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CNMS
CNMS_Computing_Resources
Commits
c5cfded1
Commit
c5cfded1
authored
Feb 01, 2018
by
Doak, Peter W
Browse files
example of explicit binding to cpu's
parent
380cc15b
Changes
1
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CADES/ARB_CODE/many_small_mpiruns.sh
0 → 100644
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c5cfded1
#!/bin/bash
##PBS -S /bin/bash
#PBS -m be
#PBS -N h2so4
#PBS -q cnms14q
#PBS -l nodes=2:ppn=32
#PBS -l walltime=24:00:00
source
/opt/modules/3.1.6/init/bash
#cd $GLOBAL_SCRATCH
cd
$PBS_O_WORKDIR
export
MODULEPATH
=
$MODULEPATH
:/projects/cnms/modules
module load whatever
export
OMP_NUM_THREADS
=
1
cd
$PBS_O_WORKDIR
#this can be useful to see from outside shells
cat
$PBS_NODEFILE
>
pbs_nodefile
cores_per_node
=
32
wcr
=(
$(
wc
pbs_nodefile
)
)
count
=
${
wcr
[0]
}
awk
-v
count
=
$count
-v
cpn
=
$cores_per_node
'BEGIN { a= 0; r=0; cores=count/2; prev_node="" }; { if (a < cpn) { print "rank " r "=" $1 " slot=" a; r = r + 1; a = a + 2; prev_node=$1 } else { if (r < cores && prev_node != $1 ) {a = 0; print "rank " r "=" $1 " slot=" a ; r = r + 1; a = a + 2} }}'
pbs_nodefile
>
rankfile
#VASP runs including significant communication especially for SCALAPACK run
#slower than they should. Refrain from using more than ~1 cpu per atom
#past 64 or 128 cores LSCALAPACK=.FALSE.
mpirun
-n
$((
count
/
2
))
-v
--report-bindings
-rf
rankfile
${
VASP_MPI_FLAGS
}
$VASP
2>&1
>
vasp_out
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