrodinger hosts file 51 hosts CKSCUMON innen een 53 setting UP ACCESS CO eee eee eee eee 60 SUDIMISSIOM e 2 4 222200000 Henn eae sne 53 testing ACCESS TO nerien 90 hosts Milera sense 49 59 batch queue configuration s s s 65 efimitl 01 UTTER Ras ERA RASER Er E 49 EXAMPLE re inensis 52 including another hosts file in 51 replacement of pera a testing s 90 validating we OO Windows installation sssesessssesossesrsnn 30 l Impact queue configuration for OpenMPI 67 Induced Fit Docking enene 11 modules to install 29 installation directory s ssssssesssssesesesesesinennnen 55 location on Mac 34 Schr dinger Software Release 2014 2 POGUE MCMUS os nu 28 selecting on Linux 18 selecting on Windows 31 setting in hosts file 52 specifying for host 55 J Job Control testing 93 K Keys RS G scssstsdasieasge sated iavdnexaesy cateenatevase 60 62 KNIME extensions addnp zen 46 installing oeren einnar 41 KNIME version s s sssssosssssosssronsorsrsrnrrnrsnnennnrn 10 UP atin nun 45 KNIME V rSlO ssss sssasssssvosesss sensdosassteses nsdsrsrsnn 10 KNIME workflows s sssssssssssesosesesesesereserenenernrnnn 47 Known hosts M nstren 61 L license Checking c0 cessessassassensovesscss
99. nd MD jobs run on a GPU require 1 CPU per GPU The NPROC placeholder will be substituted in the hosts file for the number of GPUs requested by the user at run time Therefore the same placeholder can be used for both see Section 7 3 3 on page 67 for further examples of the 3NPROC placeholder in the hosts file Here are three examples SGE Torque and LSF that can be used for GPU jobs in a very simple scheduling environment SGE name sge gpu host headnode mycluster com queue SGE qargs q myqueue q pe smp NPROC tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 gpgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Torque name torque gpu host headnode mycluster com queue Torque qargs q myqueue 1 nodes 1 ppn NPROC tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 gpgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 LSF name lsf gpu host headnode mycluster com queue LSF gargs q myqueue n NPROC R span hosts 1 tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 gpgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 Theses entries have several assumptions and characteristics e GPUs are not managed explicitly We assume that the queue called myqueue only includes hosts with GPUs e The nodes with GPUs are have
100. nd it with http You can use p port when you run these utilities to specify the port Schr dinger Software Release 2014 2 Appendix D Global Configuration File To allow settings to be made globally for all users a file named site config can be added to the installation directory The settings in this file supersede environment settings made by the user and in the hosts file The file is read by jserver but only when jserver is started If changes have been made to this file j server must be restarted The file is formatted in INI style Currently it only allows global enabling and disabling of secure transfers To globally disable or enable secure transfers use the following syntax jobcontrol secure transfers off on You can also use 0 and 1 instead of off and on Installation Guide 105 106 Schr dinger Software Release 2014 2 Appendix E Adding an Unsupported Queueing System To add support for an unsupported queueing system the following files must be created in a subdirectory of SCHRODINGER queues that is named to identify the queueing system e A submit script which is a wrapper for the queueing system s own job submission utility qsub for PBS and SGE e A cancel script which is a wrapper for the queueing system s job removal command adel for PBS and SGE e A template sh file which is a template for the shell script that is actually submitted to the batch queue and used to launch
101. nn 13 PYMOLAMAESTRO u 240452 8008420000025 25 35 SCHRODINGER amp 945e45 05 se00 5o0s drsessedestssskesnsesnen 19 SCHRODINGER BATCHID sssoststesss ssssnssnge 110 SCHRODINGER INSTALLER LOG VERBOSE farssia AE E EE E oe SCHRODINGER INSTALLER LOGFILE DIR E EEE E EE 28 SCHRODINGER LICENSE RETRY 20 66 SCHRODINGER NODEFILBE cc ccccee 110 SCHRODINGER _PDB cccssseeeeees 12 13 22 SCHRODINGER_PROXY_CONFIG 104 SCHRODINGER SCRTPTS siisii 21 SCHRODINGER SECURE TRANSFERS 88 SCHRODINGER SSH IDENTITY 113 SCHRODINGER_THIRDPARTY 12 22 SCHRODINGER TMPDIR yisististietsssesisekssnssnssr 54 SEMNE nun 97 setting default for host eee 50 TEMP sites E 57 IMP ricrea OUTEUFTTEERRITEHRFTCFTREGEHFEUBEREET ENT 57 Installation Guide 115 Index 116 TMPIER nun 57 67 USERPROFTLLE sale ee 113 Eyince VersiOi seice anssdessssnssonssnisnsssssenssness 6 execution H ST 4535664500052 005550 550 00nss sersprtnnen stt sndernns 33 F file names on DVID issssssorssssesisssessoss ensneessisnnsss 16 firewall applications to unblock on Windows 63 queue host configuration 63 88 G GE queueing system sssmnssrssssesrsrssenreresrsrrnennn annan 64 graphics Card sehn 5 graphics drivers 5 Grid ENG vs ssscvrssesinvsnssssssessssssstrantnsnsrersneteneserie 64 VEFONT E 8 H HMMER VET SION ysna E seien eine 12 WED SIE er
102. nstallation of Schr dinger Suite 2014 2 may depend on taking action on one or more of the following items e If you are using product management software you should be aware that Schrodinger software includes files with a ini extension that are not Windows ini files You may have to configure your management software to treat these files as plain files Installation Guide 27 Chapter 4 Installing the Products on Windows 28 e Check that you have enough disk space see Section 2 2 on page 8 The installer requires space on the local drive to unpack the MSI files and store a backup copy You must there fore have enough space locally to store a copy of the entire installation in addition to the space for the installed software on the drive to which you are installing and the space taken by the download e Installation log files are written by default to the following folder LOCALAPPDATA Schrodinger Installer 2014 2 These log files may be useful for troubleshooting If you want to change the location set the environment variable SCHRODINGER INSTALLER LOGFILE DIR to the desired location which must exist and have write permission See Appendix A for information on setting environment variables If you cannot find a network mounted drive that you want to use it may be due to settings made by User Access Control under which access to network shares may use the stan dard network token instead of the Administrator token
103. number of licenses reported decrease by the specified percentage The log output from the script is sent to the system logging facility syslog so you can examine the syslog to find information about the actions performed by the script More verbose information is sent to the 1ogfile which is set manually and optionally inside the script 7 4 2 3 Installing the Load Script 1 Copy the edited script into the LSF_SERVERDIR directory on the LSF master host cp SSCHRODINGER utilities elim schrodinger LSF_SERVERDIR The LSF_SERVERDIR directory is typically named something like usr 1s 6 2 linux2 6 glibc2 3 x86 etc and also contains the program melim which man ages ELIMs Installation Guide 83 Chapter 7 Preparing for Job Submission 84 2 Restart LSF with the following commands lsadmin reconfig badmin mbdrestart 3 Check that the new ELIM is active using the command lsload 1 The output should now contain the number of available tokens for each license for example HOST NAME status lt gt mem IMPACT MAIN MMLIBS hostl mycluster com ok lt gt 365M 10 15 host2 mycluster com ok lt gt 365M 10 15 LSF should now be configured to handle Schr dinger license requirements 7 4 2 4 Turning On License Checking in Job Control The final step is to instruct Job Control to specify license requirements when submitting jobs to the queue This step must be completed after the steps above otherwise jobs submi
104. o Technical Support The installation_check application runs a test program testapp that exercises all the Job Control related features of a real application You can run this program as follows testapp options Ljobname inputfile The options are described in Table 7 3 Table 7 3 Options for the testapp command Option Description DEBUG Produce debug output DIR jobdir Job launch directory The default is chosen automatically a Write auxiliary output file c time Time for subprocess to run in seconds e Write empty output file nfiles Number of extra output files Used to test file transfer g Write output file for each stage i infile Extra input file Used to test file transfer j jobname Job name k signal Send this signal to the executable at the end of the job 1 license Require the specified license If license is omitted require an MMLIBS license Used to test the license checkout mechanism The syntax for license is name version count where name is the license name version is the 2 digit software version number and count is the number of licenses Examples IMPACT GLIDE 4 IMPACT GLIDE 55 4 Installation Guide 93 Chapter 7 Preparing for Job Submission 94 Table 7 3 Options for the testapp command Continued Option Description n nsubjob Number of child jobs subjobs to spawn Default is 0 o nlines Number of lines in output file Used to test file tran
105. o install custom profiles copy them to the apps customize profiles folder in the unzipped installer folder before you install These profiles are presented along with the standard profiles when the screen for selecting profiles is displayed by the installer To install an existing hosts file rather than create a default hosts file copy the desired schrodinger hosts file to the apps customize folder in the unzipped installer folder before you install To install the license file license txt automatically copy it to the apps customize folder in the unzipped installer folder before you install e If your virus checker flags any executable in the distribution as a risk make an exception for that executable SCHROD exe is flagged by some virus checkers for example Documentation for all products is installed and uninstalled automatically along with the shared libraries mmshare 4 1 3 Installing From the DOS Command Line If you want to install the software from the command line without using the graphical inter face you can run the installer in a DOS shell in silent mode as follows setup silent exe install remove repair options The options are described in Table 4 2 To check the progress of the installation you can look at the log files which are located in lt LOCALAPPDATA Schrodinger Installer 2014 by default and contain the following information schrodingerSetup log Overall progress schrodingerInstaller l
106. o use on the host Multiple instances can be used for multiple GPUs The specification is in the form id description where id is the numerical GPU id usually starting from 0 and description is the description of the GPU for example GTX 580 Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Table 7 1 Keywords for schrodinger hosts file settings Continued Keyword Description host Host name This entry is only needed if it is different from the name set ting or if the queueing software is only available on a particular host include Name of an auxiliary hosts file to be included in the current hosts file The inclusion is done by replacing the include line with the contents of the specified file knime Path to an external KNIME installation i e an installation other than the one in the Schr dinger installation name Name of the host entry or batch queue For a host this is usually the host name This name is displayed in the Start dialog box The name must not contain spaces The value localhost is a special name that means the host on which the job is launched nodelist List of entry names used to define a multiple host entry A name may be followed by a colon and a number of processors Can be combined with a host setting parallel Specify whether the host supports MPI parallel jobs or not The value can be specified as yes or no true or false 1 or 0 port Server port to use when sending j
107. oad 3rd Stage Sharada Colony Basaveshwaranagar Bangalore 560079 India SCHR DINGER
108. obs to a server Used by KNIME only processors Number of processors available on the host If the host is part of a clus processors per node proxyhost proxyport gargs ter this number should be the total number of processors available on the cluster For multicore processors the number should be the total number of cores available The default is 1 except for the localhost entry where the default is the number of available processors or cores Number of processors cores per node available to a batch queue This setting is used by applications that support threaded parallel execution OpenMP Host on which to run jproxy This setting should be made when the host from which a job is launched cannot open a socket connection on the host on which the job is actually run By default jproxy is run on the host specified by the host keyword and is only run when using a queuing system This setting is only needed in cases where using the default is impossible or impractical Only valid when the host entry also contains a queue setting Specify the port or range of ports that j proxy may use Ports can be specified as comma or colon separated lists without spaces Ranges can specified with a dash for example 5987 5989 5992 5994 Only valid when the host entry also contains a queue setting Arguments to be used when submitting jobs to a batch queue These arguments should specify any parameters that define the queue Install
109. oes not have an Infiniband network and is used for parallel execution This setting suppresses warnings that are generated by Desmond which uses Infiniband if it can when running in parallel For Open MPI parallel use it is advisable to set one of the environment variables TMPDIR TEMP or TMP to a local file system in order to avoid performance issues with temporary files See Section 7 3 3 on page 67 for more information 7 1 9 The include Setting The include setting is a convenient way of maintaining a hosts file that can be used across multiple installations of the software For example suppose you have installations in the following locations opt schrodinger schrodinger2011 opt schrodinger schrodinger2010 opt schrodinger schrodinger2009 By adding a file opt schrodinger global hosts that contained the hosts that could be used by all software versions you can then use the include setting to refer to this file in the schrodinger hosts file for each installation Hosts file for Suite 2009 name localhost schrodinger opt schrodinger schrodinger2009 tmpdir var tmp processors 4 include opt schrodinger global hosts Because the localhost settings are inherited by all other hosts the location of the installation schrodinger setting can be specified in the hosts file for the particular release and omitted from the global hosts file Installation Guide 57 Chapter 7 Preparing for Job Submission 58
110. og Information for the product installer that was last run or is currently running Schr dinger Software Release 2014 2 Chapter 4 Installing the Products on Windows Table 4 2 Options for setup silent exe Option Description install installdir directory logpath directory plist filename profiles all1 profiles remove repair interactive mode on off user all current Install products This is the default and includes all products Installation directory If mmshare is already installed the directory in which it is installed is used and this directory is ignored the change is noted in the log file The default is C Program Files Schrodinger 2014 2 orC Program Files x86 Schrodinger 2014 2 for 32 bit executables on a 64 bit OS Directory for log files Default is SUSERPROFILE SchrodingerInstaller 2014 Full path to text file containing list of products to process The file must contain one product name per line The product names are case sensitive The product name can be obtained from the initial string up to the version string vx y on the product line in the GUIDs ini file e g maestro phase client If this option is omitted all products are processed for the specified action install remove repair Install the specified profiles given as a comma separated list Valid standard profiles are Maestro Elements BioLuminate FirstTimeUser MaterialsScience
111. optimizing cluster performance in addition to the general hardware requirements and recommendations given above A highly capable file server for the external network A high performance intra cluster network especially for Desmond Shared storage for the intra cluster network to reduce traffic to and from the external net work e Fast processors large memory and high quality motherboards and network interfaces especially on the management nodes 2 1 2 Linux Basic requirements e One of the following 64 bit operating systems e RHEL 5 9 5 10 6 3 6 5 e CentOS 5 9 5 10 6 3 6 5 e SUSE SLES 11 SP3 SLED 11 SP3 OpenSUSE 13 1 e Ubuntu 10 04 LTS and 12 04 LTS e NFS file locking must be enabled Software requirements for documentation e Adobe Reader no earlier than 7 0 5 for searching manuals e PDF reader other than Adobe Reader for viewing manuals If using Evince a version no earlier than 2 0 is required Okular is recommended if available Schr dinger Software Release 2014 2 Chapter 2 Hardware and Software Requirements RedHat CentOS requirements e The nfs utils package must be installed yum install nfs utils Ubuntu requirements e Themesa utils package must be installed sudo apt get install mesa utils 2 1 3 Windows All products and job types are supported for local use on Windows except for Desmond simu lations MCPRO Jaguar jobs using multiple selected entries Remote job submission from
112. ost The extension must be included when you specify the location of the file The default value of the USERPROFILE environment variable on Windows XP is C Documents and Settings username on Vista it is C Users username To find out what USERPROFILE is set to you can open a DOS window and enter the command set If you do not save the private key to this location you must set the environment vari able SCHRODINGER_SSH_IDENTITY to the appropriate path You must have a private key for each user name that you intend to use on remote hosts It is recommended that you generate a private key for each user name Repeat these instruc tions from Step 3 to Step 8 generate a new key for each user name 9 Open a DOS window and run the following command once for each host to which you want to establish a connection without supplying a password path to plink plink exe ssh hostname i path to ppk 1 username 1s plink exe should be in the same location as puttygen exe If the ssh server on the remote host supports only SSH 2 0 use the following command instead path to plink plink exe ssh 2 hostname i path to ppk 1 username 1s The quotes around the path to the private key are required and the ppk extension must be included This path is the one you specified in Step 8 If the remote host can be resolved on the network using both its short name and its fully qualified domain name repeat the plink command for each version of the name
113. other software that relies on the presence of this folder 4 3 Setting Up Access to PyMOL Both Maestro and Canvas can open PyMOL directly To do so PyMOL must be installed and the location communicated to the application The recommended procedure is 1 Install PyMOL in a location outside the Schr dinger software installation 2 Add the PyMOL location to the PATH environment variable 3 Set the PYMOL4MAESTRO environment variable to the PyMOL location See Appendix A for instructions on setting environment variables Canvas requires that the PyMOL location is in the PATH environment variable Maestro does not use PATH but uses the following sources to find an installation of PyMOL first in the order given 1 The registry If PyMOL is installed on Windows with an installer this version is used 2 The PYMOL4MAESTRO environment variable This environment variable should point to the PyMOL installation This is the preferred way of specifying the location of PyMOL 3 APyMOL launch script called pymol4maestro in the Schr dinger software installation This script must run PyMOL 4 APyMOL installation in the Schr dinger software installation in the pymol folder 5 The standard PyMOL environment variable PYMOL_PATH 6 A launch script called pymol in the Schr dinger software installation Installation Guide Chapter 4 Installing the Products on Windows 36 4 4 Uninstalling Schrodinger Software Before uninstalling S
114. point to this file An example of this is shown in the PBS batch script above in the if block above the SENVIRONMENT line E 4 The config File The configuration file must contains settings for the keywords QPATH QSUB QDEL QSTAT and QPROFILE These keywords define paths and commands that are used by the queueing soft ware As an example SCHRODINGER queues PBS config contains the settings QPATH usr local pbs bin QSUB qsub QDEL qdel QSTAT qstat The QPROFILE keyword specifies the absolute path on the queue host of a configuration file that needs to be sourced to set up the environment to use the queue This variable is useful for setting up an environment for the queuing system that does not affect the global environment Schr dinger Software Release 2014 2 Appendix F Setting Up Remote Access Manually on Windows This appendix describes how to manually set up access to remote hosts from Windows rather than using the Remote Access Setup tool This process involves running PuTTY gen which is provided in the Schr dinger software installation in SCHRODINGER mmshare vversion bin WIN32 x86 and uses plink exe for connection which is also provided in the Schr dinger software installation 1 Double click puttygen exe in an explorer window or run puttygen exe from the command line The window that is displayed when PuTTY gen starts is shown in Figure F 1 2 In the Parameters section select the appropriate type of key
115. pter 7 Preparing for Job Submission 66 incompatible changes in versions of some queueing systems the directories for the more recent versions have a version number appended e g PBS10 4 The Qargs setting specifies command line arguments for the queueing system s job submission command for SGE for instance this is the gsub command You must also include a host setting because the name setting is used to specify the queue Like normal remote host entries host entries for batch queues inherit settings made in the localhost entry of the schrodinger hosts file If the queueing software is available to all hosts to which users have access you can set host to localhost Otherwise you should set it to the host that runs the queueing software Batch queue entries can also have any of the other settings that host entries have such as schrodinger and tmpdir For queues on clusters the tmpdir setting is required and should refer to a directory that is available to all the nodes and writable by all users who will use that queue On shared memory machines the tmpdir setting is optional You should also add a processors Setting for submission of distributed jobs You should consider adding an env setting for the SCHRODINGER LICENSE RETRY environ ment variable particularly if there is likely to be a communication delay in obtaining a license or the license pool is oversubscribed See Appendix B of the Job Control Guide for the syntax For
116. r e Run the setup exe program that you used to install the software e Run uninstall silent exe from a DOS window not a Schrodinger Command Prompt window This program is also in the installer folder of your Schr dinger software installation It accepts the same arguments as setup silent exe given in Table 4 2 on page 31 except that the default and only allowed action is remove so you do not need to specify the action When you uninstall Schr dinger software you can choose whether to uninstall Maestro and the various applications Selecting Maestro does not uninstall other applications which must be selected separately To uninstall the entire software package you should ensure that you unin stall the other applications as well as Maestro If you have installed the third party databases required by Prime into the Schr dinger installa tion the uninstaller does not remove them and you must remove them manually from the installation You should do this before running the uninstaller otherwise the installation is not entirely removed Schr dinger Software Release 2014 2 Chapter 5 Installing the Products on a Mac This chapter covers installing and uninstalling Schr dinger software on Mac OS X Once the software is installed you must obtain and install a license If you want to run jobs on other hosts you must also configure access to those hosts using the information in Chapter 7 5 1 Installing Schr dinger Softw
117. r 3 Installing the Products on Linux 16 3 Copy the following files to the remote host e product tar files for your platform e INSTALL file e scripts in the top level directory e Maestro and mmshare tar files for your platform e data tar files for your product e third party software and databases for Prime e documentation tar file 4 Change file names if necessary If you are installing from a DVD drive on a Windows machine Windows may change the case of the file names The tar files and plat form script should be in lower case and the INSTALL script and the README file should be in upper case Use the TRANS TBL file to rename the files with the correct case If you downloaded the software You must extract the files from the archive tar file The directory to which you downloaded the software is represented by download directory in what follows cd download directory tar xvf Schrodinger Suite2014 type tar where type identifies the hardware platform that the software will be installed on and the type of institution installing the software When you have extracted the files a subdirectory named Schrodinger Suite2014 type is created and the software is in this subdirectory The installer directory is therefore download directory Schrodinger_Suite2014_ type If you want to install the software on multiple hosts you should either ensure that download direc tory is accessible to each host or copy the archive file to
118. r OpenMP 68 Torque configuration for OpenMP 71 R RedHat requirement ssssssssrsrsessesessresesrsrsrerrnr 7 remote hosts Settings LOK A A 49 59 SSH ACCESS tor users 60 testing ACCESS tO eeneenenenennennnnennenennnnennenannen 90 RSA public key authentication 60 S schrodinger hosts see hosts file 49 scratch directory specifying default during installation 18 specifying in hosts file 52 54 SCCUTE Channel seccccissceassassiveesserscsnsenssarvsccancsssszens 88 disabling in secure zones 58 tesinp ren 90 secure ZONES 58 SSCULEZ ONES en 58 SGE queueing system usnsenesenennenennenennnn 64 license checking 77 parallel configuration eeee 68 Installation Guide 117 Index 118 SLURM queueing system 64 Spotlight turning off indexing 38 ssh command use for remote jobs 49 ssh key generation uesesnsessneneesennenennen 60 62 SSH tunnel testing for file transfer oo eee 90 use for file transfer 88 stereo viewing requirements 1 00 eee eee 5 submission host ueeeseesnnennnenennnnennnennennnnn 33 T technical support generating information for 92 temporary files POT JOD serein E E E 54 from Open MP ST see also scratch directory third party databases utilities for updating 22 34 38
119. r example if the directory designated by tmpdir becomes full with files that you don t have permission to delete you can set SCHRODINGER_TMPDIR to a different directory and continue to run jobs 7 1 4 The processors and processors per node Settings For hosts with multiple processors that are not running a queueing system set processors to the number of processors on the host For batch queues set processors to the number of processors available to the queue Here processors refers to hardware units capable of running a job which for most recent hardware means cores For applications such as Jaguar that use OpenMP for threaded parallel execution set processors per node to the number of processors available on each node available to a batch queue You should ensure that the host for the queue does not have nodes with different numbers of processors Within the gargs setting you can use PPN as a variable that has the value of the processors per node setting and SNPROC PPN for the number of nodes total number of processors divided by the number of processors per node 1 On XP LOCALAPPDATA is equivalent to 3USERPROFILE Local Settings Application Data Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 71 5 The parallel Setting The parallel setting allows you to designate hosts that do or do not support MPI parallel job execution By default it is assumed that a host supports
120. rdparty database MofN zip psp pdb thirdparty database MofN zip The number of files may change as we update the databases periodically The download could take several hours because each zip file is about 600MB You only need the last zip file if you are planning to install the software outside the Schr dinger installation 3 Unzip the zip files into the desired location We recommend that you do not use the Schr dinger installation folder to install the data bases because they are very large and you would have to move them for each release Schr dinger Software Release 2014 2 Chapter 4 Installing the Products on Windows The extraction process could take an hour or two When it finishes you should have the databases in a thirdparty folder in the location you chose Some programs for unzipping files such as 7 Zip allow you to select multiple zip files to extract into a single folder 4 Set the required environment variables see Section 2 4 on page 11 and Appendix A If you are only installing the databases set SCHRODINGER PDB and PSP_BLASTDB If you are installing the software and the databases in the same location set SCHRODINGER_THIRDPARTY To install the databases from DVD you need only complete Step 3 and Step 4 Note The copy of the PDB database installed as described here does not include an all folder While this does not affect the running of Schr dinger software its absence might affect the running of
121. re available in the software distribution If you have problems with the installation please send the following files which are in the directory LOCALAPPDATA Schrodinger Installer 2014 to help schrodinger com schrodingerInstaller log SchrodingerPreInstallReg reg txt schrodingerSetup log SchrodingerPostInstallReg reg txt Schr dinger Software Release 2014 2 Chapter 4 Installing the Products on Windows You should also send the file schrodinger_machid txt which is on your desktop If you have installed software versions for more than one release there will be multiple copies of this file named schrodinger_machinfo N txt where N is a number In this case you should check that you send the correct version of the file which will usually be the latest version If Maestro fails to start send email to help schrodinger com describing the circumstances and attach the file maestro error _pid txt If Maestro fails after startup attach this file and the file maestro exe_pid_timestamp dmp These files can be found in the following folder SLOCALAPPDATAS Schrodinger appcrash On Windows XP sLOCALAPPDATA is not set by default but should correspond to C Documents and Settings username Local Settings Application Data When sending e mail messages please include the following information All relevant user input and machine output e Schr dinger software purchaser company research institution or individual e Pri
122. re listed in Section 2 2 on page 8 Installation Guide 11 Chapter 2 Hardware and Software Requirements 12 If you choose to use your own installations of the third party software the following versions are required e BLAST 2 2 16 e PSIPRED 2 61 e HMMER 3 0 and Pfam 26 0 Note The current version of Pfam is incompatible with previous versions distributed with Schr dinger software If you have been using a version of Pfam that is installed outside the Schr dinger installation you should ensure that you set the appropriate environ ment variables to point to a compatible version see Table 2 2 If you install these third party products from the DVDs supplied by Schr dinger you must run the INSTALL script for each DVD Do not change DVDs while the INSTALL script is being executed if you do the script will fail After you have installed the software you may need to set environment variables to identify the location of the software depending on where it is installed If you install all of these third party products and databases into the default location SSCHRODINGER thirdparty you do not need to set any extra environment variables However when you install a new Schr dinger software release you must make sure that these products and databases are installed in the new default location e If you install all of these third party products and databases in the same nondefault loca tion you can set SCHRODINGER_THI
123. red to as SGE LSF SLURM and Torque queueing systems in the standard software installation Below are links to information about these queueing systems e PBS http www openpbs org http www unix mcs anl gov openpbs e GE http sourceforge net projects gridscheduler http gridengine org http www univa com products grid engine php e LSF http www platform com products wm LSF e SLURM https computing linl sov linux slurm slurm html e Torque http www clusterresources com products torque resource manager php Enabling batch queue submissions to a supported queueing system only requires the addition of a few lines to the schrodinger hosts file and the specification of the queueing system and the queue name These additions are described in the next subsection Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission You should also check that the values of the QPATH and QPROFILE settings in the file SCHRODINGER queues queue config are appropriate see Section 7 3 2 on page 66 For SGE you may need to set the QPROFILE variable in the config file to point to a file that sets up the environment for the queuing software You should not use the cwd argument to qsub for SGE in the hosts file the config file the template sh file or SGE queue aliases as this causes jobs to fail It should be reasonably straightforward to configure a Schr dinger software installation to support other q
124. s The Schrodinger Nodes for Knime core extensions feature must be selected to use any Schr dinger node or renderer The 2D renderers are optional the renderer core feature is required to use any of the renderers Maestro SD and SMILES Click Next License agreements are displayed Installation Guide 43 Chapter 6 Installing and Updating KNIME Extensions 44 9 10 Accept the license agreements and click Next The installation begins Because the Schr dinger plugins are signed you will be asked to accept this information Click Restart KNIME Now KNIME restarts and you can proceed to the identification of the Schr dinger software installation to KNIME To identify the Schr dinger software installation to KNIME 1 2 6 Start KNIME if it is not already running Choose File Preferences The Preferences panel opens Under KNIME choose Schrodinger The Schrodinger preferences are displayed There are two environment variables that you can set SCHRODINGER and PYMOL4MAESTRO If either of the fields for these environ ment variables is unavailable grayed out then KNIME has picked up the variable from the environment and you do not need to set it There should be a message telling you that KNIME has done this If you want to set it in the KNIME preferences you should unset it in your environment and then start KNIME and set it Enter the path to the Schr dinger installation in the
125. s to the web For two applications getpdb which retrieves a PDB file from the web and checkupdates which checks the Schr dinger site for software updates a script has been provided that creates and stores the necessary information about the proxy server Using this script should should work for any proxy server that supports digest or basic authentication You can run this script with the following command on Windows open a Schrodinger Command Prompt window first SCHRODINGER run proxy_config py options The options are given in Table C 1 Table C 1 Options for the proxy config py script Option Description c heck url Check a specific URL f ile filename Specify the file that stores the proxy configuration h elp Display usage message and exit t est Test a previously configured proxy v ersion Display the program version and exit This script tests for access to http and https URLs and if it can access these without problems it does not ask for proxy information If access to either http or https URLs is blocked it asks for the web proxy URL If the web proxy requires a login and password the script asks for these to test the configura tion but it does not store the login and password When you run either of these applications you will be prompted for your login and password The script stores the proxy information in a file named web_proxy json The default loca tion for this file is your Sc
126. se for the products see http www schrodinger com licensing 7 Test the Maestro installation by typing SCHRODINGER maestro If jobs will be run on remote hosts 8 Set up the hosts file page 49 9 Set up communication between hosts if not already done page 60 10 Optional Prepare for Batch Queue Submission page 64 11 Test the installation and communications page 90 1 2 Windows Installation Process Summary 1 Insert the product DVD into the DVD drive or double click the installer icon The setup program should start Select an installation directory that does not contain spaces Select the products and profiles you want to install Obtain and install a license for the products see http www schrodinger com licensing a BB N Test the Maestro installation by double clicking the Maestro icon on the desktop If jobs will be run on remote hosts 6 Set up the hosts file page 49 7 Set up communication between hosts if not already done page 62 8 Optional Prepare for Batch Queue Submission page 64 9 Test the installation and communications page 90 1 3 Mac Installation Process Summary 1 Open the disk image on the product DVD or in your Downloads folder 2 Double click the installer package pkg The installer should start 3 Follow the prompts and enter a password when requested 1 For installation of Maestro only at academic institutions the license is provided in
127. sfer p usec Time in microseconds for a single step of a rapid update job s Initialize executable as if it were a subprocess t seconds Duration of test application job in seconds x code Exit code to use If no input file is specified either a run time t or a number of subjobs n needs to be spec ified If subjobs are specified then the job runs until the subjobs all finish regardless of the specified run time The standard Job Control options HOST NOLAUNCH SAVE and TMPDIR described in Table 2 1 of the Job Control Guide and the extra options INTERVAL LOCAL NOJOBID and WAIT described in Table 2 2 of the Job Control Guide are also supported Distributed computing can be tested with para_testapp The syntax of the command is para_testapp options The options are described in Table 7 4 The standard Job Control options are accepted see Table 2 1 of the Job Control Guide The DRIVERHOST option can be used to specify the host to run the driver job otherwise it is the first host specified by HOST If the number of subjobs is not specified explicitly with the n option then only a single subjob is started Likewise the number of processors to use must be specified explicitly using the HOST option For jobs submitted to a batch queue the Processors line from the hosts file entry is used if it is present LOCAL and NOLOCAL can be used to specify the location of temporary files and LOCALSUBJOB can be use
128. sly you do not need to do so again e If you plan to run parallel or distributed jobs that involve more than one host you must set up passwordless access between these hosts The special case of clusters is discussed in Section 7 5 on page 87 The domain name server DNS must be enabled to run remote jobs from Windows 7 2 1 Setting Up Access To and From Linux and Mac Hosts To use passwordless SSH the hosts to which you want to connect must be configured to satisfy the following requirements e An sshd server must be running e RSA public key authentication must be enabled and empty passphrases must be allowed in the sshd configuration Note Public key authentication is enabled in OpenSSH by default The following steps allow you to use ssh between computers that share your login directory without specifying a password 1 Open a terminal window 2 Generate a public private RSA key pair on a host of your choice whose home directory is shared with the remote hosts that you want to run jobs on cd ssh ssh keygen t rsa Note When asked for a passphrase do not enter one just press ENTER If you specify a passphrase it defeats the purpose of configuring passwordless ssh Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 3 Add your public key to the list of keys allowed to log in to your account cat id rsa pub gt gt authorized keys cat id rsa pub gt gt authorized keys2 The
129. some environment variables In addition to those listed below there may be product specific environment variables that need to be set see the requirements section for each product SCHRODINGER required for all Schr dinger products DISPLAY required for Maestro usually automatically set on login To set the SCHRODINGER environment variable enter the following command replacing install directory with the full installation path for example software Schrodinger2014 csh tesh setenv SCHRODINGER install directory bash ksh export SCHRODINGER install directory To avoid using the wrong installation when a new installation is made or when you use different installations we recommend that you do not add a SCHRODINGER definition to your shell startup script file or add SCHRODINGER to your path definition Instead you can use aliases to set SCHRODINGER to the appropriate location for example csh tesh alias schro2014 setenv SCHRODINGER installdir bash ksh alias schro2014 export SCHRODINGER installdir You can also set aliases to specific programs that substitute the current SCHRODINGER so that you do not have to type SCHRODINGER to run a program For example csh tesh alias maestro SSCHRODINGER maestro bash ksh alias maestro SSCHRODINGER maestro Installation Guide Chapter 3 Installing the Products on Linux 20 An alternative to setting the environment variables directly is to use environment management
130. sor script automatically after you have made the load_sensor setting and also restarts it automatically if you modify or update the script flexlm_sensor p1 The command ghost F h hostname displays all of the resource attributes for hostname If the load sensor is running and working properly you should see your licenses in this list For example gl IMPACT MAIN 20 000000 qg1 MMLIBS 20 000000 SGE should be now configured to handle Schr dinger licenses properly Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 7 4 1 4 Turning On License Checking in Job Control The final step is to instruct Job Control to specify license requirements when submitting jobs to the queue This step must be completed after the steps above otherwise jobs submitted to the queue will fail because the license software will assume that the required licenses are not avail able 1 Open the file SSCHRODINGER queues SGE config in a text editor 2 Change the LICENSE CHECKING line to read LICENSE CHECKING yes 3 Save the modified file and close the editor 7 4 2 Configuring License Checking for LSF 7 4 2 1 Adding License Attributes A resource attribute representing each license must be defined in the queueing system configu ration The utility licutil can be used to parse your license file or query the license server and generate the configuration text that needs to be added to the queueing system configuration files
131. suitable locations and extract it or copy the files described in Step 3 above to suitable locations Note If you do not want to install all modules of the software the modules that you do not want must be removed from the directory from which you install prior to starting the installation The installation installs all modules that are in the same directory as the INSTALL script 3 2 Verifying System Compliance Before starting the installation verify that the systems that you are installing on satisfy the minimum requirements to run Schr dinger software You should follow this procedure for each host on which you plan to run the software When you have verified the system compliance proceed to the software installation Schr dinger Software Release 2014 2 Chapter 3 Installing the Products on Linux 1 Log on to the desired host 2 Change to the installer directory which contains the platform script cd installer dir 3 Enter the following command platform s The script indicates whether your system meets the requirements or needs to be updated If you receive an error message postpone installation of your Schr dinger software until you have updated your system For help obtaining any missing libraries see the appropri ate product specific section of this guide 4 Optional To see a summary of the platform information enter platform 1 The script checks the operating system and distribution CPU type number o
132. sure your parallel environment orte_rr in the example has your desired allocation_rule e g round robin fill_up Next create a complex resource representing the number of cores in each node In this example we call the resource dedicated To set up the complex run the following command and fill in the table with the row given below Installation Guide 69 Chapter 7 Preparing for Job Submission 70 qconf mce name shortcut type relop requestable consumable default urgency Pen ENE SE EE E EE E EE EE E E EE E E E E E A dedicated ded INT lt YES YES 1 0 Finally add the appropriate complex value to each execution host with the value of dedicated equal to the number of slots on the host qconf me computehost 0 3 hostname computehost 0 3 local load_scaling NONE complex values dedicated 12 slots 12 7 3 3 2 PBS Family configuration The TM API is used to allocate slots and launch processes in Open MPI for all of the family of PBS queuing systems For more information of running jobs on PBS Pro or Torque check the OpenMPI FAQs at http www open mpi org fag category tm PBS Pro Tight integration for PBS Pro 9 1 should work without any configuration It might also work for older version of PBS Pro If the bundled components do not work on your queuing system you can remove those components and use loose integration cd SCHRODINGER mmshare vversion openmpi lib openmpi rm mca_plm tm la mca_plm tm so mca_ras_tm
133. t at a time so you must select each host and initialize access to it If several hosts share a common home file system you only need to initialize access to one of those hosts but you should test all of them Likewise you only need to initialize access to a queue host for one of the hosts file entries for the queues on that host To test access to a host select a host in either table and click Test Results are shown in the Status area If you want to initialize access to a host that is not in the hosts file for example before adding it to the hosts file you can add it to the User Specified hosts table select it and click Initialize 7 2 3 Configuring the Firewall If you have a firewall some configuration needs to be made in order to run remote jobs If you do not have a firewall this section is not applicable 7 2 3 1 Linux and Mac Firewalls For simple remote job submission i e submitted directly to the remote host and not via a queueing system you must open ports above 1024 on the remote host For submission to a queueing system the Secure Channel mechanism is used by default See Section 7 5 2 on page 88 for more information If your queue host has a firewall the recom mended procedure is to block all ports above 1024 Communication between the job submis sion host and the queue host is carried out over port 22 via an SSH tunnel 7 2 3 2 Windows Firewalls With Windows firewalls you will often see a popup dialog bo
134. t the Schr dinger extensions will continue to work Click Next The detailed list of items to be upgraded is shown including any dependencies Click Next License agreements are displayed Accept the license agreement and click Finish The download begins As the Schr dinger plugins are signed you will be asked to accept this information Restart KNIME when prompted If you do not have direct access to the web you can update existing extensions from a down loaded archive of the update site by following the procedure for adding extensions 6 3 Adding New Schrodinger Extensions Adding new Schr dinger extensions uses a very similar mechanism to installing the Schr dinger extensions into an existing KNIME installation You can do this from the Schr dinger KNIME update web site or from a downloaded archive of this web site 1 2 Start KNIME Choose Help Install New Software The Install Available Software panel opens Ensure that Show only the latest versions of available software is selected If you are installing the new extensions from the web site do the following a Open the Schr dinger site The URL should be https support schrodinger com releases knime extensions This URL is automatically added when you install KNIME as part of the Schr dinger software You are prompted to log on to the Schr dinger web site b Enter your email address and password as you normally do to log on
135. tail below 1 Click Generate Keys The default key generation is for SSH 2 RSA protocol and 1024 bit encryption You should not need to change these choices but if you do need to change them click Options The keys are written to SUSERPROFILES The private key is stored as user ppk and the public key is stored as publickey txt 2 Click Initialize Host Access A second panel opens In this panel the available hosts are listed in two tables In the first you can edit the table cells to enter a host name and a user name The second table contains a list of all hosts in the hosts file in the installation schrodinger hosts 3 Select a host from the second list A host does not need to be initialized if a it has a home drive that is shared with the host on which you are running the configuration tool or b it has already been initialized Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission 4 Click Initialize You will be prompted to enter your password for the host unless it is already initialized A connection is opened to this host and the public key is appended to the authorized keys file on the host Progress and results of the connection are displayed in the Status area A dialog box opens asking if you want to add this host to the list of known hosts 5 Click Yes 6 Repeat Step 3 and Step 5 for each host that you want to initialize access to You can only initialize access to one hos
136. talling to has plenty of space This is because Windows caches the installers to the primary disk before installing so you must have enough space on your primary disk You can remove the download zip file once you have extracted it if you downloaded it to your local disk You can also remove the download zip files and folders for previous releases to free some disk space If you need more log information when you install the software you can set the environ ment variable SCHRODINGER_INSTALLER_LOG VERBOSE before running the installer Verbose logging can significantly increase the time for installation For information on setting environment variables see Appendix A e If you are editing the schrodinger hosts file and cannot save it this usually means that the editor application is running without administrator privilege Windows does not allow you to modify files under Program Files without administrator privilege You can save the file in a location where you have write permission then move it to the installa tion When editing files in the installation you should start your editor with administrator privilege for example by right clicking and choosing Run as Administrator e If Maestro fails to start and the DOS startup window shows the following error The system cannot execute the specified program the Visual C libraries are probably not installed These libraries need to be installed by a user with administrator privileges and a
137. tch ID of each submitted job so that the ID can be used for cancelling jobs The cancel script should return a nonzero exit status if the operation fails for Job Control to be able to detect the failure If you are creating your own cancel script to support a new queueing system you can use the cancel scripts provided for PBS SGE and LSF as templates Use the QDEL variable rather than the actual submission command in your script and define QDEL in the config file E 3 The Job Script Template File The template sh file is a skeleton for the Bourne shell script that is actually submitted to the batch queue The Schr dinger job launching mechanism reads this file and inserts the commands necessary to launch the user s job and then submits the resulting file to the queueing system using the submit command described above The following information from the template sh file supplied for the PBS system illustrates how the template sh file works bin sh PBS N PBSNAME PBS j oe PBS r n PBS 1 nodes NPROC Batch submission script for OpenPBS system PATH usr bin bin usr bsd usr sbin sbin usr local bin PATH QPATH usr local pbs bin curdir echo 0 sed e s S if curdir config then curdir config fi PATH SQPATH PATH Schr dinger Software Release 2014 2 Appendix E Adding an Unsupported Queueing System SCHRODINGER BATCHID PBS JOBID export SCHRODINGER BA
138. te key pair Load an existing private key file Save the generated key mM Parameters Type of key to generate C SSH 1 RSA SSH 2RSA SSH 2DSA Number of bits in a generated key fi 024 Figure F 1 PuTTYgen window before key generation Z PuTTY Key Generator x File Key Conversions Help r Key Public key for pasting into OpenSSH authorized keys file Key fingerprint ssh rsa 1023 81 b0 33 71 95 7b 39 3b 42 47 83 c3 e0 dd 7e a Key comment Jisa key 20050808 Key passphrase PC O O Confirm passphrase Doo O O m Actions Generate a public private key pair Generate Load an existing private key file Load Save the generated key Save public key Save private key 7 Parameters Type of key to generate C SSH 1 RSA SSH 2 RSA SSH 2DSA Number of bits in a generated key fi 024 Figure F 2 PuTTYgen window after key generation with key selected 112 Schr dinger Software Release 2014 2 Appendix F Setting Up Remote Access Manually on Windows 6 In the PuTTYgen window leave the Key passphrase and Confirm passphrase fields empty Specifying the passphrase would defeat the purpose of this whole procedure which is to avoid the password prompt 7 Click Save private key 8 Save the private key to SHOME unixusername ppk if SHOMES is set otherwise save it to SUSERPROFILES unixusername ppk where unixusername is the user name on the Unix h
139. terface 2 1 1 2 Graphics Card and Monitor Required e 16 bit color Strongly recommended e 1280 x 1024 minimum resolution e Graphics card that supports hardware accelerated OpenGL e Up to date vendor supplied graphics driver The driver supplied with the operating system is usually inadequate If you upgrade the operating system the driver must be reinstalled e Monitor with a refresh rate of 100 Hz or more For hardware stereo viewing one of the following requirements must be met in addition to the recommendations e A graphics card that supports quad buffered OpenGL stereo or e A monitor that supports interlaced stereo On Mac OS X only interlaced stereo is supported Installation Guide 5 Chapter 2 Hardware and Software Requirements Not meeting the recommendations can significantly degrade Maestro performance Note An out of date graphics driver is the most common cause of Maestro display prob lems An inadequate graphics card is the second most common cause 2 1 1 3 GPGPU Computing GPGPU computing with CUDA is supported on Linux only with the following graphics cards e NVidia Tesla all models e NVidia Quadro Fermi and Kepler models e NVidia GeForce Fermi and Kepler models 3GB of video memory is required and a Compute Capability of at least 2 0 See https devel oper nvidia com cuda gpus for the full list of available models 2 1 1 4 Clusters The following components are recommended for
140. the processors per node setting in the hosts file General arithmetic is supported with these variables For example NPROC TTP NPROC 2 NPROC 2 1 TPP 4 Integer division is rounded down so NPROC 8 evaluates to 0 if NPROC is less than 8 Examples are given below for each queueing system 7 3 3 1 SGE configuration Any SGE queue to which parallel jobs are submitted must be configured to support multi processor jobs The schrodinger hosts file must include an entry to describe the queue For SGE queuing systems this entry should look like the following Name my queue name Queue SGE Qargs q SGE queue name pe pe NPROC Host my cluster name processors processors in queue where pe is the name of the parallel environment The value to use for pe depends on the queueing system configuration and it may be necessary to consult the documentation for the queueing system to determine how to select a suitable value The command qconf spl provides a list of defined parallel environments An example of the output of this command is as follows lam mpi mpich Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission These names are merely labels and may have no particular significance for example choosing the mpich environment does not mean that you must run MPICH You can find out more information about a defined particular parallel environment using the command qconf sp pe The SGE man pa
141. the same location as the setup program and should be copied to the installation directory Schr dinger Software Release 2014 2 Chapter 1 Installation Notes 4 Obtain and install a license see http www schrodinger com licensing 5 Test the Maestro installation by double clicking the Maestro icon on the desktop If jobs will be run on remote hosts 6 Set up the hosts file page 49 7 Set up communication between hosts if not already done page 60 8 Optional Prepare for Batch Queue Submission page 64 9 Test the installation and communications page 90 2 For installation of Maestro only at academic institutions the license is provided in the installation Installation Guide 3 4 Schr dinger Software Release 2014 2 Chapter 2 Hardware and Software Requirements 2 1 General Requirements This section lists the general minimum system requirements and recommendations for Schr dinger products If the product specific requirements differ from those listed below they are given in Section 2 3 on page 9 2 1 1 Hardware 2 1 1 1 CPU Memory and Disk e x86_64 compatible processor e 1 GB memory minimum 2 GB recommended per core e For software installation 9 GB disk space see below e For computational jobs 4 GB scratch disk space minimum 60 GB recommended at 10000 RPM e Larger cache size for improved performance of most Schr dinger software e Network card with a configured network in
142. the same number and type of GPUs e g 3 Tesla C2050 s The job does not span nodes The drawback to these configurations is that they make reservations based on CPUs and there may be more CPUs or more properly slots available on each node than GPUs Since the GPU resources are not being requested directly then for these options you should set the number of slots in each node equal to the number of GPUs That will ensure that the node is not over loaded by GPU tasks Alternatively you could arrange for the resource request to reserve the entire node outright If this type of scheduling proves inadequate you will need to manage the GPU resources explicitly For SGE Torque and LSF you can define a consumable resource named gpus for example and configure each host in the cluster to have the appropriate number of gpus Then you would adjust your hosts file entry to request not only the proper number of CPUs but also the proper number of GPUs as in the following examples Installation Guide 75 Chapter 7 Preparing for Job Submission 76 SGE name sge gpu host headnode mycluster com queue SGE qargs q myqueue q pe smp NPROC 1 gpus 1 tmpdir usr local tmp schrodinger opt bin schrodinger2014 2 pgpu 0 Tesla C2050 gpgpu 1 Tesla C2050 gpgpu 2 Tesla C2050 Note that for SGE you set gpus 1 not gpus NPROC The reason for this is that SGE inter prets the resource request as for every slot r
143. to generate Select SSH 1 RSA if the remote ssh server only supports ssh protocol 1 0 Otherwise select SSH 2 RSA Leave the number of bits in a generated key as 1024 3 Click Generate then move the pointer around in the blank area of the Key section You must move the pointer around as PuTTYgen uses these movements to generate a random key When the key is generated it appears in a noneditable text box at the top of this area along with some other text boxes see Figure F 2 4 Copy and paste the key into the authorized keys file in your HOME ssh directory on the UNIX host You must copy and paste do not use Save Public Key Append this public key to the authorized keys2 file if the ssh server supports only SSH 2 0 proto col If your home directory is not cross mounted on all desired UNIX hosts you must copy and paste the key for each independent home directory If you prefer you can use PuTTY to connect to the UNIX host A version of PuTTY is provided in the software installation in the subdirectory mmshare vver sion bin WIN32 x86 5 Make sure you do not have write permissions for group or others on your HOME and HOME ssh directory on the UNIX host chmod go w HOME HOME ssh HOME ssh authorized_keys Installation Guide 111 Appendix F Setting Up Remote Access Manually on Windows if PuTTY Key Generator x File Key Conversions Help r Key No key Actions Generate a public priva
144. to the Schr dinger web site Schr dinger Software Release 2014 2 Chapter 6 Installing and Updating KNIME Extensions Otherwise if you are installing the new extensions from a downloaded archive of the site do the following a In the Available Software tab click Add The Add Repository dialog box opens b Click Archive c Navigate to and select the downloaded zip file d Click OK in the file selector e Click OK in the Add Repository dialog box The available extensions should now be displayed under the URL 5 Select the Schr dinger nodes you want to install 6 Click Next License agreements are displayed 7 Accept the license agreement and click Next The installation begins As the Schr dinger plugins are signed you will be asked to accept this information 8 Restart KNIME when prompted You can also use this panel to update or install nodes from sources other than Schr dinger 6 4 Installing Knime Workflows KNIME workflows that have been wrapped to run from Maestro can be installed for the use of all users into the installation The standard location for these workflows is in the mmshare vversion python workf lows directory of the installation The installation can be performed with one of the following commands SCHRODINGER run installscripts py k c z workflowzipfile zip SCHRODINGER run installscripts py k c d workflowsourcedir The zip file workflowzipfile zip or the directory workflowsource
145. tor privileges you can install Schr dinger software in single user OnlyForMe mode To do so you must have permission to write in the User folder of the registry and permission to create a directory that does not have spaces in the path see below You can also install for all users from a non administrator account with RunAs on XP but you should install the patch available at http support micro soft com kb 949860 en us FR 1 first If Schr dinger software is installed by an administrator in OnlyForMe mode the mode cannot be changed to AllUsers Instead the software must be uninstalled and reinstalled in AllUsers mode If you are repairing or removing software you must ensure that none of the programs that are part of the installation are running at the time as this will prevent the operation from finishing successfully After you have installed the software you must then obtain a license If you are an academic user installing only Maestro the license is included and installed automatically To install Schr dinger software e If you have a DVD setup exe starts automatically after the DVD is placed in the drive e If you have downloaded the software first unzip the downloaded zip archive Schrodinger Internet _Download zip then double click the installer icon or run setup exe Note Do not try to install the msi files directly They must be installed using setup exe 4 1 1 Preparing for Installation Successful i
146. tribution directory contains the data directory Default SSCHRODINGER thirdparty database pdb BLAST database directory contains directories nr and pdb Default SSCHRODINGER thirdparty database blast BLAST executable directory Default SSCHRODINGER thirdparty bin platform blast bin BLAST matrices directory Default SSCHRODINGER thirdparty bin platform blast data HMMER executable directory Default SSCHRODINGER thirdparty bin platform hmmer Pfam database directory Default SSCHRODINGER thirdparty database pfam PSIPRED installation contains bin and data directories Default SCHRODINGER thirdparty bin platform psipred Identity of PSIPRED sequence database Allowed values are nr and pdb Default pdb Identity of SSPRO sequence database Allowed values are nr and pdb Default pdb Information on the third party software and databases can be found at the following locations e BLAST http www ncbi nlm nih gov blast e HMMER http hmmer wustl edu e Pfam http pfam sanger ac uk e PDB http www rcsb org pdb e PSIPRED http bioinf cs ucl ac uk psipred 2 5 Documentation Requirements Manuals are distributed in PDF format and require a PDF reader To view the manuals you must have a PDF reader installed and it must support links between documents otherwise the documentation index is unusable e Adobe Reader is required on all platforms to use the search index and to op
147. ts of this output there should be one line for each license in your license file To add the new license attributes follow the instructions in the output The files you need to modify 1sf shared and ls f cluster lt your_cluster_name gt are located in the LSF_CONFDIR directory which is usually something like usr 1lsf conf If this directory is not cross mounted between all of the hosts to which LSF can submit jobs you will have to make these changes in the configuration files on each host To verify that the changes were made correctly restart LSF with the commands lsadmin reconfig badmin mbdrestart and then list the resources LSF recognizes using the command lsload 1 The output should include a column for each of the new license resources for example HOST_NAME status lt gt mem IMPACT MAIN MMLIBS hostl mycluster com ok lt gt 365M host2 mycluster com ok lt gt 362M 7 4 2 2 Configuring the Load Script A script is provided that queries the FLEXIm license server and reports the number of tokens available for each license in a format that the queueing software can understand To make sure the 1mutil utility and license file can be found when the script is run by the queueing soft ware you need to add the locations of the program and the license file to the script by editing the configuration section at the top of the script You must have permission to change this file 1 Use a text editor to edit th
148. tted to the queue will fail because the license software will assume that the required licenses are not avail able 1 Open the file SCHRODINGER queues LSF config in a text editor 2 Change the LICENSE CHECKING line to read LICENSE CHECKING yes 3 Save the modified file and close the editor 7 4 3 Configuring License Checking for PBS Pro 7 4 3 1 Adding License Attributes A resource attribute representing each license must be defined in the queueing system configu ration The utility 1icutil can be used to parse your license file or query the license server and generate the configuration text that needs to be added to the queueing system configuration files The syntax is SSCHRODINGER utilities licutil pbsconf f license file The f license file option is not required if your license file is in the default location SCHRODINGER license or if it is already specified by one of the environment variables SCHROD LICENSE FILE or LM LICENSE FILE If you want to query the server directly you must not use the f option and the environment variable you use must be set to the server location Schr dinger Software Release 2014 2 Chapter 7 Preparing for Job Submission Note If you specify multiple servers only the first is queried Licenses on other servers will therefore not be used The output from licutil should consist of lines like the following Copy the text between the dashed lines below into your lt PBS_HOME gt
149. two separate files are necessary to support both OpenSSH 1 5 and OpenSSH 2 0 pro tocols Some versions use just one or the other of these files Remove your known hosts file rm known_hosts This is necessary so that the new RSA key pair mechanism is used for every host Other wise hosts to which you previously connected using passwords might not use the new system automatically Make sure your home directory cannot be written by anyone but you chmod go w This is required before SSH will allow passwordless access to your account For each home directory that is not shared with that of the chosen host run the following command ssh copy id user remote host This command copies the keys and performs the necessary setup and permissions changes If for some reason this does not work you can do the setup manually as follows 1 Copy the public and private keys to that home directory scp ssh id_rsa other host ssh Connect to the host on which that home directory is mounted and change to the ssh directory cd ssh Repeat Step 3 through Step 5 above Ensure that id_rsa the private key is readable and writable only by the user chmod go rwx ssh id_rsa To test that passwordless SSH has been set up properly you can execute a command on a remote host for which it is set up as follows ssh username remotehost date Installation Guide 61 Chapter 7 Preparing for Job Submission 62
150. uested from the queueing system for the execution of a single program For distributed jobs this is set to 1 for MPI parallel jobs this is set to greater than 1 Installation Guide 109 Appendix E Adding an Unsupported Queueing System 110 Table E 1 Batch script variables Continued Variable Variable action lt LOGDIR The directory in which log files are written SHOMES Home directory on the submission host COMMAND Command that launches the Schr dinger j monitor program which sets up runs and cleans up after your calculation The ENVIRONMENT and COMMANDS lines are the only lines that are absolutely required in this script and they must appear in this order These variables are assigned by the job control system and are not configurable by the user Another important component of this script is the two line section that sets the SCHRODINGER_BATCHID environment variable to the actual batch ID assigned to this job The batch ID is usually provided by the queueing system in a special environment variable such as the PBS JOBID variable used by PBS The jmonitor program checks for the SCHRODINGER_BATCHID environment variable and saves the batch ID in the job record where the user can look it up If you want to run MPI parallel jobs the list of host names assigned to the job by the queuing system must be made available in a file and the SCHRODINGER_NODEFILE environment vari able must be set in the script to
151. ueueing systems as well The components required to support a batch system are a few text files that can be added or modified after installation The nature of these files is explained in the following subsection 7 3 1 Setting Up the Hosts File for Batch Queues To enable job submissions to a batch queue on a supported queueing system you must add host entries that define the available queues to the schrodinger hosts file The command syntax is described in Table 7 1 on page 50 There are two settings that define the queue the Queue setting and the Qargs setting A sample of the host entries to be inserted into the hosts file is shown below Batch submission to bigjobs queue under PBS Name bigg Host cluster Queue PBS Qargs q bigjobs processors 128 tmpdir storage TMPDIR Batch submission to shortjobs queue under PBS Name shortq Host cluster Queue PBS Qargs q shortjobs processors 16 tmpdir storage TMPDIR This example defines two entries named bigq and shortq to which jobs can be sent on the host cluster The Job Control facility distinguishes batch queues from hosts by the presence of the Queue setting which specifies the queueing system The Queue setting must be set to the subdirectory of SCHRODINGER queues that contains the support files for the queueing system The subdi rectories for the supported queueing systems are PBS SGE SLURM and LSF Because of Installation Guide 65 Cha
152. un jobs on the local host only no additional configuration is needed but you should test your installation as described in Section 7 6 on page 90 To run jobs on remote hosts run distributed jobs run jobs on remote hosts or submit jobs to batch queues you must first set up the hosts file schrodinger hosts This task is described in Section 7 1 Next you must enable access to these remote hosts using the ssh command or equivalent without specifying a password see Section 7 2 For batch queues additional configuration is needed see Section 7 3 and for some queueing systems it is also possible to set up license checking Section 7 4 Finally this chapter provides information on configuring clusters Section 7 5 and checking the installation and connections Section 7 6 7 1 The Hosts File The Job Control facility obtains information about the hosts on which it will run jobs from the hosts file The default name for this file is schrodinger hosts Maestro also uses the hosts file to set up the menus in the Start dialog box This file must contain information on all hosts to which jobs can be submitted and a copy of this file must be accessible on all hosts from which jobs will be submitted The copy of the file that is stored in the installation directory provides the default settings for all users and all hosts To customize job submission for a user copy schrodinger hosts to the directory HOME schrodinger on UNIX or USERPROFILE
153. x asking you if you wish to block or unblock a specific application Below are the scenarios where you need to unblock certain applications and the list of applications in each case Unless noted below these instructions apply to all versions of Windows operating systems These application lists are followed by requirements for various firewalls Installation Guide 63 Chapter 7 Preparing for Job Submission 64 Launching jobs e perl exe SCHRODINGER mmshare vversion bin platform perl exe e python exe 3SCHRODINGER mmshare vversion bin platform python exe e sh exe SCHRODINGER unxutils sh exe Running remote jobs e plink exe Windows XP Service Pack 2 or 3 Windows XP SP2 has a built in firewall An additional exception needs to be made beyond the above mentioned ones 1 Open port 113 for the TCP packets in the firewall 2 Run Security from the Control Panel and specify port 113 as an exception McAfee Add the remote machine to the Trusted IP list using the settings You can configure the firewall to trust all the machines in your LAN as well but make sure the subnet mask is properly set Norton Should work when the internet access prompts to unblock the packets are answered But make sure you trust your LAN in this case too 7 3 Preparing for Batch Queue Submission Schr dinger supplies support for the PBS SGE Sun Grid Engine now Grid Engine GE here it will continue to be refer
154. your calculation on the execution host e A config file which contains settings for the keywords QPATH QSUB QDEL QSTAT and QPROFILE The name of the subdirectory that contains these files is used as the name of the queueing system in the hosts file E 1 The submit Script The submit script needs to support the command line syntax submit job script qsub options where job script is the name of a shell script that starts a job on the queue This is always the first and possibly only command line argument to submit Anything else on the command line must be passed on as arguments to the actual job submission command If job submission is successful submit should extract the batch ID from the output of the underlying job submission command and report it in its output in the form BatchId batchid If job submission fails for some reason the script should exit with a non zero exit code If you are creating your own submit script to support a new queueing system you can use the submit scripts provided for PBS SGE and LSF as templates Use the QSUB variable rather than the actual submission command in your script and define QSUB in the config file Installation Guide 107 Appendix E Adding an Unsupported Queueing System 108 E 2 The cancel Script The cancel script must support the command line syntax cancel batchid where batchid is a batch ID assigned by the queueing system Job Control keeps track of the ba

Installation Guide for Schrödinger Software Release

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Installation Guide for Schr&ouml;dinger Software Release

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Installation Guide for Schrödinger Software Release