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updated pbs script for gcc
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glessin committed May 17, 2021
1 parent dc1c334 commit d7d2258
Showing 1 changed file with 23 additions and 48 deletions.
Original file line number Diff line number Diff line change
@@ -1,15 +1,16 @@
#!/bin/bash
#SBATCH --job-name=AMM7_ERSEM_test
#SBATCH --time=00:20:00
#SBATCH --nodes=2
##SBATCH --nodes=1
#SBATCH --ntasks=124
##SBATCH --ntasks=2
#SBATCH --account=n01
##SBATCH --time=00:20:00
#SBATCH --time=00:45:00
##SBATCH --nodes=2
#SBATCH --nodes=12
#SBATCH --ntasks=1224
##SBATCH --ntasks=100
#SBATCH --account=n01-PML
#SBATCH --partition=standard
#SBATCH --qos=standard
##BATCH --reservation=shortqos
##BATCH --qos=short
##SBATCH --reservation=shortqos
##SBATCH --qos=short

# NOTE:
# the simulation year and month must be passed to this slurm script at runtime
@@ -18,40 +19,21 @@
# "sbatch MYH2020slurm.sh 1981 1"
#

module -s restore /work/n01/shared/acc/n01_modules/ucx_env
export OMP_NUM_THREADS=1

#cat > myscript_wrapper.sh << EOFB
##!/bin/ksh
##
#set -A map ./xios_server.exe ./nemo.exe
#exec_map=( 0 1 )
##
#exec \${map[\${exec_map[\$SLURM_PROCID]}]}
###
#EOFB
#chmod u+x ./myscript_wrapper.sh

#
cat > myscript_wrapper2.sh << EOFB
#!/bin/ksh
#
set -A map ./xios_server.exe ./nemo.exe
exec_map=( 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 )
#
exec \${map[\${exec_map[\$SLURM_PROCID]}]}
##
EOFB
chmod u+x ./myscript_wrapper2.sh
#
#export OMP_NUM_THREADS=1

module restore /etc/cray-pe.d/PrgEnv-gnu
module load cray-hdf5-parallel
module load cray-netcdf-hdf5parallel
module unload craype-network-ofi
module unload cray-mpich
module load craype-network-ucx
module load cray-mpich-ucx
module load libfabric
module load gcc
module swap gcc/10.1.0 gcc/9.3.0

set -u

#NNODES=64
#NNODES=7
#NCORES=$(( NNODES*24 ))

#number of month to launch:
nmmax=31

@@ -185,17 +167,9 @@ do
exit
fi

# echo "Launching $y0 $m0 at $(date +%s) seconds since 1970-01-01 00:00:00 on $NCORES cores"

# aprun -b -n 1 -N 1 -S 1 ./xios_server.exe : -n $NCORES -N 24 ./nemo.exe
# aprun -n 192 -N 24 ./nemo.exe

#srun --mem-bind=local \
# --cpu-bind=v,mask_cpu:0x1,0x2 ./myscript_wrapper.sh

srun --mem-bind=local --cpu-bind=v,map_cpu:00,0x4,0x8,0xa,0xc,0xe,0x10,0x12,0x14,0x16,0x18,0x1a,0x1c,0x1e,0x20,0x22,0x24,0x26,0x28,0x2a,0x2c,0x2e,0x30,0x32,0x34,0x36,0x38,0x3a,0x3c,0x3e,0x40,0x42,0x44,0x46,0x48,0x4a,0x4c,0x4e,0x50,0x52,0x54,0x56,0x58,0x5a,0x5c,0x5e,0x60,0x62,0x64,0x66,0x68,0x6a,0x6c,0x6e,0x70,0x72,0x74,0x76,0x78,0x7a,0x7c,0x7e,00,0x4,0x8,0xa,0xc,0xe,0x10,0x12,0x14,0x16,0x18,0x1a,0x1c,0x1e,0x20,0x22,0x24,0x26,0x28,0x2a,0x2c,0x2e,0x30,0x32,0x34,0x36,0x38,0x3a,0x3c,0x3e,0x40,0x42,0x44,0x46,0x48,0x4a,0x4c,0x4e,0x50,0x52,0x54,0x56,0x58,0x5a,0x5c,0x5e,0x60,0x62,0x64,0x66,0x68,0x6a,0x6c,0x6e,0x70,0x72,0x74,0x76,0x78,0x7a,0x7c,0x7e, ./myscript_wrapper2.sh
echo "Launching $y0 $m0 at $(date +%s) seconds since 1970-01-01 00:00:00"

# srun --mem-bind=local --cpu-bind=v,map_cpu:00,0x10,0x20,0x22,0x24,0x26,0x28,0x2a,0x2c,0x2e,0x30,0x32,0x34,0x36,0x38,0x3a,0x3c,0x3e,0x40,0x42,0x44,0x46,0x48,0x4a,0x4c,0x4e,0x50,0x52,0x54,0x56,0x58,0x5a,0x5c,0x5e,0x60,0x62,0x64,0x66,0x68,0x6a,0x6c,0x6e,0x70,0x72,0x74,0x76,0x78,0x7a,0x7c,0x7e,00,0x10,0x20,0x22,0x24,0x26,0x28,0x2a,0x2c,0x2e,0x30,0x32,0x34,0x36,0x38,0x3a,0x3c,0x3e,0x40,0x42,0x44,0x46,0x48,0x4a,0x4c,0x4e,0x50,0x52,0x54,0x56,0x58,0x5a,0x5c,0x5e,0x60,0x62,0x64,0x66,0x68,0x6a,0x6c,0x6e,0x70,0x72,0x74,0x76,0x78,0x7a,0x7c,0x7e, ./myscript_wrapper2.sh
./amm7standard.slurm

echo "Finished $y0 $m0 at $(date +%s) seconds since 1970-01-01 00:00:00"

@@ -218,6 +192,7 @@ do
mv amm7_1m_${d0}_[1-2]???????_ptrc_T.nc $ARCHIVEDIR
mv amm7_1m_${d0}_[1-2]???????_grid_?.nc $ARCHIVEDIR
bzip2 ocean.output && mv -f ocean.output.bz2 $ARCHIVEDIR
#mv timing.output $ARCHIVEDIR
mv -f time.step $ARCHIVEDIR

#archive:

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