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 -fumask 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}