GAMESS-2012May01 for PRIMERGY RX300 | Research Center for Computational Science

Webpage

http://www.msg.ameslab.gov/GAMESS/GAMESS.html

Version

May 1, 2012

Tools for Compiling

Intel Compiler 12.1.2.273
Intel MPI 4.0.2.003

Necessary Files for Compiling

gamess-2012May01.tar.gz (from GAMESS webpage)
rungms.patch

Content of rungms.patch

--- rungms.orig    2012-08-14 16:33:58.481954000 +0900
+++ rungms    2012-08-14 16:34:15.780440000 +0900
@@ -56,10 +56,10 @@
#       both Sun Grid Engine (SGE), and Portable Batch System (PBS).
#       See also a very old LoadLeveler "ll-gms" for some IBM systems.
#
-set TARGET=sockets
-set SCR=/scr/$USER
-set USERSCR=~$USER/scr
-set GMSPATH=/u1/mike/gamess
+set TARGET=mpi
+set SCR=/work/users/$USER/scr.$$
+if (! -d $SCR) mkdir $SCR
+set GMSPATH=/local/apl/pg/gamess2012May01
#
set JOB=$1      # name of the input file xxx.inp, give only the xxx part
set VERNO=$2    # revision number of the executable created by 'lked' step
@@ -89,16 +89,10 @@
    uniq $TMPDIR/machines
endif
if ($SCHED == PBS) then
-   set SCR=/scratch/$PBS_JOBID
+#   set SCR=/scratch/$PBS_JOBID
    echo "PBS has assigned the following compute nodes to this run:"
    uniq $PBS_NODEFILE
endif
-#
-echo "Available scratch disk space (Kbyte units) at beginning of the job is"
-df -k $SCR
-echo "GAMESS temporary binary files will be written to $SCR"
-echo "GAMESS supplementary output files will be written to $USERSCR"
-
#        this added as experiment, February 2007
#        its intent is to detect large arrays allocated off the stack
limit stacksize 8192
@@ -131,6 +125,15 @@
    endif
endif

+set dir=`dirname $JOB`
+set USERSCR=`cd $dir; pwd`
+
+#
+echo "Available scratch disk space (Kbyte units) at beginning of the job is"
+df -k $SCR
+echo "GAMESS temporary binary files will be written to $SCR"
+echo "GAMESS supplementary output files will be written to $USERSCR"
+
#    define many environment variables setting up file names.
#    anything can be overridden by a user's own choice, read 2nd.
source $GMSPATH/gms-files.csh
@@ -583,13 +586,13 @@

    #
    if ($NCPUS == 1) then
-      echo "-n $NPROCS -host `hostname` /home/mike/gamess/gamess.$VERNO.x" >> $PROCFILE
+      echo "-n $NPROCS -host `hostname` $GMSPATH/gamess.$VERNO.x" >> $PROCFILE
    else
       if ($NNODES == 1) then
              # when all processes are inside a single node, it is simple!
              # all MPI processes, whether compute processes or data servers,
              # are just in this node.   (note: NPROCS = 2*NCPUS!)
-         echo "-n $NPROCS -host `hostname` /home/mike/gamess/gamess.$VERNO.x" >> $PROCFILE
+         echo "-n $NPROCS -host `hostname` $GMSPATH/gamess.$VERNO.x" >> $PROCFILE
       else
              # For more than one node, we want PPN compute processes on
              # each node, and of course, PPN data servers on each.
@@ -602,7 +605,7 @@
          while ($n <= $NNODES)
             set host=`sed -n -e "$n p" $HOSTFILE`
             set host=$host[1]
-            echo "-n $PPN2 -host $host /home/mike/gamess/gamess.$VERNO.x" >> $PROCFILE
+            echo "-n $PPN2 -host $host $GMSPATH/gamess.$VERNO.x" >> $PROCFILE
             @ n++
          end
       endif
@@ -666,7 +669,7 @@
    setenv I_MPI_DEBUG 0
    setenv I_MPI_STATS 0
    setenv I_MPI_FABRICS dapl
-   setenv I_MPI_DAT_LIBRARY libdat2.so
+   setenv I_MPI_DAT_LIBRARY libdat2.so.2
    #      in case someone wants to try the "tag matching interface",
    #      an option which unfortunately ignores the WAIT_MODE in 4.0.2!
    #--setenv I_MPI_FABRICS tmi
@@ -758,7 +761,7 @@
    # Now, at last, we can actually kick-off the MPI processes...
    #
    echo "MPI kickoff will run GAMESS on $NCPUS cores in $NNODES nodes."
-   echo "The binary to be executed is /home/mike/gamess/gamess.$VERNO.x"
+   echo "The binary to be executed is $GMSPATH/gamess.$VERNO.x"
    echo "MPI will run $NCPUS compute processes and $NCPUS data servers,"
    echo "    placing $PPN of each process type onto each node."
    echo "The scratch disk space on each node is $SCR, with free space"
@@ -790,7 +793,7 @@
       setenv I_MPI_HYDRA_ENV all
       setenv I_MPI_PERHOST $PPN2
       mpiexec.hydra -f $PROCFILE -n $NPROCS \
-            /home/mike/gamess/gamess.$VERNO.x < /dev/null
+            $GMSPATH/gamess.$VERNO.x < /dev/null
       unset echo
       breaksw
    case default:
@@ -1040,6 +1043,7 @@
echo Files used on the master node $master were:
ls -lF $SCR/$JOB.*
rm -f $SCR/$JOB.F*
+rm -f $SCR/$JOB.nodes.mpd
#
#   Clean/Rescue any files created by the VB2000 plug-in
if (-e $SCR/$JOB.V84)        mv $SCR/$JOB.V84     $USERSCR
@@ -1051,13 +1055,13 @@
if (-e $SCR/$JOB.molf)       mv $SCR/$JOB.molf    $USERSCR
if (-e $SCR/$JOB.mkl)        mv $SCR/$JOB.mkl     $USERSCR
if (-e $SCR/$JOB.xyz)        mv $SCR/$JOB.xyz     $USERSCR
-ls $SCR/${JOB}-*.cube > $SCR/${JOB}.lis
+(ls $SCR/${JOB}-*.cube > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.cube $USERSCR
rm -f $SCR/${JOB}.lis
-ls $SCR/${JOB}-*.grd > $SCR/${JOB}.lis
+(ls $SCR/${JOB}-*.grd > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.grd $USERSCR
rm -f $SCR/${JOB}.lis
-ls $SCR/${JOB}-*.csv > $SCR/${JOB}.lis
+(ls $SCR/${JOB}-*.csv > $SCR/${JOB}.lis) >& /dev/null
if (! -z $SCR/${JOB}.lis) mv $SCR/${JOB}*.csv $USERSCR
rm -f $SCR/${JOB}.lis
#
@@ -1091,37 +1095,37 @@
#    We have inherited a file of unique node names from above.
#    There is an option to rescue the output files from group DDI runs,
#    such as FMO, in case you need to see the other group's outputs.
-if ($TARGET == mpi) then
-   set nnodes=`wc -l $HOSTFILE`
-   set nnodes=$nnodes[1]
-   @ n=1
-   set master=`hostname`
-           # burn off the .local suffix in our cluster's hostname
-   set master=$master:r
-   while ($n <= $nnodes)
-      set host=`sed -n -e "$n p" $HOSTFILE`
-           # in case of openMPI, unwanted stuff may follow the hostname
-      set host=$host[1]
-      if ($host != $master) then
-         echo Files used on node $host were:
-         #---------FMO rescue------
-         #--if ($GDDIjob == true) then
-         #--   echo "========= OUTPUT from node $host is =============="
-         #--   ssh $host -l $USER "cat $SCR/$JOB.F06*"
-         #--endif
-         #---------FMO rescue------
-         ssh $host -l $USER "ls -l $SCR/$JOB.*"
-         ssh $host -l $USER "rm -f $SCR/$JOB.*"
-      endif
-      @ n++
-   end
-#          clean off the last file on the master's scratch disk.
-   rm -f $HOSTFILE
-   #
-   if ($?I_MPI_STATS) then
-      if ($I_MPI_STATS > 0) mv $SCR/stats.txt ~/$JOB.$NCPUS.stats
-   endif
-endif
+###if ($TARGET == mpi) then
+###   set nnodes=`wc -l $HOSTFILE`
+###   set nnodes=$nnodes[1]
+###   @ n=1
+###   set master=`hostname`
+###           # burn off the .local suffix in our cluster's hostname
+###   set master=$master:r
+###   while ($n <= $nnodes)
+###      set host=`sed -n -e "$n p" $HOSTFILE`
+###           # in case of openMPI, unwanted stuff may follow the hostname
+###      set host=$host[1]
+###      if ($host != $master) then
+###         echo Files used on node $host were:
+###         #---------FMO rescue------
+###         #--if ($GDDIjob == true) then
+###         #--   echo "========= OUTPUT from node $host is =============="
+###         #--   ssh $host -l $USER "cat $SCR/$JOB.F06*"
+###         #--endif
+###         #---------FMO rescue------
+###         ssh $host -l $USER "ls -l $SCR/$JOB.*"
+###         ssh $host -l $USER "rm -f $SCR/$JOB.*"
+###      endif
+###      @ n++
+###   end
+####          clean off the last file on the master's scratch disk.
+###   rm -f $HOSTFILE
+###   #
+###   if ($?I_MPI_STATS) then
+###      if ($I_MPI_STATS > 0) mv $SCR/stats.txt ~/$JOB.$NCPUS.stats
+###   endif
+###endif
#
#   IBM SP cleanup code...might need to be something other than 'rsh'.
#

Procedure of Compiling

#!/bin/csh -f
umask 022
set file_gamess=/home/users/${USER}/build/gamess2012May01/gamess-2012May01.tar.gz
set work=/work/users/${USER}
set gamess=gamess2012May01
set patch_rungms=/home/users/${USER}/build/gamess2012May01/ccpg/rungms.patch
#----------------------------------------------------------------------------
cd ${work}
if (-d ${gamess}) then
mv ${gamess} ${gamess}-erase
rm -rf ${gamess}-erase &
endif
#----------------------------------------------------------------------------
tar xzf ${file_gamess}
mv gamess ${gamess}
cd ${work}/${gamess}
expect <<EXPECT
spawn ./config
expect "After the new window is open"
send "\r"
expect "please enter your target machine name:"
send "linux64\r"
expect "GAMESS directory?"
send "\r"
expect "GAMESS build directory?"
send "\r"
expect "Version?"
send "\r"
expect "Please enter your choice of FORTRAN:"
send "ifort\r"
expect "Version?"
send "12\r"
expect "hit <return> to continue after digesting this message."
send "\r"
expect "hit <return> to continue to the math library setup."
send "\r"
expect "Enter your choice of 'mkl' or 'atlas' or 'acml' or 'none':"
send "mkl\r"
expect "MKL pathname?"
send "/opt/intel/mkl\r"
expect "MKL version (or 'skip')?"
send "skip\r"
expect "hit <return> after you have digested this warning."
send "\r"
expect "please hit <return> to compile the GAMESS source code activator"
send "\r"
expect "please hit <return> to set up your network for Linux clusters."
send "\r"
expect "communication library ('sockets' or 'mpi')?"
send "mpi\r"
expect "Enter MPI library (impi, mvapich2, mpt, sockets):"
send "impi\r"
expect "Please enter your impi's location:"
send "/opt/intel/impi/4.0.2.003\r"
expect eof
EXPECT
#----------------------------------------------------------------------------
cd ${work}/${gamess}/ddi
./compddi >& compddi.log
cd ${work}/${gamess}
./compall >& compall.log
./lked >& lked.log
#----------------------------------------------------------------------------
chmod -R o-rwx source object
find . -name "src" | xargs chmod -R o-rwx
#----------------------------------------------------------------------------
patch -p0 < ${patch_rungms}

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