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_contrib/jmc_script/run_gnu.pbs,v 1.1 2012/10/25 21:17:10 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 , host="`hostname`

#- 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"

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

 module add gcc
if test $mpi = 0 ; then
 EXE="./mitgcmuv > std_outp"
else
 module add openmpi
 EXE="mpirun -v"
 if [ $mth -ge 1 ] ; then EXE="$EXE -x OMP_NUM_THREADS -x GOMP_STACKSIZE" ; fi
 #- select which MPI procs to use
 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 $PBS_NODEFILE | sort | uniq > mf
   EXE="$EXE -hostfile mf -npernode $npn ./mitgcmuv"
 else
   EXE="$EXE -np $mpi ./mitgcmuv"
 fi
fi

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

echo "" ; echo " run ended at: "`date`
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_contrib/jmc_script/run_gnu.pbs,v 1.1 2012/10/25 21:17:10 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 , host="`hostname`
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	if [ $mth -ge 1 ] ; then
44	export OMP_NUM_THREADS=$mth
45	export GOMP_STACKSIZE=400m
46	fi
47
48	module add gcc
49	if test $mpi = 0 ; then
50	EXE="./mitgcmuv > std_outp"
51	else
52	module add openmpi
53	EXE="mpirun -v"
54	if [ $mth -ge 1 ] ; then EXE="$EXE -x OMP_NUM_THREADS -x GOMP_STACKSIZE" ; fi
55	#- select which MPI procs to use
56	nn=`cat $PBS_NODEFILE \| sort \| uniq \| wc -l`
57	if [ $nn -gt 1 ] ; then dd=`expr $mpi % $nn` ; else dd=1 ; fi
58	if [ $dd -eq 0 ] ; then
59	npn=`expr $mpi / $nn`
60	echo " Nb of nodes=$nn , nb of process per node=$npn"
61	cat $PBS_NODEFILE \| sort \| uniq > mf
62	EXE="$EXE -hostfile mf -npernode $npn ./mitgcmuv"
63	else
64	EXE="$EXE -np $mpi ./mitgcmuv"
65	fi
66	fi
67
68	echo "list of loaded modules:"
69	module list 2>&1
70	echo " "
71	echo "run command: $EXE"
72	eval $EXE
73
74	echo "" ; echo " run ended at: "`date`