PDF - Molpro
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1. containing a directory that users may write on There are parts of the program in which demanding I O is performed simultane ously on two different files and it is therefore helpful to provide at least two filesystems on different physical disks if other solutions such as striping are not available The directory names should be stored in the environment variables TMPDIR TMPDIR2 STMPDIR3 These variables should be set before the program is installed preferably in profile or cshrc since at some stages the installation procedures will check for them cf section 3 5 6 If the program is to be built for parallel execution then the Global Arrays toolkit or the MPI 2 library is needed For building MOLPRO with the Global Arrays toolkit we rec ommend the latest stable version although earlier versions may also work This is avail able from and should be installed prior to compil ing MOLPRO For building MOLPRO with the MPI 2 library we recommend to use the built in MPI 2 library which may have advantages of optimization on some platforms If there is no built in one on the platform a fresh MPI 2 library e g MPICH2 see http http www mpich org should be installed prior to compiling MOLPRO Many MPI 2 libraries including Intel MPI Bull MPI MPICH2 and Open MPI have been tested and others untested could also work 7 The source distribution of MOLPRO which consists of a compressed tar archive with a file name of the2. make ca certificates Net download boost curl Net token download Table 1 Cygwin requirments for user install contains a list of potentially useful packages With the above steps configure can be run and the Molpro built in the normal way 3 INSTALLATION FROM SOURCE FILES Vili Package Package Group Reason bison Devel bison gdb Devel gdb git Devel git libxslt Libs xsltproc openssh Net ssh vim Editors vi Table 2 Cygwin packages for developers
3. source tree can then be archived and deleted The overall effect of this is to create a shell script in the INSTBIN directory The name should relate to the architecture type of build integer etc Symbolic links relating to the type of build are then made and finally providing that INSTBIN molpro is not a file a symbolic link is created to the new script In some cases it is preferable to create a localized script in INSTBIN molpro which will not be over written The overall effect of this cascade of links is to provide in the normal case the commands molpro and one or both of molpros serial and molprop parallel for normal use with the long names remaining available for explicit selection of particular variants 3 INSTALLATION FROM SOURCE FILES vii For normal single variant installations none of the above has to be worried about and the molpro command will be available from directory INSTBIN During the install process the key from HOME molpro token is copied to PREFIX token so that the key will work for all users of the installed version 3 9 Installation of documentation The documentation is available on the web at http www molpro net info users It is also in cluded with the source code The PDF user s manual is found in the directory Molpro doc manual pdf with the HTML version in the directory Molpro doc manual index html After make install the documentation is installed in the doc subdirectory of PRE
4. suite with all internal tests run successfully For the case of using the MPI 2 library one example can be configur nable mpp usr local mpich2 install include and the directory should contain file mpi h Please ensure the built in or freshly built MPI 2 library fully supports MPI 2 standard and works properly For desktop or single node installations there are a series of options prefixed with auto which build any prerequisites and can be passed to enable mpp eg configur nable mpp auto ga mpich 2 For good performance it is important to use appropriate BLAS libraries in particular a fast implementation of the matrix multiplication dgemm is very important for MOLPRO Therefore you should use a system tuned BLAS library whenever available MOLPRO will automatically detect the most appropriate BLAS library in many cases In certain cases in particular when the BLAS library is installed in a non default location configure should be directed to the appropriate directory with configur with blas path path to lib dir 3 The Molpro installation directory can be given with prefix 3 4 Compilation and linking After configuration the remainder of the installation is accomplished using the GNU make command Remember that the default make on many systems will not work and that it is essential to use GNU make cf section 3 2 Everything needed to make a functioning program together with all ancillary fil
5. ALLATION FROM SOURCE FILES iv libblas dev provides a BLAS library liblapack dev provides a LAPACK library which will be used instead of compiling the equivalent MOLPRO routines Set up password less ssh by running the following commands and not entering a password when prompted ssh keygen t rsa cat ssh id_rsa pub gt gt ssh authorized_keys This must be done for each user account which will be running MOLPRO 3 2 4 Mac OSX It is recommended to install and manage the additional compilers and utilities needed for build ing and running MOLPRO using the Homebrew system Visit and copy the installation command into a terminal window On an empty system you will be prompted to in stall command line tools do this first Then accept all prompts from the Homebrew installation script The following will install all utilities that might be needed for building and running MOLPRO either as a developer or installer brew unlink mpich2 not needed if mpich has not been installed brew install molpro ga ga Caskroom cask xquartz homebrew x11 grace open babel doxygen automake wget Caskroom cask java homebrew science jmol Assuming usr local bin is in your path configure CXX mpicxx FC mpif90 enable mpp usr local lib will configure MOLPRO 3 3 Configuration Once the distribution has been unpacked change to the Mol pro directory that has been created Having changed to the Molpro directory you should check that the dire
6. FIX specified in CONFIG file generated by the configure command Numerous example input files are in cluded in the manual and can alternatively be seen in the directory Molpro examples 3 10 Simple building for single workstations Linux or Mac OSX The following instructions are quick instructions for installing MOLPRO on a single workstation Linux or Mac OS X system The instructions assume GNU compilers have been installed de tails of getting GNU compilers for common Linux distributions are contained in the prerequi sites section but these can be substituted with alternative compilers For serial MOLPRO configure CXX g FC gfortran make For parallel MOLPRO one can use configure CXX g FC gfortran enable mpp path to ga install lib make if Global Arrays has already been built There is a simpler option providing the curl utility is installed and the machine is connected to the internet configure CXX gtt FC gfortran nable mpp auto ga mpich make which will automatically download and install MPICH and Global Arrays 3 11 Installation on a Cygwin system On a Windows machine Cygwin should be installed In addition to the default package list one should also install the packages listed in table I If undertaking development work table 2 Package Package Group Reason gcc core Devel compiling C files gcec fortran Devel compiling Fortran files gcc g t Devel compiling C files make Devel need GNU
7. MOLPRO Installation Guide Version 2015 1 Pfaffenwaldring 55 D 70569 Stuttgart Federal Republic of Germany P J Knowles School of Chemistry Cardiff University Main Building Park Place Cardiff CF10 3AT United Kingdom SHAI 5c514783246ecbhc6a54d953dfc47c9a50b9c4 9fc Copyright 2015 TTI GmbH Stuttgart Germany 1 OBTAINING THE DISTRIBUTION MATERIALS i 1 Obtaining the distribution materials MOLPRO is distributed to licensees on a self service basis using the world wide web Those enti tled to the code should obtain it from https www molpro net download supplying the username and password given to them The web pages contain both source code and binaries although not everyone is entitled to source code and binaries are not available for every platform Execution of MOLPRO whether a supplied binary or built from source requires a valid licence key Note that the key consists of two components namely a list of comma separated key value pairs and a password string and these are separated by amp In most cases the licence key will be automatically downloaded from the website when building or installing the software 2 Installation of pre built binaries Binaries are given as self extracting tar archives which are installed by running them on the command line There are binaries tuned for several architectures These also support parallel execution The parallel binaries are built using GA with MPI The tar ar
8. chives are fully relocatable the location can be changed when running the script interactively the default is usr local If the script finds a licence key which has been cached in SHOME molpro token from a previous install then that key will be installed with the software If the script cannot find a key or automatically download it from the molpro website then the script will prompt that this part of the install has failed All files of Molpro are installed but the user must then manually install the key with the library files in a file named token e g usr local lib molpro mpptype arch lib t Other configuration options as described in section 5 may also be specified in the script file usr local bin molpro 3 Installation from source files 3 1 Overview There are usually four distinct stages in installing MOLPRO from source files Configuration A shell script that allows specification of configuration options is run and creates a configuration file that drives subsequent installa tion steps Compilation The program is compiled and linked and other miscellaneous utilities and files including the default options file are built The essential resulting components are 1 The molpro shell script which launches the main executable In serial case one can directly run the main executable 2 Themolpro exe executable which is the main program For parallel computation multiple copies of molpro exe are started by a s
9. ctory containing the Fortran compiler you want to use is in your PATH Then run the command configure which creates the file CONFIG This file contains machine dependent parameters such as com piler options Normally CONFIG will not need changing but you should at the least examine it and change any configuration parameters which you deem necessary Any changes made to CONFIG will be lost next time configure is invoked so it is best to supply as many of these as possible via the command line The configure procedure may be given command line options and some commonly used options include 3 INSTALLATION FROM SOURCE FILES v 1 In the case of building for parallel execution the option enable mpp must be given on the command line This enables both mpp and mppx parallelism for the distinction between these two parallelism modes please refer to the user manual section 2 The option enable mpp must be set to the location of the Global Arrays library directory or the MPI 2 library include directory For the case of using the Global Arrays toolkit one example can be configur nable mpp usr local ga install lib If using a Global Arrays build with an MPI library the appropriate MPI executable should appear first in PATH when more than one is available Queries regarding Global Arrays installations should be sent directly to the Global Arrays team any Molpro related queries will assume a fully functional Global Arrays
10. es is carried out by default simply by issuing the command make in the MOLPRO base directory Most of the standard options for GNU make can be used safely in particular j can be used to speed up compilation on a parallel machine The program can then be accessed by making sure the bin directory is included in the PATH and issuing the command molpro If MPI library is used for building Global Arrays or building MOLPRO directly please be aware that some MPI libraries use mpd daemons to launch parallel jobs In this case mpd daemons must already be running before make 3 INSTALLATION FROM SOURCE FILES vi 3 5 Adjusting the default environment for MOLPRO The default running options for MOLPRO are stored in the script bin molpro After program installation either using binary or from source files this file should be reviewed and adjusted if necessary to make system wide changes 3 6 Tuning MOLPRO can be tuned for a particular system by running in the root directory the command make tuning This job automatically determines a number of tuning parameters and appends these to the file bin molpro Using these parameters MOLPRO will select the best BLAS routines depending on the problem size This job should run on an empty system It may typically take 10 minutes depending on the processor speed and you should wait for completion of this run before doing the next steps 3 7 Testing At this stage it is essential to check that the pr
11. form molpro 2015 1 tar gz The archive can be unpacked using gunzip and tar 3 INSTALLATION FROM SOURCE FILES lil 3 2 1 Fedora packages To build using GNU compilers one should ensure the following packages are installed via dnf gcc c provides GNU C and C compiler gcc gfortran provides GNU Fortran compiler libxml2 devel provides libxml2 library amp headers make provides GNU make Optionally one can choose to install blas devel provides a BLAS library lapack devel provides a LAPACK library which will be used instead of compiling the equivalent MOLPRO routines 3 2 2 openSUSE packages To build using GNU compilers one should ensure the following packages are installed via YaST gcc c provides GNU C and C compiler gcc fortran provides GNU Fortran compiler libxml2 devel provides libxml2 library amp headers make provides GNU make Optionally one can choose to install blas provides a BLAS library lapack provides a LAPACK library which will be used instead of compiling the equivalent MOLPRO routines 3 2 3 Ubuntu packages To build using GNU compilers one should ensure the following packages are installed via apt get build essential provides GNU C compiler curl provides curl for downloading patches gfortran provides GNU Fortran compiler libxml2 dev provides libxml2 library amp headers openssh server provides ssh access to localhost Optionally one can choose to install 3 INST
12. ingle instance of molpro shell script using the appropri ate system utility e g mpi run 3 Machine ready basis set and other utility libraries 3 INSTALLATION FROM SOURCE FILES ii Validation A suite of self checking test jobs is run to provide assurance that the code as built will run correctly Installation The program can be run directly from the source tree in which it is built but it is usually recommended to run the procedure that installs the essential components in standard system directories 3 2 Prerequisites The following are required or strongly recommended for installation from source code 1 A Fortran 2003 compiler On HPC systems the latest vendor supplied compiler should be used The program is regularly tested with recent versions of GNU and Intel Fortran compilers 2 GNU make freely available from http www fsf org and mirrors GNU make must be used most system standard makes do not work In order to avoid the use of a wrong make it may be useful to set an alias e g alias make gmake s A recent version of GNU make is required 3 80 or above 3 Libxml2 library and header files 4 About 10GB disk space strongly system dependent more with large blocksize file sys tems and where binary files are large during compilation Typically 100Mb is needed for the finally installed program Large calculations will require larger amounts of disk space 5 One or more large scratch file systems each
13. ogram has compiled correctly The makefile target test i e command make test will do this using the full suite of test jobs and although this takes a significantly long time it should always be done when porting for the first time A much faster test which checks the main routes through the program can be done using make quicktest For parallel installation it is highly desirable to perform this validation with more than one running process This can be done conveniently through the make command line as for example make MOLPRO_OPTIONS n2 test If any test jobs fail the cause must be investigated If after due efforts to fix problems of a local origin the problem cannot be resolved the developers of MOLPRO would appreciate receiving a report There is a web based mechanism at https www molpro net bugzilla at which as many details as possible should be filled in It may also be helpful to attach a copy of the CONFIG file along with the failing output Please note that the purpose of such bug reports is to help the developers improve the code and not for providing advice on installation or running 3 8 Installing the program for production Although the program can be used in situ it is usually convenient to copy only those files needed at run time into appropriate installation directories as specified at configuration time see section and stored in the file CONFIG To install the program in this way do make install The complete
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