Cpmd

CPMD

The CPMD version 3.13.2 package was built using the Intel v11.1 compilers, and the OpenMPI v1.4.1 library.

Patched with the latest available patch. In the SOURCE directory:

  patch -p2 < ../../cpmd-3.13.2_01.patch

Basic configuration used:

<source lang="bash">

1. INFO#
2. INFO# Configuration to build a parallel cpmd executable for a linux machine
3. INFO# with an AMD64/EM64T cpu (Opteron/AthlonFX/Athlon64/Xeon-EM64T) using
4. INFO# the Intel Fortran Compiler with EM64T extensions.
5. INFO#
6. INFO# For optimal performance you should use a specifically tuned BLAS/LAPACK
7. INFO# library. This example uses the Intel MKL library.
8. INFO#
9. INFO# see http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-linux.html
10. INFO# for more information on compilind and running CPMD on linux machines.
11. INFO#
12. INFO# NOTE: CPMD cannot be compiled with the GNU Fortran compiler.
13. INFO#

    IRAT=2
    CFLAGS='-O2 -Wall -m64'
    CPP='/lib/cpp -P -C -traditional'
    CPPFLAGS='-D__Linux -D__PGI -DFFT_DEFAULT -DPOINTER8 -DLINUX_IFC \
       -DPARALLEL -DMYRINET'
    FFLAGS='-pc64 -O2 -unroll'
    LFLAGS=' -L. -L${MKLPATH} ${MKLPATH}/libmkl_solver_lp64_sequential.a -Wl,--start-group \
       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread'
    FFLAGS_GROMOS='-Dgood_luck $(FFLAGS)'
    if [ $debug ]; then
      FC='mpif77 -c -g'
      CC='mpicc -g -Wall -m64'
      LD='mpif77 -g'
    else
      FC='mpif77 -c '
      CC='mpicc'
      LD='mpif77 -static-intel '
    fi

</source>

In the SOURCE directory do:

  ./config.sh LINUX_INTEL64_INTEL_MPI > Makefile
  Make >& make.out

Created cpmd/3.13.2 module:

<source lang="tcl">

1. %Module -*- tcl -*-

1. CPMD 3.13.2

proc ModulesHelp { } {

 puts stderr "\tThis module adds CPMD environment variables"

}

module-whatis "adds CPMD environment variables"

1. CPMD was compiled with Intel compilers and OpenMPI

prereq intel prereq openmpi

setenv SCINET_CPMD_HOME /scinet/gpc/Applications/cpmd/3.13.2 setenv SCINET_CPMD_BIN /scinet/gpc/Applications/cpmd/3.13.2/bin append-path PATH /scinet/gpc/Applications/cpmd/3.13.2/bin setenv CPMD_PP_LIBRARY_PATH /scinet/gpc/Applications/cpmd/3.13.2/PPLIBNEW </source>

Running CPMD

- Load the necessary modules: gcc, intel, intelmpi, nwchem (best done in your .bashrc)

  # module load intel openmpi cpmd

- The CPMD executable is in $SCINET_CPMD_BIN/cpmd.x

- For multinode runs, use the sample IB script futher below

- Create a torque script to run CPMD. Here is an example for a calculation on a single 8-core node:

<source lang="bash">

1. !/bin/bash
2. MOAB/Torque submission script for Scinet GPC (ethernet)
3. PBS -l nodes=1:ppn=8,walltime=00:30:00
4. PBS -N cpmdjob
5. load the cpmd and other required modules if not in .bashrc already

module load intel openmpi cpmd

1. If not an interactive job (i.e. -I), then cd into the directory where
2. I typed qsub.

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then

  if [ -n "$PBS_O_WORKDIR" ]; then
    cd $PBS_O_WORKDIR
  fi

fi

mpirun -np 8 -hostfile $PBS_NODEFILE $SCINET_CPMD_BIN/cpmd.x inp1 /home/mgalib/uspp/uspp-736/Pot >out1 </source>

Here is a similar script, but this one uses 2 InfiniBand-connected nodes:

<source lang="bash">

1. !/bin/bash
2. PBS -l nodes=2:ib:ppn=8,walltime=48:00:00,os=centos53computeA
3. PBS -N cpmdjob

1. 1. To submit type: qsub nwc.sh (where nwc.sh is the name of this script)

1. If not an interactive job (i.e. -I), then cd into the directory where
2. I typed qsub.

if [ "$PBS_ENVIRONMENT" != "PBS_INTERACTIVE" ]; then

  if [ -n "$PBS_O_WORKDIR" ]; then
    cd $PBS_O_WORKDIR
  fi

fi

mpirun -np 16 -hostfile $PBS_NODEFILE $SCINET_CPMD_BIN/cpmd.x inp1 /home/mgalib/uspp/uspp-736/Pot >out1 </source>

-- dgruner 3 September 2010