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GAMESS-2012May01 for UV1000

Webpage

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

Version

May 1, 2012

Tools for Compiling

  • Intel Compiler 12.1.2.273

Necessary Files for Compiling

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

Content of rungms.patch

--- rungms.orig    2012-08-15 14:07:02.535168674 +0900
+++ rungms    2012-08-15 14:10:11.368169006 +0900
@@ -57,9 +57,9 @@
 #       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 SCR=/work/users/$USER/scr.$$
+if (! -d $SCR) mkdir $SCR
+set GMSPATH=/local/apl/uv/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 +89,11 @@
    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 +126,15 @@
    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 $GMSPATH/gms-files.csh
@@ -255,53 +259,55 @@
 #                       NODE= physical enclosure (box/blade)
 #
 #       1. Sequential execution is sure to be on this very same host
-   if ($NCPUS == 1) then
+###   if ($NCPUS == 1) then
+###      set NNODES=1
+###      set HOSTLIST=(`hostname`)
+###   endif
+####
+####       2. This is an example of how to run on a multi-core SMP enclosure,
+####          where all CPUs (aka COREs) are inside a -single- NODE.
+####     At other locations, you may wish to consider some of the examples
+####     that follow below, after commenting out this ISU specific part.
+###   if ($NCPUS > 1) then
+###      switch (`hostname`)
+###         case se.msg.chem.iastate.edu:
+###         case sb.msg.chem.iastate.edu:
+###            if ($NCPUS > 2) set NCPUS=2
+###            set NNODES=1
+###            set HOSTLIST=(`hostname`:cpus=$NCPUS)
+###            breaksw
+###         case br.msg.chem.iastate.edu:
+###            if ($NCPUS > 4) set NCPUS=4
+###            set NNODES=1
+###            set HOSTLIST=(`hostname`:cpus=$NCPUS)
+###            breaksw
+###         case cd.msg.chem.iastate.edu:
+###         case zn.msg.chem.iastate.edu:
+###         case ni.msg.chem.iastate.edu:
+###         case co.msg.chem.iastate.edu:
+###         case pb.msg.chem.iastate.edu:
+###         case bi.msg.chem.iastate.edu:
+###         case po.msg.chem.iastate.edu:
+###         case at.msg.chem.iastate.edu:
+###         case sc.msg.chem.iastate.edu:
+###            if ($NCPUS > 4) set NCPUS=4
+###            set NNODES=1
+###            set HOSTLIST=(`hostname`:cpus=$NCPUS)
+###            breaksw
+###         case ga.msg.chem.iastate.edu:
+###         case ge.msg.chem.iastate.edu:
+###         case gd.msg.chem.iastate.edu:
+###            if ($NCPUS > 6) set NCPUS=6
+###            set NNODES=1
+###            set HOSTLIST=(`hostname`:cpus=$NCPUS)
+###            breaksw
+###         default:
+###            echo I do not know how to run this node in parallel.
+###            exit 20
+###      endsw
+###   endif
       set NNODES=1
-      set HOSTLIST=(`hostname`)
-   endif
-#
-#       2. This is an example of how to run on a multi-core SMP enclosure,
-#          where all CPUs (aka COREs) are inside a -single- NODE.
-#     At other locations, you may wish to consider some of the examples
-#     that follow below, after commenting out this ISU specific part.
-   if ($NCPUS > 1) then
-      switch (`hostname`)
-         case se.msg.chem.iastate.edu:
-         case sb.msg.chem.iastate.edu:
-            if ($NCPUS > 2) set NCPUS=2
-            set NNODES=1
-            set HOSTLIST=(`hostname`:cpus=$NCPUS)
-            breaksw
-         case br.msg.chem.iastate.edu:
-            if ($NCPUS > 4) set NCPUS=4
-            set NNODES=1
-            set HOSTLIST=(`hostname`:cpus=$NCPUS)
-            breaksw
-         case cd.msg.chem.iastate.edu:
-         case zn.msg.chem.iastate.edu:
-         case ni.msg.chem.iastate.edu:
-         case co.msg.chem.iastate.edu:
-         case pb.msg.chem.iastate.edu:
-         case bi.msg.chem.iastate.edu:
-         case po.msg.chem.iastate.edu:
-         case at.msg.chem.iastate.edu:
-         case sc.msg.chem.iastate.edu:
-            if ($NCPUS > 4) set NCPUS=4
-            set NNODES=1
-            set HOSTLIST=(`hostname`:cpus=$NCPUS)
-            breaksw
-         case ga.msg.chem.iastate.edu:
-         case ge.msg.chem.iastate.edu:
-         case gd.msg.chem.iastate.edu:
-            if ($NCPUS > 6) set NCPUS=6
-            set NNODES=1
-            set HOSTLIST=(`hostname`:cpus=$NCPUS)
-            breaksw
-         default:
-            echo I do not know how to run this node in parallel.
-            exit 20
-      endsw
-   endif
+      set HOSTLIST=(`hostname`:cpus=$NCPUS)
 #
 #       3. How to run in a single computer, namely the "localhost", so
 #          this computer needn't have a proper Internet name.
@@ -353,90 +359,90 @@
 #          names into the HOSTLIST string for the kickoff program,
 #          and to request the host name of the fast network adapters.
 #
-    if ($?PBS_JOBID) then
-#
-#         The IBM cluster has two Gigabit adapters in each 4-way SMP,
-#         while the AXP cluster is based on a Myrinet network.
-      if (`uname` == AIX)   set NETEXT=".gig,.gig2"
-      if (`uname` == Linux) set NETEXT=".myri"
-#
-#         repeated host names in the PBS host file indicate being assigned
-#         CPUs in the same SMP enclosure, which we must count up correctly.
-#         Fortunately PBS gives duplicate host names in a row, not scrambled.
-#         The number of hosts in the PBS node file (nmax) should equal the
-#         requested processor count, NCPUS.  We need to count duplicates
-#         in order to learn the number of SMP enclosures, NNODES, and how
-#         many CPUs inside each SMP were assigned (NSMPCPU).  For example,
-#         if we are assigned the host names "a a a b b c c c" we must build
-#         the string "a:cpus=3 b:cpus=2 c:cpus=3" so that ddikick.x will
-#         know the SMP structure of the assigned node names.  (C-shell handles
-#         variable substitution followed by colon gracefully by ${HOST}:cpus.)
-#
-      set HOSTLIST=()
-      set nmax=`wc -l $PBS_NODEFILE`
-      set nmax=$nmax[1]
-      if ($nmax != $NCPUS) then
-         echo There is processor count confusion
-         exit
-      endif
-#            1st host in the list is sure to be a new SMP enclosure
-      set MYNODE=`sed -n -e "1 p" $PBS_NODEFILE`
-      set MYNODE=`echo $MYNODE | awk '{split($0,a,"."); print a[1]}'`
-#            IPROC counts assigned processors (up to NCPUS),
-#            NNODES counts number of SMP enclosures.
-#            NSMPCPU counts processors in the current SMP enclosure
-      @ IPROC = 2
-      @ NNODES = 1
-      @ NSMPCPU = 1
-      set spacer1=":cpus="
-      set spacer2=":netext="
-      while($IPROC <= $nmax)
-         set MYPROC=`sed -n -e "$IPROC p" $PBS_NODEFILE`
-         set MYPROC=`echo $MYPROC | awk '{split($0,a,"."); print a[1]}'`
-         if($MYPROC != $MYNODE) then
-            set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
-            set MYNODE=$MYPROC
-            @ NSMPCPU = 0
-            @ NNODES++
-         endif
-         @ IPROC++
-         @ NSMPCPU++
-      end
-      set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
-   endif
-#
-#        we have now finished setting up a correct HOSTLIST.
-#        uncomment the next two if you are doing script debugging.
-#--echo "The generated host list is"
-#--echo $HOSTLIST
-#
-#
-#        choose remote shell execution program.
-#    Parallel run do initial launch of GAMESS on remote nodes by the
-#    following program.  Note that the authentication keys for ssh
-#    must have been set up correctly.
-#    If you wish, choose 'rsh' using .rhosts authentication on next line.
-   setenv DDI_RSH ssh
-#
-   if($DDI_RSH == ssh) then
-      setenv DDI_RCP scp
-   else
-      setenv DDI_RCP rcp
-   endif
-
-#        One way to be sure that the master node of each subgroup
-#        has its necessary copy of the input file is to stuff a
-#        copy of the input file onto every single node right here.
-   if ($GDDIjob == true) then
-      @ n=2   # master in master group already did 'cp' above
-      while ($n <= $NNODES)
-         set host=$HOSTLIST[$n]
-         set host=`echo $host | cut -f 1 -d :` # drop anything behind a colon
-         echo $DDI_RCP $SCR/$JOB.F05 ${host}:$SCR/$JOB.F05
-              $DDI_RCP $SCR/$JOB.F05 ${host}:$SCR/$JOB.F05
-         @ n++
-      end
-   endif
+###    if ($?PBS_JOBID) then
+####
+####         The IBM cluster has two Gigabit adapters in each 4-way SMP,
+####         while the AXP cluster is based on a Myrinet network.
+###      if (`uname` == AIX)   set NETEXT=".gig,.gig2"
+###      if (`uname` == Linux) set NETEXT=".myri"
+####
+####         repeated host names in the PBS host file indicate being assigned
+####         CPUs in the same SMP enclosure, which we must count up correctly.
+####         Fortunately PBS gives duplicate host names in a row, not scrambled.
+####         The number of hosts in the PBS node file (nmax) should equal the
+####         requested processor count, NCPUS.  We need to count duplicates
+####         in order to learn the number of SMP enclosures, NNODES, and how
+####         many CPUs inside each SMP were assigned (NSMPCPU).  For example,
+####         if we are assigned the host names "a a a b b c c c" we must build
+####         the string "a:cpus=3 b:cpus=2 c:cpus=3" so that ddikick.x will
+####         know the SMP structure of the assigned node names.  (C-shell handles
+####         variable substitution followed by colon gracefully by ${HOST}:cpus.)
+####
+###      set HOSTLIST=()
+###      set nmax=`wc -l $PBS_NODEFILE`
+###      set nmax=$nmax[1]
+###      if ($nmax != $NCPUS) then
+###         echo There is processor count confusion
+###         exit
+###      endif
+####            1st host in the list is sure to be a new SMP enclosure
+###      set MYNODE=`sed -n -e "1 p" $PBS_NODEFILE`
+###      set MYNODE=`echo $MYNODE | awk '{split($0,a,"."); print a[1]}'`
+####            IPROC counts assigned processors (up to NCPUS),
+####            NNODES counts number of SMP enclosures.
+####            NSMPCPU counts processors in the current SMP enclosure
+###      @ IPROC = 2
+###      @ NNODES = 1
+###      @ NSMPCPU = 1
+###      set spacer1=":cpus="
+###      set spacer2=":netext="
+###      while($IPROC <= $nmax)
+###         set MYPROC=`sed -n -e "$IPROC p" $PBS_NODEFILE`
+###         set MYPROC=`echo $MYPROC | awk '{split($0,a,"."); print a[1]}'`
+###         if($MYPROC != $MYNODE) then
+###            set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
+###            set MYNODE=$MYPROC
+###            @ NSMPCPU = 0
+###            @ NNODES++
+###         endif
+###         @ IPROC++
+###         @ NSMPCPU++
+###      end
+###      set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
+###   endif
+####
+####        we have now finished setting up a correct HOSTLIST.
+####        uncomment the next two if you are doing script debugging.
+####--echo "The generated host list is"
+####--echo $HOSTLIST
+####
+####
+####        choose remote shell execution program.
+####    Parallel run do initial launch of GAMESS on remote nodes by the
+####    following program.  Note that the authentication keys for ssh
+####    must have been set up correctly.
+####    If you wish, choose 'rsh' using .rhosts authentication on next line.
+###   setenv DDI_RSH ssh
+####
+###   if($DDI_RSH == ssh) then
+###      setenv DDI_RCP scp
+###   else
+###      setenv DDI_RCP rcp
+###   endif
+###
+####        One way to be sure that the master node of each subgroup
+####        has its necessary copy of the input file is to stuff a
+####        copy of the input file onto every single node right here.
+###   if ($GDDIjob == true) then
+###      @ n=2   # master in master group already did 'cp' above
+###      while ($n <= $NNODES)
+###         set host=$HOSTLIST[$n]
+###         set host=`echo $host | cut -f 1 -d :` # drop anything behind a colon
+###         echo $DDI_RCP $SCR/$JOB.F05 ${host}:$SCR/$JOB.F05
+###              $DDI_RCP $SCR/$JOB.F05 ${host}:$SCR/$JOB.F05
+###         @ n++
+###      end
+###   endif
 
 #
 #        Just make sure we have the binaries, before we try to run
@@ -455,9 +461,10 @@
 #
    if ($DDI_VER == new) then
       set echo
-      $GMSPATH/ddikick.x $GMSPATH/gamess.$VERNO.x $JOB \
-          -ddi $NNODES $NCPUS $HOSTLIST \
-          -scr $SCR < /dev/null
+###      $GMSPATH/ddikick.x $GMSPATH/gamess.$VERNO.x $JOB \
+###          -ddi $NNODES $NCPUS $HOSTLIST \
+###          -scr $SCR < /dev/null
+         $GMSPATH/ddikick.x dplace -s1 $GMSPATH/gamess.$VERNO.x $JOB -ddi $NNODES $NCPUS ${HOSTLIST} -scr $SCR < /dev/null
       unset echo
    else
       set path=($GMSPATH $path)
@@ -1051,13 +1058,13 @@
 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
 #

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/ccuv/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 "10.2.5.035\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 "sockets\r"
expect eof
EXPECT
#----------------------------------------------------------------------------
cd ${work}/${gamess}/ddi
sed -e 's/MAXCPUS  = 16/MAXCPUS  = 1024/' -e 's/MAXNODES = 256/MAXNODES = 2/' compddi > compddi1024
csh ./compddi1024 >& compddi.log
mv ddikick.x ../
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}