Документ взят из кэша поисковой машины. Адрес оригинального документа : http://classic.chem.msu.su/gran/gamess/ff_openmpi.pdf Дата изменения: Tue Aug 21 19:06:00 2012 Дата индексирования: Mon Oct 1 19:53:34 2012 Кодировка:

Firelfy 8 with OpenMPI 1.4 (32-bit)

Installing Firefly with OpneMPI (32-bit) libraries
by Pavlo Solntsev (pavlo.solntsev@gmail.com)
An idea of this tutorial is to provide easy to use and comprehensive instructions to setup Firefly on GNU/Linux OS (cluster, workstation, desktop computer laptop etc.). Since 64-bit OS's become more and more popular and Firefly is a 32-bit program yet, 32-bit libraries should be available to run Firefly not only in parallel but on single processor as well. This tutorial was tested on 64-bit Ubuntu 12.04 LTS (3.2.0-29-generic #46-Ubuntu SMP) but of course can be used for any GNU/Linux OS. The installation consist of the following steps: 1. Compilation and installation 32-bit libraries of OpenMPI 2. Creating appropriate settings withing script file to run Firefly 1. Installing dependencies for 32-bit libraries OpenMPI To compile 32-bit libraries additional packages should be available. In Ubuntu 12.04 LTS they are: g++-4.6-multilib g++-multilib gcc-4.6-multilib gcc-multilib gfortran-4.6-multilib gfortran-multilib Basically, these libraries provide 32-bit standard libraries to link 32-bit applications. You can check, if they are present or not (in an Debian based distribution) by command: $ dpkg -l | grep multilib An equivalent command should be used in case of RPM package manager: rpm -qa | grep Unfortunately, name of the packages with 32-bit libraries may vary from distribution to distribution. Of course, all compiler (C, C++, Fortran90/95, Fortran 77) also should be available. First of all we need to download OpenMPI source code from www.open-mpi.org. For Firefly version 8 OpenMPI 1.4 should be used, while 1.2 versions of OpenMPI should be used for earlier versions of Firefly. In this tutorial openmpi-1.4.5 (http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.5.tar.bz2) was used together with Firefly 8.. In a terminal we need to do the following actions:


Firelfy 8 with OpenMPI 1.4 (32-bit)

# Unpack archive with source code $ tar xvfj openmpi-1.4.5.tar.bz2 $ cd openmpi-1.4.5 # configure our Makefile. A value for --prefix variable can be different. It is a place where your # program will be installed. Default /usr/local # We need also to specify 32-bit compilation via additional flag "-m32" that should be passed # to ALL compilers. f $ ./configure --prefix=/opt/soft/openmpi-1.4.5 CFLAGS=-m32 CXXFLAGS=-m32 FFLAGS=m32 FCFLAGS=-m32 # Standard compilation $ make # Installation. Root rights or equivalents are needed. $ sudo make install In the presented example. OpenMPI is installed in /opt/soft/openmpi-1.4.5, but location can be easy changed via --prefix variable at ./configure stage. 2. Creating appropriate settings withing script file to run Firefly To run Firefly, the best way (at least for me) is to make script. Script below is suitable to run Firefly on desktop computer or workstation (without task manager, such as PBS). Suppose Firefly is installed in folder /home/user/progs/ff8 then script file to start Firefly looks (all contents of the script file highlighted as blue): #!/bin/bash # $1 - number of processors for parallel run # $2 - input file without extension # $3 - basis set file export PROJNAME=$2 export FFINPUT="" export FFOUTPUT=$PROJNAME.out export WORKDIR=$PWD if [ -f $PROJNAME.inp ]; then export FFINPUT=$PROJNAME.inp elif [ -f $PROJNAME.INP ]; then export FFINPUT=$PROJNAME.INP else echo "Can't find input file $PROJNAME.inp or $PROJNAME.INP in $PWD" exit fi


Firelfy 8 with OpenMPI 1.4 (32-bit)

# Check for basis set file export BASISF=$3 echo $3 if [ $# -eq 3 ];then if [ -f $3 ]; then BASISF=$3 elif [ -f $PWD/$3 ]; then BASISF=$PWD/$3 else echo "Can't find basis file $3 in $PWD. Exit..." exit fi fi # Check for number of processors on workstation MAXCPUS=`cat /proc/cpuinfo | grep processor | wc -l` echo "Maxcpu's = $MAXCPUS" export NCPUS=$1 if [ $NCPUS -gt $MAXCPUS ]; then echo "You requested CPU's more then you have installed" echo "Number of CPU's will be $MAXCPUS" NCPUS=$MAXCPUS fi # Firefly settings . You can change them according to your ystem export FF8_HOME=$HOME/progs/ff8x export FF8_TEMP=$HOME/tmp/ if [ ! -d $FF8_TEMP ]; then mkdir -p $FF8_TEMP; if [ $? -ne 0 ]; then echo "Can't create $FF8_TEMP dirrectory" ; fi; exit fi # OpenMPI settings . See OpenMPI installation section.. export OMPI_HOME=/opt/soft/openmpi-1.4.5 export PATH=$OMPI_HOME/bin:$PATH # If you have 64-bit libraries installed in your system it better to overwrite LD_LIBRARY_PATH # as in line below export LD_LIBRARY_PATH=$OMPI_HOME/lib # We are ready to go. Make sure name of executable file is correct. mpirun -np $NCPUS $FF8_HOME/firefly8.openmpi14.ex -f -r -p -stdext -ex $FF8_HOME -i $WORKDIR/$FFINPUT -o $WORKDIR/$FFOUTPUT -b $BASISF -t $FF8_TEMP # Cleaning scratch folder rm -rf $FF8_TEMP rm -rf $FF8_TEMP.* exit Firefly can also be placed into any directory being already in PATH variable, such as $HOME/bin, for instance or /usr/local/bin for system wide access. However, it strongly recommended to put the script in to a PATH variable mentioned above. After that Firefly can be started via command


Firelfy 8 with OpenMPI 1.4 (32-bit)

ourscript Input file also should be in the same folder. Of course we need OpenMPI compiled version of Firefly. Depending on your need you can adjust script. It is just example for beginners. To run Firefly on clusters via PBS you need add appropriate PBS parameters to your file: #!/bin/bash #PBS -N #PBS -l nodes=1:ppn=4 # Number of nodes and cpu's #PBS -l pmem=450mb # memmory #PBS -l walltime=48:00:00 # Time for job #PBS -o $PBS_JOBID.o # Standard output for PBS #PBS -e $PBS_JOBID.e # Standard error output for PBS export OMPI_HOME=/opt/soft/openmpi-1.4.5 # change according to your system export PATH=$OMPI_HOME/bin:$PATH export LD_LIBRARY_PATH=$OMPI_HOME/lib export FF8_HOME=$HOME/progs/ff8x # change according to your system export NCPU=`wc -l < $PBS_NODEFILE` export WORKDIR=$PBS_O_WORKDIR export TEMP_DIR=/scratch/$USER/$PBS_JOBID # change according to your settings $OMPI_HOME/ mpirun -np $NCPU $FF8_HOME/firefly -f -r -p -stdext -ex $FF8_HOME -i $WORKDIR/$FFINPUT -o $WORKDIR/$FFOUTPUT -b $BASISF -t $FF8_TEMP rm -rf $TEMP_DIR rm -rf $TEMP_DIR.* exit Based on this tutorial, you should be able to setup Firefly using another version of MPI. Good luck with Firefly. If you have any suggestions, questions or corrections fill free to write me e-mail (see above)