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BioGeometry.OptEOnTopsail
r1.1 - 11 Feb 2009 - 18:08 - Main.guest
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UNC getting started on Topsail page http://help.unc.edu/6214 * Load the gcc development suit module =module load hpc/mvapich-gcc= * get mini source onto the scratch partition On a local machine <verbatim> cd /tmp svn checkout https://svn.rosettacommons.org/source/trunk/mini mini cd mini svn checkout https://svn.rosettacommons.org/source/trunk/minirosetta_database database cd .. tar -czf mini.tar.gz mini scp mini.tar.gz yourOnyen@topsail.unc.edu:/ifs1/scr/yourOnyen/ ssh yourOnyen@topsail.unc.edu cd /ifs1/scr/yourOnyen mkdir mini_optE tar -xzf mini.tar.gz mini_optE/mini cd mini_optE mv mini/database minirosetta_database </verbatim> The scratch directory is auto-cleans files over 21 days old, so backup stuff to mass storage or afs edit mini/tools/build/basic.settings by changing in the "gcc, mpi" section =mpicc= -> =/opt/lam/gnu/bin/mpicc= and =mpiCC= -> =/opt/lam/gnu/bin/mpiCC= <verbatim> cd mini_optE/mini/external/lib wget http://www.zlib.net/zlib-1.2.3.tar.gz tar -xzf zlib-1.2.3.tar.gz python scons.py extras=mpi mode=release bin </verbatim> ---++ Getting MPI working with Topsail <verbatim> $cd ifs1/scr/momeara/mini_optE/mini $bsub -n 1 -q debug -o out_fixbb.%J -e err_fixbb.%J -a mvapich mpirun ./bin/fixbb.linuxgccrelease \ -s ifs1/scr/momeara/momeara/mini_optE/mini/test/integration/tests/fixbb/1l2y.pdb # prints what job this submission is $bjobs <job number> $cat err_fixbb.<job number> #returns this #----------------------------------------------------------------------------- # #It seems that there is no lamd running on the host cmp-51-9.local. # #This indicates that the LAM/MPI runtime environment is not operating. #The LAM/MPI runtime environment is necessary for MPI programs to run #(the MPI program tired to invoke the "MPI_Init" function). # #Please run the "lamboot" command the start the LAM/MPI runtime #environment. See the LAM/MPI documentation for how to invoke #"lamboot" across multiple machines. #----------------------------------------------------------------------------- </verbatim> When <verbatim> module load hpc/mvapich-gcc </verbatim> all sorts of stuff happen: * set environment variables: compiler locations, PMICH_HOME, PATH, MANPATH, LD_LIBRARY_PATH, INCLUDE. In particular "which mpiCC" returns "/usr/local/ofed/mpi/gcc/bin/mpiCC" <verbatim> [momeara@topsail-login1 ~]$ echo $LD_LIBRARY_PATH /usr/local/ofed/lib64:/usr/local/ofed/lib:/usr/local/ofed/mpi/gcc/lib:/opt/lsfhpc/6.2/linux2.6-glibc2.3-x86_64/lib:/opt/intel/fce/9.1.041/lib:/opt/intel/cce/9.1.047/lib [momeara@topsail-login1 ~]$ echo $INCLUDE /usr/local/ofed/include:/usr/local/ofed/mpi/gcc/include </verbatim> Put all of those paths in site.settings in the "prepends" section so it looks like this: <verbatim> settings = { "site" : { "prepends" : { # Location of standard and system binaries "program_path" : [ "/usr/local/ofed/mpi/gcc/", # Path to GCC compiler if not in the os rule # Path to Intel C++ compiler if not in the os rule ], # Location of standard and system header files if not in the os rule "include_path" : [ "/usr/local/ofed/include", "/usr/local/ofed/mpi/gcc/include", # ], # Location of standard and system libraries if not in the os rule. "library_path" : [ "/opt/lsfhpc/6.2/linux2.6-glibc2.3-x86_64/lib", "/opt/intel/fce/9.1.041/lib", "/opt/intel/cce/9.1.047/lib", "/usr/local/ofed/lib64", "/usr/local/ofed/lib", "/usr/local/ofed/mpi/gcc/lib", "/opt/lsfhpc/6.2/linux2.6-glibc2.3-x86_64/lib", "/opt/intel/fce/9.1.041/lib", "/opt/intel/cce/9.1.047/lib" # ], }, "appends" : { }, "overrides" : { }, "removes" : { }, } } </verbatim> Then run =./scons.py extras=mpi,static mode=release -j7 bin= I get this warning message <verbatim> /opt/mpich/gnu/lib/libmpich.a(p4_secure.o)(.text+0x278): In function `start_slave': : warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking /opt/mpich/gnu/lib/libmpich.a(p4_sock_util.o)(.text+0xcd8): In function `gethostbyname_p4': : warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking Install file: "build/src/release/linux/2.6/64/x86/gcc/mpi-static/inv_kin_lig_loop_design.linuxgccrelease" as "bin/inv_kin_lig_loop_design.linuxgccrelease" </verbatim> According to this [[http://www.mail-archive.com/bug-findutils@gnu.org/msg00941.html][bug report]] this is a problem with an out dated version of glibc. To check if it built ok test it on an application that uses mpi: <verbatim> $bsub -q debug -o output.%J -e err.%J -n 2 -a mvapich mpirun ./bin/optE_parallel.linuxgccrelease $bjobs #to see how the job is running $cat output.<job number> ... The output (if any) follow: core.init: command: ./optE_parallel.linuxgccrelease core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1556917344 seed_offset=0 real_seed=1556917344 core.init.random: RandomGenerator:init: Normal mode, seed=1556917344 RG_type=mt19937 core.options.util: Use either -s or -l to designate one or more start_files core.init: command: ./optE_parallel.linuxgccrelease core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-537361992 seed_offset=0 real_seed=-537361992 core.init.random: RandomGenerator:init: Normal mode, seed=-537361992 RG_type=mt19937 core.options.util: Use either -s or -l to designate one or more start_files ... </verbatim> -- Main.MatthewOmeara - 04 Feb 2009
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