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User's Guide to the HPC-Systems at ZIH
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1. Leave all other optimization options We can not generally give advice as to which option should be used even 00 sometimes leads to a fast code To gain maximum performance please test the compilers and a few combinations of optimization flags In case of doubt you can also contact ZIH and ask the staff for help Sifort only flushes denormalized numbers to zero On Itanium 2 an underflow raises an underflow exception that needs to be handled in software This takes about 1000 cycles 4 2 Parallel Programming 17 4 2 Parallel Programming 4 2 1 MPI 4 2 1 1 Mars This installation of the Message Passing Interface supports the MPI 1 2 standard with a few MPI 2 features see man mpi There is no command like mpicc instead you just have to append Impi to the linker command line Since the include files as well as the library are in standard directories there is no need to append additional library or include paths Note for C programmers You additionally need to link with 1mpi 4 2 1 2 Deimos When loading a compiler module on Deimos the module for the MPI implementation OpenMPl is also loaded Use the wrapper commands mpicc mpiCC mpif77 and mpif90 to compile MPI source code They use the currently loaded compiler To reveal the commandlines behind the wrappers use the option show For running your code you have to load the same compiler module as for compiling the program 4 2 2 OpenMP To achieve the b
2. idb dbx gdb pid process_id exec_file core_file 4 3 3 GNU Debugger gdb ddd This debugger offers only limited support for MPI parallel application and Fortran90 However it might be the debugger you are most used to gdb exec_file core_filelprocess_id The graphical frontend ddd for gdb can be used after module load ddd ddd debugger name exec_file core_file process_id 4 4 Performance Tuning 19 4 4 Performance Tuning 4 4 1 Basics There are many possible reasons for performance problems This chapter is only intended to provide a short overview and some entry points where to start CPU bound processes Performing many slow operations sqrt fp divides Non pipelined operations Switching between adds and mults Memory bound processes Poor memory strides Page thrashing Cache misses Poor data placement in NUMA systems 1 0 bound processes Performing synchronous I O Performing formatted 1 0 Library and system level buffering 4 4 1 1 Floating Point Performance on Itanium 2 The Itanium 2 CPU Altix is capable of delivering 2 floating point multiply adds per clock cycle i e peak performance of 6 GFlops This performance can slow down due to two reasons getting data to the processor cannot be done quickly enough or the FP unit is throwing exceptions Denormal numbers underflow numbers are defined in the IEEE stan
3. ee 25 4 CONTENTS 5 Applications 26 5 1 Quantum Chemistry Molecular Modeling 26 SLI A ae ee ef a EES 26 A EAN 26 A CSI 27 A a o ea we in rn na him HS 27 521 EEE 27 542 ELTA u andorra ina eRe eR 27 A ARRE 27 524 NCBI ToolKit essa nikes umpire eee 28 Da Enmen A p ad a aa pe 28 BAR AU aras es PERAZA ke 28 Dae A EN ESkEES 28 BIS AWE A 29 SIA A 29 5 4 Mathematics aa RA A A AA 29 SAL MATLAE 2 4 6 meee te ee Oe oe we RS a amp 29 5 4 2 Mathematica co curar a nenne 30 5 4 3 Maple 6 06025 eh dn See dk ba weed Bae ee a 30 6 Support from ZIH 31 51 Support Meqesis e cs ccs ed masea uis Dee eee ee EEw RA 31 7 Further Documentation 32 7 1 SGI developer forum ce eo oe ee da 32 LA OPAMP 24263 aes ceed Se ARA ASA ee RX 32 Oe oo hee ee ee ee ee ee eee ee eee 32 TA We RI 32 7 5 Libraries and Compilers oo oaa rss e 33 T MM in ad a Se A a 33 A Appendix 34 A 1 Problems with Intel Compilers 2 222222 nn nn 34 1 Introduction The Center for Information Services and High Performance Computing ZIH is a cen tral scientific unit of TU Dresden with a strong competence in parallel computing and software tools We have a strong commitment to support real users collaborating to create new algorithms applications and to tackle the problems that need to be solved to create new scientifc insight with computational methods Our new compute com plex Hochleistungs Rechner Speicher Komplex HRSK
4. For interactive jobs please submit Ansys via the batch system like bsub ansys110 g p aa_t_a 5 3 3 Ansys CFX Version 10 0 Vendor http www ansys com Module cfx Machines Deimos General ANSYS CFX is a powerful finite volume based program package for modelling general fluid flow in complex geometries The main components of the CFX package are the flow solver cfx5solve the geometry and mesh generator cfx5pre and the post processor cfx5post 5 3 4 Fluent Version 6 3 26 Vendor http www fluent com Module fluent Machines Deimos General Fluent is a general purpose package for modeling fluid flow and heat transfer It can simulate two three dimensional steady unsteady compressible incompressible flows in structured and unstructured grids The Mach number of Fluent simulation ranges from subsonic to hypersonic lts capabilities include simulating non isothermal flows disperse phase droplets combustion and radiation heat transfer and flow through porous media For parallel jobs we have provided a wrapper function fluent Isf which adds the necesary options for parallel runs over multiple nodes You can start a compute session like this bsub oo out txt oe error txt x n 4 m dual _hosts fluent lsf 3d g i INPUTFILE 5 4 Mathematics 5 4 1 MATLAB Version 2007b Vendor http www mathworks com Module matlab Machines Deimos General MATLAB is a numerical computing environment and programm
5. One can submit a Gaussian job with options like this bsub n 1 R span hosts 1 rusage mem MEM MB MEMMB memory usage in MB x for exclusive usage m NODE_TYPE NODE_TYPE can be dual_hosts quad_hosts or fat_quads needed wallclock time General single_hosts W hh mm script sh 5 1 2 CPMD Version 3 11 Vendor http www cpmd org Module cpmd Machines Deimos General The Car Parrinello Molecular Dynamics better known as CPMD is a package for performing ab initio quantum mechanical molecular dynamics MD using pseudopo tentials and a plane wave basis set This code is a parallelized implementation of Density functional theory Please submit a parallel job like this bsub n 32 a openmpi o out mpirun lsf cpmd x bp_110_wf inp or a sequential job with 5 2 Bioinformatics 27 bsub cpmd seq bp_110_wf inp 5 13 NAMD Version 2 6 Vendor http www ks uiuc edu Research namd Module namd Machines Deimos General NAMD is a parallel molecular dynamics code designed for high performance simulation of large biomolecular systems On Deimos NAMD scales well up to 64 CPUs depending on the size of the problem You can use a call like bsub a openmpi x oo output n 32 mpirun lsf namd _2 6 _tcl run100 conf 5 2 Bioinformatics 5 2 1 PHYLIP Version 3 66 Vendor J Felsenstein University of Washington Module phylip Machines Deimos Mars General
6. n 8 number of processors BSUB o out J output file BSUB u vorname nachname tu dresden de email address echo Starting Program cd HOME work a out e g an OpenMP program echo Finished Program LSF sets the user environment according to the environment at the time of submission Based on the given information the job scheduler puts your job into the appropriate queue These queues are subject to permanent changes You can check the current situation using the command bqueues 1 There are a couple of rules and restrictions to balance the system loads One idea behind them is to prevent users from occupying the machines unfairly An indicator for the priority of a job placement in a queue is therefore the ratio between used and granted CPU time for a certain period 3 4 1 Interactive Jobs Interactive activities like editing compiling etc are normally limited to the boot CPU set Mars or to the master nodes Deimos If you want to start a parallel interactive job you again have to use the batch system Use the additional bsub options Is to start an interactive job like bsub Is matlab You can check the current usage of the system with the command bhosts to estimate the time to schedule 3 4 2 Monitoring The command bhosts shows the load on the hosts For a little more information use 1sf info in usr local bin for a short summary on the job situation on the system For a more convenient overview t
7. vngd is analyzing the tracefiles and a front end vng provides a GUI The correct envi ronment can be set with module load vng The daemon is a multithreaded program it has to be started in a queue like bsub n 4 I vngd n 4 After scheduling this job the daemon prints the number of the port it is serving like Listen port 30088 If the daemon started in a non interactive queue without bsub option I then the used port can be determined by looking in the file HOME vnga cat HOME vngd In another shell the user can after loading the module module load vng start the front end with bsub I vng a localhost p 30088 Please make sure you shut down the daemon after finishing your work with the front end 4 4 4 2 VampirTrace VampirTrace is a performance monitoring tool that produces tracefiles during a program run These tracefiles can be analyzed and visualized by the tool Vampir see above Before using VampirTrace set up the correct environment with module load vampirtrace To make measurements with VampirTrace the user s application program needs to be instrumented i e at specific important points events VampirTrace measurement calls have to be activated By default VampirTrace handles this automatically In order to enable instrumentation of function calls MPI as well as OpenMP events the user only needs to replace the compiler and linker commands with VampirTrace s wrappe
8. heeds SHE SEE A 9 3 Operating Systems 9 Oe A ce u es daa hee eee a eee 9 3 2 Customize your environment 0 000000 0 9 Sl DOI naeh ras 10 3 4 Batch Systems ee oe RO RR SEEKER RE KE Re SRS 10 3 4 1 Interactive Jobs vo 22 445485 Phe Ye ee ee oye 11 A A 11 3 4 3 Parallel Jobs wehbe hewn dara 12 3 4 4 Placing Threads or Processes on CPUs 13 4 Software Development 14 AL CARES e a a ee ES 15 ALI Templer Fass amp was jodas Ra 15 4 2 Parallel Programming 2 4242 25 5 kw Rew Ree eR RS 17 EL ME scsi dera Pe eed amp teh oR ORS ae ee Se a 17 422 TOUR es ae hms Ree niare eRe SG ORS eS 17 A a a a a ai ee e ae Barden na 17 32 Allinea DDT 244 405 442 rra 18 4 3 2 Intel Debugger idb 2 2 2 2 ee 18 4 3 3 GNU Debugger gdb ddd 18 4 4 Performance Tuning lt 2 440446435 4825 Ge BRE ee ae 19 Mee WON ee seen eg a 19 4 4 2 Analyzing Profiles Comm 19 4 43 Determining Data Access Patterns 20 AJA Wamp a o ts a a A a A 20 4 5 Mathematical Libraries 22 22 Con rn nn 22 4 5 1 Math Kernel Library MKL 222222222 23 BEZ ALME esc agro ae ne a ce kan 23 A 5 in ee Se a a a ee ae ee de 24 a MI 24 BEE PEIN a bee ee ae ee ele are i 24 4 6 Miscellaneous 2 22 aa 24 4 6 1 1 O with from to binary files 24 162 Fat Oon Fle nn nd a A a 24 4 6 3 Memory Corruption on Altix 2 222 o o
9. is focused on data intensive computing High scalability big memory and fast O systems are the outstanding prop erties of this project aside from the significant performance increase cf fig 1 The infrastructure is provided not only to TU Dresden but to all universities and research institutes in Saxony PC Farm PC SAN 68 TB h Tape Archive 1PB Figure 1 Overview over the HRSK system 6 2 HARDWARE 2 Hardware This chapter should provide you with basic information about the hardware installed at ZIH between 2005 and 2007 2 1 HPC Component SGI Altix The SGI Altix 4700 is a shared memory system with dual core Intel Itanium 2 CPUs Montecito operated by the Linux operating system SuSE SLES 10 with a 2 6 kernel Currently the following Altix partitions are installed at ZIH name total cores compute cores Memory per core Mars 384 348 1 GB Jupiter 512 506 4 GB Saturn 512 506 4 GB Uranus 512 506 4 GB Neptun 128 128 1 GB The jobs for these partitions except Neptun are scheduled by a LSF batch system running on mars hrsk tu dresden de The actual placement of a submitted job may depend on factors like memory size number of processors time limit cf chapter 3 4 All partitions share the same CXFS filesystem 2 1 1 ccNuma Architecture The SGI Altix has a ccNUMA architecture which stands for Cache Coherent Non Uniform Memory Access It
10. to the man pages 4 Software Development This section should provide you with the basic knowledge and tools to get you out of trouble It will tell you How to compile your code Using mathematical libraries Find caveats and hidden errors in application codes Handle debuggers Follow system calls and interrupts Understand the relationship between correct code and performance Some hints that are helpful Stick to standards wherever possible Computers are short living creatures migrat ing between platforms can be painful In addition running your code on different platforms greatly increases the reliabily You will find many bugs on one platforms that never will be revealed on another Before and during performance tuning Make sure that your code delivers the correct results Some questions you should ask yourself Given that a code is parallel are the results independent from the numbers of threads or processes Have you ever run your Fortran code with array bound and subroutine argument checking check all traceback Have you checked that your code is not causing floating point exceptions Does your code work with a different link order of objects Have you made any assumptions regarding storage of data objects in memory 4 1 Compilers 15 4 1 Compilers The following compilers are available on our platforms Intel 10 GNU 4 1 PGI 7 0 Pathscale 3 0 icc gcc pgcc pathcc
11. NT 4 4 3 Determining Data Access Patterns on Altix The command dlook allows you to display the memory map and CPU usage for a specified process dlook a c h 1 o outfilel s secs command command args dlook a c h 1 o outfile s secs pid For each page in the virtual address space of the process dlook prints the following information The object that owns the page such as a file SysV shared memory a device driver etc The type of page such as random access memory RAM FETCHOP IOSPACE etc For RAM pages the following are also listed memory attributes SHARED DIRTY etc node that the page is located on physical address of page if option a is specified 4 4 4 Vampir Vampir is a graphical analysis framework that provides a large set of different chart representations of event based performance data generated through source code instru mentation These graphical displays including state diagrams statistics and timelines can be used by developers to obtain a better understanding of their parallel programs inner working and to subsequently optimize it Vampir allows for quick focusing on appropriate levels of detail which allows the detection and explanation of various perfor mance bottlenecks such as load imbalances and communication deficiencies The Vampir tool has been developed at the Center for Applied Mathematics of Re search Center J lich and
12. PHYLIP the PHYLogeny Inference Package is a package of programs for inferring phylogenies evolutionary trees Methods that are available in the package in clude parsimony distance matrix and likelihood methods including bootstrapping and consensus trees Data types that can be handled include molecular sequences gene frequencies restriction sites and fragments distance matrices and discrete characters CLUSTALW is automatically loaded together with the PHYLIP module in order to create PHYLIP input data 5 2 2 CLUSTALW Version 1 83 Vendor http ww ebi ac uk clustalw Module clustalw Machines Deimos Mars General Multiple alignments of protein sequences are important tools in studying se quences The basic information they provide is the identification of conserved sequence regions This is very useful in designing experiments to test and modify the function of specific proteins in predicting the function and structure of proteins and in identify ing new members of protein families ClustalW is a general purpose multiple sequence alignment program for DNA or proteins It produces biologically meaningful multiple se quence alignments of divergent sequences It calculates the best match for the selected sequences and lines them up so that the identities similarities and differences can be seen 5 2 3 HMMER Version 2 3 2 Vendor http hmmer janelia org Module hmmer hmmer pthread Machines Deimos Mars 28 5 APPLICATION
13. S General Profile hidden Markov models profile HMMs can be used to do sensitive database searching using statistical descriptions of a sequence family s consensus HM MER is a freely distributable implementation of profile HMM software for protein se quence analysis The PThread version of HMMER should be used with 2 CPUs Using more than two CPUs will not improve performance Make sure that the number of CPUs that is speci fied in the bsub call is identical to the number of CPUs that is specified in the command line parameter when calling hmmpfam 5 2 4 NCBI ToolKit Version 3 66 Vendor http www ncbi nlm nih gov Module ncbitoolkit Machines Deimos Mars General Molecular biology is generating a host of data which are dramatically altering and deeping our understanding of the processes which underlie all living things This new knowledge is already affecting medicine agriculture biotechnology and basic science in fundamental and sweeping ways However the data on which our growing understand ing is based is being accumulated and analyzed in thousands of laboratories all over the world from large genome centers to small university laboratories from large pharmacuti cal companies to small biotech startups It is being managed and analyzed on machines from small personal computers to supercomputers on systems from a few disk files to large commercial database systems These essential new data require specialized to
14. User s Guide to the HPC Systems at ZIH Version 2 3 Ulf Markwardt November 14 2007 Fu IH Zentrum f r nformationsdienste und Hochleistungsrechnen Disclaimer This booklet is mainly directed at the users of the new HPC systems However users of our smaller Opteron and Itanium clusters may find it usefull too SGI Altix and Origin are registered trademarks of Silicon Graphics International Other brands and names may be claimed a the property of others This manuscript is work in progress since we try to incorporate more information with increasing experience and with every question you ask us Please tell us if you miss something or find incorrect information You can find this document and further infor mation at the web site http www tu dresden de zih Publikationen Schriften Benutzerinforma t onen Acknowledgements would like to thank the following people for contributing to this manual Matthias M ller Reiner Vogelsang SGI Matthias Jurenz Matthias Lieber Guido Juckeland Michael Kluge Robert Henschel CONTENTS 3 Contents 1 Introduction 5 2 Hardware 6 2 1 HPC Component SGI Altix nen 6 2411 zeMums AYERBE occ eek rss Ge RES Ee BES 4 6 212 Compute Module u amp u ua 0 ina sera eee aa 6 E A 7 2 2 Linux Networx PC Farm Deimos 24 4 6 54 240 bowie es 8 Be CPU 2 kh i ek RO a ee an A 8 2 3 Linux Networx PC Cluster Phobos 2 2222 222er 8 eee CPU ee phe
15. ardware Linux Networx PC Farm Linux Networx PC Cluster phobos hrsk tu dresden de 3 2 Customize your environment To allow the user to switch between different versions of installed programs and libraries we use the so called module concept A module is a user interface that provides utilities for the dynamic modification of a user s environment e users do not have to manually modify their environment variables PATH LD_LIBRARY_PATH to access the compilers loader libraries and utilities lFor security reasons this port is only accessible for hosts within the domains of TU Dresden Guests from other research institutes can either use one of the central login servers or the VPN gateway of ZIH Information on these topics can be found on our web pages http www tu dresden de zih 10 3 OPERATING SYSTEMS Command Description module help show all module options module list list all user installed modules module porge remove all user installed modules module avail list all available modules module load lt modname gt load module modname module switch lt mod1 gt lt mod2 gt unload module mod1 load module mod2 Please note we have set ulimit c 0 as a default to prevent you from filling the disk with the dump of a crashed program bash users can use ulimit c unlimited to enable the debugging via analyzing the core file limit coredumpsize unlimited for tcsh 3 3 Backup An automated backup
16. can be considered as a SM MIMD shared memory mul tiple instruction multiple data machine The SGI ccNuma system has the following properties Memory is physically distributed but logically shared Memory is kept coherent automatically by hardware Coherent memory memory is always valid caches hold copies Granularity is L3 cacheline 128 B Bandwidth of NumaLink4 is 6 4 GB s The ccNuma is a compromise between a distributed memory system and a flat symmetric multi processing machine SMP Altough the memory is shared the access properties are not the same 2 1 2 Compute Module The basic compute module of an Altix system is shown in fig 2 It consists of one dual core Intel Itanium 2 Montecito processor the local memory of 4 GB 2 GB on Mars and the communication component the so called SHUB All resources are shared by both cores They have a common front side bus so that accumulated memory bandwidth for both is not higher than for just one core The SHUB connects local and remote ressources Via the SHUB and NUMAlink all CPUs can access remote memory in the whole system Naturally the fastest access provides local memory fig 3 There are some hints and commands that may help you 2 1 HPC Component SGI Altix 7 Intel empty Itanium 2 socket NUMAlink E SHUB 6 4 GB s NUMAlink 6 4 GB s Figure 2 Altix compute blade to get optimal memory allocation and process placement cf c
17. chip nodes 384 dual nodes 230 quad nodes 88 quad nodes 32 GB RAM 24 All nodes share a 68 TB filesystem on DDN hardware Each node has per core 40 GB local diskspace for scratch mounted on tmp The jobs for the compute nodes are scheduled by a LSF batch system from the login nodes deimos hrsk tu dresden de Two separate Infiniband networks 10 Gb s with low cascading switches provide the communication and O infrastructure for low latency high throughput data traffic An additional gigabit Ethernet network is used for control and service purposes Users with a login on the Altix can access their home directory via NFS below the mount point hpc_work 2 2 1 CPU The cluster is based on dual core AMD Opteron X85 processor One core has the following basic properties clock rate 2 6 GHz floating point units 2 peak performance 5 2 GFLOPS L1 cache 2 x 64 kB L2 cache 1 MB memory bus 128 bit x 200 MHz The CPU belongs to the x86_64 family Since it is fully capable of running x86 code one should compare the performances of the 32 and 64 bit versions of the same code 2 3 Linux Networx PC Cluster Phobos Phobosis a cluster based on AMD Opteron CPUs The nodes are operated by the Linux operating system SuSE SLES 9 with a 2 6 kernel Currently the following hardware is installed CPUs AMD Opteron 248 single core total peak performance 563 2 Gflops nodes 64 compute 1 master CPUs per node 2 RAM per n
18. dard for floating point as those below the normal range Operations involving these numbers cannot be performed on the processor and need to be performed by the operating system and there is a huge penalty about 1 000 cycles in doing this The system logs some of these events The user can identify them by using the command dmesg grep assist She will get events like namd2 19416 floating point assist fault at ip 4000000000590941 isr 0000020000000008 namd2 19416 floating point assist fault at ip 4000000000590941 isr 0000020000000008 namd2 19416 floating point assist fault at ip 4000000000590941 isr 0000020000000008 namd2 19462 floating point assist fault at ip 4000000000410941 isr 0000020000000008 The commandline tool addr2line might help to localize te corresponding source code Please be aware that its result might be disturbed by optimizations If you are sure the underflows are no problems for your application you should compile with the option ftz 4 4 2 Analyzing Profiles A very convenient way to select the focus for further optimization is to analyze the frequencies and durations of function calls To do this one has to compile the code with the appropriate flags pg for Pathscale PGI or GNU compilers and p for icc At the end of the execution of the program the collected data is written into a file The user can then use a profiling tool like gprof or kprof to display the data 20 4 SOFTWARE DEVELOPME
19. e complex data types Fast scalar vector and array math transcendental library routines optimized for high performance on AMD Opteron processors Random Number Generators in both single and double precision 24 4 SOFTWARE DEVELOPMENT 4 5 3 ATLAS The ATLAS Automatically Tuned Linear Algebra Software project is an ongoing re search effort focusing on applying empirical techniques in order to provide portable per formance At present it provides C and Fortran77 interfaces to a portably efficient BLAS implementation as well as a few routines from LAPACK 4 5 4 SGI SCSL For the SGI Altix SCSL provides similar functionality as the Intel MKL One advantage is that there is a version for programs requiring 64 Bit integers The SCSL routines can be linked and loaded by using the 1scs or the 1s8cs mp options Try man scsl for more information 4 5 5 FFTW FFTW is a C subroutine library for computing the discrete Fourier transform DFT in one or more dimensions of arbitrary input size and of both real and complex data as well as of even odd data i e the discrete cosine sine transforms or DCT DST Before using this library please check out the functions of vendor specific libraries ACML and or MKL 4 6 Miscellaneous 4 6 1 1 O with from to binary files This section is only important for users migrating from other architectures The Itanium and Opteron CPUs use so called little endian order to store numbers most si
20. e free calls 26 5 APPLICATIONS 5 Applications The following applications are available on the HRSK systems General descriptions are taken from the vendor s web site or from Wikipedia org Before running an application you normally have to load the given module e g module load ansys Please read the instructions given while loading th emodule they are more up to date than this manual 5 1 Quantum Chemistry Molecular Modeling 5 1 1 Gaussian Version G03 Vendor http www gaussian com Module gaussian Machines Deimos Starting from the basic laws of quantum mechanics Gaussian predicts the en ergies molecular structures and vibrational frequencies of molecular systems along with numerous molecular properties derived from these basic computation types It can be used to study molecules and reactions under a wide range of conditions including both stable species and compounds which are difficult or impossible to observe experimentally such as short lived intermediates and transition structures To be able to run Gaussian you have to be in the user group gauss To check this use the Linux command groups which lists all groups you are a member of With module load gaussian you can set the environment according to the needs of Gaussian For temporary data GAUSS _SCRDIR please use your own fastfs direc tory We have a queue named gauss which can be used for time intensive computing that can not be checkpointed
21. e or bsub Is xmaple 31 6 Support from ZIH Over the last 10 years since the founding of the former Center for High Performance Compution ZHR the staff has been supporting users developing tools and collecting experience in the field of high performance computing We are currently using the following tools for code instrumentation and analysis Vampir NG 1 4 ZIH tool Intel VTune UPI Universal Profiling Interface tool in development by ZIH If you think what your application needs is a little speed up don t hesitate to ask the authors to organize some support Experience tells that during the code development phase you are in constant need for help to make your program run correctly For a leading edge computational science code it is normal to be under constant development 6 1 Support Requests The status of our machines and messages concerning maintainance shutdowns etc can be found at http www tu dresden de zih aktuelles betriebsstatus For support requests and other questions regarding HPC the email address hpcsupport zih tu dresden de has been established This email address is served by a trouble ticket system 32 7 FURTHER DOCUMENTATION 7 Further Documentation You can find detailed documentation in the doc directory of the installed products e g opt intel cc_90 doc At the web site http www tu dresden de zih Publikationen Schriften Benutzerinformationen you can find these l
22. elp Reading the man pages is a good idea too The user benefits from the nearly same set of compiler flags for optimization for the C C and Fortran compilers In the following table only a couple of important compiler dependant options are listed For more detailed information the user should refer to the man pages or use the option help to list all options of the compiler Use module avail to list the installed versions on the platform The names of these modules may change without further notice 16 4 SOFTWARE DEVELOPMENT Intel PGI Pathscale Description openmp mp mp turn on OpenMP support mp Kieee no fast math use this flag to limit floating point optimizations and maintain declared precision mpi Knoieee ffast math some floating point optimizations are allowed less performance impact than mp fpe lt n gt Ktrap Controls the behavior of the pro ftz cessor when floating point exceptions occur tp amd64 mcpu opteron optimize for Opteron processor axW fastsse msse2 generally optimal flags for support ing SSE instructions Opteron only ipo Mipa ipa inter procedure optimization across files ip Mipa inter procedure optimization within files parallel Mconcur apo Auto parallelizer prof gen Mpfi fb create lt FN gt Create intrumented code to generate profile in file lt FN gt prof use Mpfo fb opt lt FN gt Use profile data for optimization
23. ers relative to current cpumemset x lt mask gt A bitmask for specifying threads to skip placing See following examples s lt count gt Skip placement of the first count threads Use s1 to skip placing the shepherd thread in MPI programs q Displays static load information dplace without ar guments will avoid loaded cpus e Exact placement When you run OpenMP applications you have to be aware that the run time library uses the second thread for internal management purposes You therefore need to use dplace x 2 c 0 lt N gt The use of profiling tools may require modification of placement flags 14 4 SOFTWARE DEVELOPMENT dplace x5 c0 15 histx o prof a out histx skip 1 a out master place 0 OpenMP monitor skip 1 a out slavel place 0 a out slave2 place 0 place 0 You can use dplace in conjunction with MPI mpirun np lt gt dplace s 1 a out An easier approach is to set the environment variable export MPI_DSM_DISTRIBUTE 1 3 4 4 2 taskset on Farm and Cluster To place tasks on the PC farm you can use the standard linux tool taskset which allows to bond a process to a given set of CPUs on the system The Linux scheduler will honor the given CPU aff nity and the process will not run on any other CPUs This only makes sense when you submit the job with bsub x to exclusively use the hosts For forther information on taskset please refer
24. est performance the compiler needs to exploit the parallelism in the code Therefore it is sometimes necessary to provide the compiler with some hints Some possible directives are Fortran style CDEC ivdep ignore assumed vector dependences CDEC swp try to software pipeline CDEC noswp disable softeware pipeling CDEC loop count NN hint for optimzation CDEC distribute point split this large loop CDEC unroll n unroll n times CDEC nounroll do not unroll CDEC prefetch a prefetch array a CDEC noprefetch c do not prefetch array a The compiler directives are the same for ifort and icc The syntax for C C is like pragma ivdep pragma swp and so on More detailled sources of information are listed in chapter 7 4 4 3 Debuggers This short User s Guide only describes how to start the debuggers on our HPC systems For detailed information refer to 7 6 General advices for debugging are You need to compile your code with the flag g to enable debugging It is also recommendable to reduce or even disable optimizations 00 For parallel applications try to reconstruct the problem with less processes before using a debugger DDT behaves slower with larger number of processes The flag traceback of the Intel Fortran compiler causes to print stack trace and source code location when the program terminates abnormally 18 4 SOFTWARE DEVELOPMENT 4 3 1 Allinea DDT The Allinea Debugger is avai
25. gnificant byte with highest memory address So if you access files written in binary mode on big endian platforms they may not work on an Itanium platform without con version Due to the little endian representation you normally have to convert binary files written on big endian architectures before reading them For Fortran applications there is however the option to do this conversion automatically Big endian systems are SGI MIPS Irix Origin 3000 2000 HP PA Risc Sun Sparc IBM Power RISC NEC vector systems Cray vector systems For the use with Intel compilers you can read write big endian binary data by the fol lowing means set the environment variable F_UFMTENDIAN big applies to all units or F_UFMTENDIAN big 10 20 applies to unit 10 and 20 only or compile with convert big Intel compilers or Mbyteswapio PGI Pathscale 4 6 2 Fast I O on Altix The ffread and ffwrite functions provide flexible file O FFIO to record oriented or byte stream oriented data in an application transparent manner see man ffread 4 6 Miscellaneous 25 4 6 3 Memory Corruption on Altix The MALLOC_CHECK_ environent variable controls some basic protection against memory corruption see man malloc Value Description 0 silently ignore any heap corruption 1 print diagnostic message when heap corruption detected 2 abort immediately upon heap corruption This only detects simple errors such as one byte overruns and multipl
26. hapter 3 4 4 1 Four of these blades are grouped together with a NUMA router in a compute brick All bricks are connected with NUMAlink4 in a fat tree topology Figure 3 Remote memory access via SHUBs and NUMAlink 2 1 3 CPU The current SGI Altix is based on the dual core Intel Itanium 2 processor codename Montecito One core has the following basic properties clock rate 1 6 GHz integer units 6 floating point units multiply add 2 peak performance 6 4 GFLOPS L1 cache 2x16 kB 1 clock latency L2 cache 256 kB 5 clock latency L3 cache 9 MB 12 clock latency front side bus 128 bit x 200 MHz The theoretical peak performance of all Altix partitions is hence about 13 1 TFLOPS The processor has hardware support for efficient software pipelining For many scientific applications it provides a high sustained performance exceeding the performance of RISC CPUs with similar peak performance On the down side is the fact that the compiler has to explicetly discover and exploit the parallelism in the application 8 2 HARDWARE 2 2 Linux Networx PC Farm Deimos The PC farm Deimos is a heterogenous cluster based on dual core AMD Opteron CPUs The nodes are operated by the Linux operating system SuSE SLES 10 with a 2 6 kernel Currently the following hardware is installed CPUs AMD Opteron X85 dual core RAM per core 2 GB Number of cores 2584 total peak performance 13 4 TFLOPS single
27. he command showjobs displays information on the LSF status like this You have 1 running job using 64 cores You have 1 pending job AA A AR A E A A A nodes available 714 714 nodes damaged 0 A ea in ed ehe E jobs running 1797 cores closed exclusive jobs 94 jobs wait 3361 cores closed by ADMIN 129 jobs suspend 0 cores working 2068 jobs damaged 0 ee Sh eS ET eae EZ fre ee OE SS ee normal working cores 2556 cores free for jobs 265 With the command bqueues 1 lt queuename gt you can get information about available queues With bqueues 1 you get a detailed listing of the queue properties The command bjobs allows to monitor your running jobs It has the following options 12 3 OPERATING SYSTEMS bjobs option Description r Displays running jobs s Displays suspended jobs together with the sus pending reason that caused each job to become suspended p Displays pending jobs together with the pend ing reasons that caused each job not to be dis patched during the last dispatch turn a Displays information on jobs in all states in cluding finished jobs that finished recently 1 job_id Displays detailed information for each job or for a particular job 3 4 3 Parallel Jobs For submitting parallel jobs a few rules have to be understood and followed In general they depend on the type of parallelization and the architecture 3 4 3 1 OpenMP Jobs An SMP parallel job can on
28. icpc gtt pgCc pathCc ifort gfortran pgf95 pathf95 Mars x x Deimos x x x x Phobos 9 1 4 1 6 2 2 4 GNU compilers are installed on the Altix but they reach significantly less performance on IA64 Please do not use them without urgency All C compiler support ANSI C and C99 with a couple of different language options The support for Fortran77 Fortran90 Fortran95 and Fortran2003 differs from one compiler to the other Please check the man pages to verify that your code can be compiled Please note that the linking of C files normally requires the C version of the compiler to link the correct libraries For serious problems with Intel s compilers please refer to Appendix A 1 p 34 4 1 1 Compiler Flags Common options are g to include information required for debugging pg to generate gprof style sample based profiling information during the run 0 lt 0111213 gt to customize the optimization level from no 00 to aggressive 03 optimization I to set search path for header files L to set search path for libraries Please note that aggressive optimization allows deviation from the strict IEEE arithmetic Since the performance impact of options like mp is very hard the user herself has to balance speed and desired accuracy of her application There are several options for profiling profile guided optimization data alignment and so on You can list all available compiler options with the option h
29. ing language Created by The MathWorks MATLAB allows easy matrix manipulation plotting of func tions and data implementation of algorithms creation of user interfaces and interfacing with programs in other languages Although it specializes in numerical computing an optional toolbox interfaces with the Maple symbolic engine allowing it to be part of a full computer algebra system To use Matlab in an interactive session please submit your job with bsub Is matlab 30 5 APPLICATIONS 5 4 2 Mathematica Version 6 0 Vendor http www wolfram com Module mathematica Machines Deimos General Mathematica is a general computing environment organizing many algorith mic visualization and user interface capabilities within a document like user interface paradigm To use Mathematica in an interactive session please submit your job with bsub Is mathematica 5 4 3 Maple Version 11 Vendor http www maplesoft com Module maple Machines Deimos General Maple is an all purpose mathematics software tool Maple provides an ad vanced high performance mathematical computation engine with fully integrated nu merics and symbolics all accessible from a WYSIWYG technical document environment Live math is expressed in its natural 2D typeset notation linked to state of the art graph ics and animations with full document editing and presentation control To use Maple in an interactive session please submit your job with bsub Is mapl
30. inks further information and updates The most recent information is available at the web sites of our machines at http tu dresden de zih hrsk 7 1 SGI developer forum The web sites behind http www sgi com developers resources tech_pubs html are full of most detailed information on SGI systems Have a look onto the section Linux Publications You will be redirected to the public part of SGI s technical publication repository Linux Application Tuning Guide Linux Programmer s Guide The Linux Device Driver Programmer s Guide Linux Kernel Internals and more 7 2 OpenMP You will find a lot of information at the following web pages http www openmp org http www compunity org 7 3 MPI The following sites may be interesting http www mcs anl gov mpi the MPI homepage http www mpi forum org Message Passing Interface MPI Forum Home Page http www open mpi org the dawn of a new standard for a more fail tolerant MPI The manual for SGI MPI installed on Mars can be found at http techpubs sgi com library manuals 3000 007 3773 003 pdf 007 3773 003 pdf 7 4 Intel Itanium There is a lot of additional material regarding the Itanium CPU http www intel com design itanium manuals iiasdmanual htm http www intel com design archives processors itanium index htm http www intel com design itanium2 documentation htm 7 5 Libraries and Compilers 33 You wi
31. kup lan guage VML More specifically it contains the following components BLAS Level 1 BLAS vector vector operations 48 functions Level 2 BLAS matrix vector operations 66 functions Level 3 BLAS matrix matrix operations 30 functions LAPACK linear algebra package solvers and eigensolvers hundreds of routines more than 1000 user callable routines FFTs fast Fourier transform one and two dimensional with and without fre quency ordering bit reversal There are wrapper functions to provide an interface to use MKL instead of FFTW VML vector math library set of vectorized transcendental functions Parallel Sparse Direct Linear Solver Pardiso Please note MKL comes in a OpenMP parallel version If you want to use it make sure you know how to place your jobs chapter 3 4 4 1 4 5 2 ACML Opteron based systems only The AMD Core Math Library is a collection of the following routines A full implementation of Level 1 2 and 3 Basic Linear Algebra Subroutines BLAS with key routines optimized for high performance on AMD Opteron processors A full suite of Linear Algebra LAPACK routines As well as taking advantage of the highly tuned BLAS kernels a key set of LAPACK routines has been fur ther optimized to achieve considerably higher performance than standard LAPACK implementations A comprehensive suite of Fast Fourier Transforms FFTs in both single double single complex and doubl
32. lble with module load ddt It is quite intuitive usable and provides great support for MPI parallel applications For serial applications run DDT with ddt PROGRAM PROGRAM ARGS Select none as MPI implementation in the DDT session control window via the Change button and start the program with the Run button 4 3 1 1 Debugging MPI applications on Mars For parallel applications on Mars replace mpirun np lt N gt in your job submission by ddt e g bsub W 1 00 I n 8 ddt a out Select altix mpi as MPI implementation and set the number of processes Click Run to start the program Alternatively you can start an interactive batch session a shell on compute CPUs and start DDT from there This is especially useful when you plan to do several consecutive debug sessions bsub W 1 00 Is n 8 bash ddt a out 4 3 1 2 Debugging MPI applications on Deimos Using DDT on Deimos is similar to Mars For OpenMPI submit the job the following bsub x W 1 00 I n 8 a openmpi ddt a out Then set the number of processes in the DDT session control window and click the Submit button DDT also works in an interactive batch session on the compute nodes bsub W 1 00 Is n 8 a openmpi bash ddt a out 4 3 2 Intel Debugger idb The Intel debugger available with module load idb can be used for programs compiled with an Intel compiler
33. lel programs With a combination of the above mentioned approaches hybrid applications can be instrumented original mpif90 openmp hybrid F90 o hybrid instrumented vtf90 vt f90 mpif90 openmp hybrid F90 o hybrid By default running a VampirTrace instrumented application should result in a tracefile in the current working directory where the application was executed Consult the documentation for more detailed information e g manual source code instrumentation important environment variables recording hardware counter by using PAPI library memory allocation tracing I O tracing function filtering and grouping The installed documentation can be found on Mars and Deimos in the folder licsoft tools vampirtrace lt VERSION gt share vampirtrace doc 4 5 Mathematical Libraries The following mathematical are available on our platforms including the two seperate clusters 4 5 Mathematical Libraries 23 Mars Deimos Phobos MKL 8 1 8 1 9 1 ACML 3 6 3 6 ATLAS 3 6 3 6 SCSL 1 6 1 4 5 1 Math Kernel Library MKL The Intel Math Kernel Library is a collection of basic linear algebra subroutines BLAS and fast fourier transformations FFT It contains routines for Solvers such as linear algebra package LAPACK and BLAS Eigenvector eigenvalue solvers BLAS LAPACK PDEs signal processing seismic solid state physics FFTs General scientific financial vector transcendental functions vector mar
34. ll find the following manuals Intel Itanium Processor Floating Point Software Assistance handler FPSWA Intel Itanium Architecture Software Developer s Manuals Volume 1 Application Architecture Intel Itanium Architecture Software Developer s Manuals Volume 2 System Ar chitecture Intel Itanium Architecture Software Developer s Manuals Volume 3 Instruction Set Intel Itanium 2 Processor Reference Manual for Software Development and Opti mization Itanium Architecture Assembly Language Reference Guide Libraries and Compilers http www intel com software products mk1 index htm http www intel com software products ipp index htm http www ball project org http www intel com software products compilers Intel Compiler Suite http www pgroup com doc PGI Compiler http pathscale com ekopath html PathScale Compilers Tools http www allinea com downloads userguide pdf Allinea DDT Manual http www intel com software products compilers docs linux idb_manual_ 1 html Intel Debugger http www gnu org software gdb documentation GNU Debugger http vampir ng de official homepage of Vampir an outstanding tool for performance analysis developed at ZIH http www fz juelich de zam kojak homepage of KOJAK at the FZ Julich Parts of this project are used by Vampirtrace http www intel com software products threading index htm 34 A APPENDIX A Appendix A 1 Problems with Intel Com
35. ly run within a node or a par tition so it is neccessary to include the option R span hosts 1 The maximum number of processors for an SMP parallel program is 506 on an Altix partition and 8 on a quad node on Deimos A simple example of a job file for an OpenMP job can be found above section 3 4 3 4 3 2 MPI Jobs There are major differences for submitting MPI parallel jobs on the systems Please refer to chapter 4 2 1 for compiling MPI programs It is essential to use the same modules at compile and run time Mars The MPI library running on the Altix is provided by SGI and highly optimized for the ccNUMA architecture of this machine However communication within a partition is faster than across partitions Take this into consideration when you submit your job Single partition jobs can be started like this bsub R span hosts 1 n 16 mpirun np 16 a out Really large jobs with over 256 CPUs might run over multiple partitions Cross partition jobs can be submitted via PAM like this bsub n 1024 pamrun a out Deimos Most MPI implementations on normal clusters communicate via ethernet fabrics On Deimos and Phobos we have a high bandwidth low latency Infiniband network for communication Yet it is a bit tricky to handle from the user s point of view Per default when you specify a compiler module the corresponding OpenMPI library can 3 4 Batch Systems 13 be used without much tr
36. ode 4 GB All nodes share a 4 4 TB SAN filesystem Each node has additional local diskspace mounted on scratch The jobs for the compute nodes are scheduled by a LSF batch system running on the login node phobos hrsk tu dresden de Two seperate Infiniband networks 10 Gb s with low cascading switches provide the infrastructure for low latency high throughput data traffic An additional GB Ether network is used for control and service purposes 2 3 1 CPU Phobosis based on single core AMD Opteron 248 processor It has the following basic properties clock rate 2 2 GHz floating point units 2 peak performance 4 4 GFLOPS L1 cache 2x 64 kB L2 cache 1 MB memory bus 128 bit x 200 MHz The CPU belongs to the x86_64 family Although it is fully capable of running x86 code one should always try to use 64 bit programs due to their potentially higher performance 3 Operating Systems Make sure you know how to work with a Linux system Documentations and tutorials can be easily found in the internet or in your library 3 1 Login The only way to login to the machines is via ssh From a Linux console the command syntax is ssh lt user gt lt host gt The option X enables X11 forwarding for graphical applications The default shell is bash Hostname Description mars hrsk tu dresden de neptun hrsk tu dresden de deimos hrsk tu dresden de SGI Altix 4700 LSF SGI Altix 4700 with FPGA and graphic h
37. ols for analysis and management so software tools are being developed in all these different environments at once The GenInfo Software Toolbox is a set of software and data ex change specifications that are used by NCBI to produce portable modular software for molecular biology 5 3 Engineering 5 3 1 Abaqus Version ABAQUS 6 6 1 Vendor http www hks com Module abaqus Machines Deimos General ABAQUS is a general purpose finite element program designed for advanced linear and nonlinear engineering analysis applications with facilities for linking in user developed material models elements friction laws 5 3 2 Ansys Version Ansys 11 0 Vendor http www ansys com Module ansys Machines Deimos General ANSYS is a general purpose finite element program for engineering analysis and includes preprocessing solution and postprocessing functions ANSYS is used in a wide range of disciplines for solutions to mechanical thermal and electronic problems 5 4 Mathematics 29 Please do not run Ansys on the login node Use a call like this for a pure computation bsub n lt N gt R span hosts 1 ansys110 np lt N gt b p aa_t_a o lt output txt gt i lt input txt gt If your problem needs the Research license substitute aat_a by aar The usage of more than N 4 CPUs is not advisable by CADFEM Make sure to include R span hosts 1 in your job submission Ansys only runs on a single SMP node
38. ouble E g module load pathscale changes the environment so that you can use mpicc to compile and link MPI parallel C codes built with pathcc mpiCC and mpif90 for C and Fortran90 codes resp Please pay attention to the messages you get loading the module They are more up to date than this manual To submit a job the user has to use a script or a command line like this bsub n lt N gt a openmpi mpirun lsf a out Phobos Per default when you specify a compiler module the corresponding MVAPICH library is loaded automatically E g module load pgi changes the environment so that you can use mpicc to compile and link MPI parallel C codes built with pathcc mpiCC and mpif90 for C and Fortran90 codes resp Please pay attention to the messages you get loading the module They are more up to date than this manual To submit a program compiled with PGI compiler the user has to use a script or a command line like this module load pgi if not already loaded bsub n lt N gt a mvapich mpirun lsf a out You can switch the MPI library manually like module load pgi if not already loaded module switch mvapich_pgi openmpi_pgi bsub n lt N gt a openmpi mpirun lsf a out 3 4 4 Placing Threads or Processes on CPUs 3 4 4 1 dplace on Altix To bind threads to CPUs you can use the dplace command Important flags are Flag Description c lt cpulist gt CPU numbers are logical numb
39. pilers If you encounter a bug in one of the intel compilers we ask you to report this issue to hpcsupport zih tu dresden de We have a support contract with Intel to get bugs fixed Please apply the following procedure to report the bug 1 Create one single source file C C use the E option to produce a single file icc E myfile c gt bug c Fortran use fgather fgather myfile F90 Run the compiler under the control of cesr compiler command cesr icc 03 bug c or cesr ifort 03 cesrgathered F90 Please read the man page for a more detailled description Be aware that this may take a long time The tool will print out a summary containing the compiler command required to reproduce the error and the outputfile that was generated Please provide us with the summary and the outputfile This procedure has the following advantages 1 lt protects your intellectual property because you don t have to send in your complete source code It reduces the amount of code you have to send it makes life easier for the engineers and this will reduce the amount of time required to fix this bug Please also report whether you have found a workaround e g using a different compiler version or using different compiler flags We need to know how critical this issue is for you
40. rs The following list shows some examples depending on the parallelization type of the program 22 4 SOFTWARE DEVELOPMENT e Serial programs Compiling serial code is the default behavior of the wrappers Simply replace the compiler by VampirTrace s wrapper original gfortran a f90 b f90 o myprog with instrumentation vtf90 a f90 b f90 o myprog This will instrument user functions if supported by compiler and link the Vam pir Trace library e MPI parallel programs If your MPI implementation uses MPI compilers this is the case on Deimos and Phobos you need to tell VampirTrace s wrapper to use this compiler instead of the serial one original mpicc hello c o hello instrumented vtcc vt cc mpicc hello c o hello MPI implementations without own compilers as on the Altix require the user to link the MPI library manually In this case you simply replace the compiler by VampirTrace s compiler wrapper original icc hello c o hello 1mpi instrumented vtcc hello c o hello lmpi If you want to instrument MPI events only creates smaller trace files and less overhead use the option vt inst manual to disable automatic instrumentation of user functions e OpenMP parallel programs When VampirTrace detects OpenMP flags on the command line OPARI is invoked for automatic source code instrumentation of OpenMP events original ifort openmp pi f o pi instrumented vtf77 openmp pi f o pi e Hybrid MPI OpenMP paral
41. system provides security for the HOME directories on Mars Deimos and Phobos on a daily basis This is the reason why we urge our users to store large temporary data like checkpoint files on the fastfs Filesystem or at local scratch disks 3 4 Batch Systems Both HRSK systems are operated with the batch system LSF running on Mars and Deimos resp The job submission can be done with the command bsub bsub_options lt job gt Some options of bsub are shown in the following table bsub option Description n lt N gt set number of processors to N default 1 W lt hh mm gt set maximum wallclock time to hh mm R rusage mem MEM_MB needed memory size in MB J lt name gt assigns the specified name to the job eo lt errfile gt writes the standard error output of the job to the specified file overwriting o lt outfile gt appends the standard output of the job to the specified file R span hosts 1 use only one SMP node for OpenMP jobs x disable other jobs to share the node Deimos You can use the J macro to merge the job ID into names It is more convenient to put the options directly in a job file you can submit with bsub lt my_jobfile An example job file may look like this 3 4 Batch Systems 11 bin bash BSUB W 4 00 BSUB R rusage mem 1500 memory for the job in MB max wall clock time 4h BSUB R span hosts 1 run on a single node BSUB
42. the Center for High Performance Computing of the Technische Universit t Dresden Vampir is available as a commercial product since 1996 and has been enhanced in the scope of many research and development projects In the past it was distributed by the German Pallas GmbH which became later a part of Intel Corpora tion The cooperation with Intel ended in 2005 but the development is continued by ZIH A growing number of performance monitoring environments like VampirTrace see be low TAU or KOJAK can produce tracefiles that are readable by Vampir Since version 5 0 Vampir supports the new Open Trace Format OTF that is developed by ZIH as well and is especially designed for massively parallel programs A detailed documentation on Vampir can be found at http www vampir eu Before using Vampir set up the correct environment with module load vampir Start the GUI with bsub I vampir 4 4 Performance Tuning 21 R meals Vampir Timeline lt mars gt 5 Processo SET CU_INIT Process 1 CU_INIT Process 2 CU_INIT Process 3 CU_INIT N Process 4 CU_INIT Process 5 CU_INIT Process 6 CU_INIT iy Process 7 CU_INIT i Process 8 CU_INIT y Process 9 CU_INIT i Process 10 PUTE 37 CU_INIT Process 11 SAGE CU_INIT Process 12 5137 CU_INIT i Process 135 CUNT Process MAA CU_INIT Process 15 SHE CU_INIT Figure 4 Vampir Global Timeline 4 4 4 1 Vampir Server on Mars Vampir Server comes in two parts a daemon
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