MITgcm_contrib/jmc_script/run_gnu.pbs

#!/bin/bash
#
#PBS -q four-twelve
#PBS -N run_gnu_1
#PBS -l nodes=1:ppn=12
#PBS -e run_gnu.stderr
#PBS -o run_gnu.stdout

#- batch parameters are specified above (lines starting with #PBS); note that after 1rst
#        blank line (above), anything folowing "#" character is treated as comments
#
# example of a PBS batch script to run MITgcm on new (x86_64) acesgrid cluster
#         using executable compiled with gfortran (and OpenMPI if using MPI)
#         and running on /data/ disk(/net/eaps-80-11/data/)

# $Header: /u/gcmpack/MITgcm/tools/example_scripts/ACESgrid/test_aces_gnu_mpi,v 1.10 2012/08/26 18:07:38 jmc Exp $
# $Name:  $

sfx=1    # directory suffix
mpi=0    # number of MPI procs (=0 for non MPI run)
mth=0    # number of OMP threads (=0 for non Multi-thread run)

if test -f /etc/profile.d/modules.sh ; then
    . /etc/profile.d/modules.sh
fi

HERE=`pwd`
echo "start from HERE='$HERE' at: "`date`
echo " sfx=$sfx , mpi=$mpi , mth=$mth"

#- dir where to run mitgcmuv (batch job starts in home dir; need to "cd" to run dir):
runD="/net/eaps-80-11/data/jm_c/exp/atm_gray/run_$sfx"
echo -n " run in runD='$runD' on nodes: "
cat $PBS_NODEFILE | sort | uniq
cd $runD
echo " sfx=$sfx , mpi=$mpi , mth=$mth" > mf_run
cat $PBS_NODEFILE >> mf_run

umask 0022
#- to get case insensitive "ls" (and order of tested experiments)
export LC_ALL="en_US.UTF-8"

 module add gcc
if test $mpi = 0 ; then
 EXE="./mitgcmuv > std_outp"
else
 module add openmpi
 nn=`cat $PBS_NODEFILE | sort | uniq | wc -l`
 if [ $nn -gt 1 ] ; then dd=`expr $mpi % $nn` ; else dd=1 ; fi
 if [ $dd -eq 0 ] ; then
   npn=`expr $mpi / $nn`
   echo " Nb of nodes=$nn , nb of process per node=$npn"
   cat $PBS_NODEFILE | sort | uniq > mf
   EXE="mpirun -v -hostfile mf -npernode $npn ./mitgcmuv"
 else
   EXE="mpirun -v -np $mpi ./mitgcmuv"
 fi
fi

if [ $mth -ge 1 ] ; then
 export OMP_NUM_THREADS=$mth
 export GOMP_STACKSIZE=400m
fi

echo "list of loaded modules:"
module list 2>&1
echo " "
echo "run command: $EXE"
eval $EXE

echo "" ; echo " run ended at: "`date`
1	jmc	1.1	#!/bin/bash
2			#
3			#PBS -q four-twelve
4			#PBS -N run_gnu_1
5			#PBS -l nodes=1:ppn=12
6			#PBS -e run_gnu.stderr
7			#PBS -o run_gnu.stdout
8
9			#- batch parameters are specified above (lines starting with #PBS); note that after 1rst
10			# blank line (above), anything folowing "#" character is treated as comments
11			#
12			# example of a PBS batch script to run MITgcm on new (x86_64) acesgrid cluster
13			# using executable compiled with gfortran (and OpenMPI if using MPI)
14			# and running on /data/ disk(/net/eaps-80-11/data/)
15
16			# $Header: /u/gcmpack/MITgcm/tools/example_scripts/ACESgrid/test_aces_gnu_mpi,v 1.10 2012/08/26 18:07:38 jmc Exp $
17			# $Name: $
18
19			sfx=1 # directory suffix
20			mpi=0 # number of MPI procs (=0 for non MPI run)
21			mth=0 # number of OMP threads (=0 for non Multi-thread run)
22
23			if test -f /etc/profile.d/modules.sh ; then
24			. /etc/profile.d/modules.sh
25			fi
26
27			HERE=`pwd`
28			echo "start from HERE='$HERE' at: "`date`
29			echo " sfx=$sfx , mpi=$mpi , mth=$mth"
30
31			#- dir where to run mitgcmuv (batch job starts in home dir; need to "cd" to run dir):
32			runD="/net/eaps-80-11/data/jm_c/exp/atm_gray/run_$sfx"
33			echo -n " run in runD='$runD' on nodes: "
34			cat $PBS_NODEFILE \| sort \| uniq
35			cd $runD
36			echo " sfx=$sfx , mpi=$mpi , mth=$mth" > mf_run
37			cat $PBS_NODEFILE >> mf_run
38
39			umask 0022
40			#- to get case insensitive "ls" (and order of tested experiments)
41			export LC_ALL="en_US.UTF-8"
42
43			module add gcc
44			if test $mpi = 0 ; then
45			EXE="./mitgcmuv > std_outp"
46			else
47			module add openmpi
48			nn=`cat $PBS_NODEFILE \| sort \| uniq \| wc -l`
49			if [ $nn -gt 1 ] ; then dd=`expr $mpi % $nn` ; else dd=1 ; fi
50			if [ $dd -eq 0 ] ; then
51			npn=`expr $mpi / $nn`
52			echo " Nb of nodes=$nn , nb of process per node=$npn"
53			cat $PBS_NODEFILE \| sort \| uniq > mf
54			EXE="mpirun -v -hostfile mf -npernode $npn ./mitgcmuv"
55			else
56			EXE="mpirun -v -np $mpi ./mitgcmuv"
57			fi
58			fi
59
60			if [ $mth -ge 1 ] ; then
61			export OMP_NUM_THREADS=$mth
62			export GOMP_STACKSIZE=400m
63			fi
64
65			echo "list of loaded modules:"
66			module list 2>&1
67			echo " "
68			echo "run command: $EXE"
69			eval $EXE
70
71			echo "" ; echo " run ended at: "`date`