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scratch_output [2017/06/28 21:16]
root
scratch_output [2017/06/28 21:22]
root
Line 24: Line 24:
 module purge module purge
 module load intel/​14.0.3 mkl/14.0.3 fftw/3.3.6 impi/5.1.2 module load intel/​14.0.3 mkl/14.0.3 fftw/3.3.6 impi/5.1.2
 +
 +#copy files
 #run to scratch if output bigger than $OUTPUT_SIZE here 90MB #run to scratch if output bigger than $OUTPUT_SIZE here 90MB
 OUTPUT_SIZE=90000000 OUTPUT_SIZE=90000000
Line 39: Line 41:
 cd .. cd ..
 mkdir -p "/​${SCRATCH}/​${Zbas}"​ mkdir -p "/​${SCRATCH}/​${Zbas}"​
-rsync -av --exclude=outputs "​${Zbas}/"​ "/​${SCRATCH}/​${Zbas}"+rsync -av --exclude=outputs "./${Zbas}/"​ "/​${SCRATCH}/"​
 cd "/​${SCRATCH}/​${Zbas}/"​ cd "/​${SCRATCH}/​${Zbas}/"​
 +
 +#compute step
 sort -u $PBS_NODEFILE >​hostfile sort -u $PBS_NODEFILE >​hostfile
-mpirun -ppn 4 -hostfile hostfile -genv OMP_NUM_THREADS 4 -genv MKL_NUM_THREADS 4   ​/​share/​apps/​espresso/​qe-6.1-intel-mkl-impi/​bin/​pw.x -npools 1 <​ausurf.in >​ausurf.log+mpirun -ppn 4 -hostfile hostfile -genv OMP_NUM_THREADS 4 -genv MKL_NUM_THREADS 4 /​share/​apps/​espresso/​qe-6.1-intel-mkl-impi/​bin/​pw.x -npools 1 <​ausurf.in >​ausurf.log 
 + 
 +#copy files back 
 +#not rsync/​remove if cd failed and in original dir 
 cd .. cd ..
 Zpwd=`pwd` Zpwd=`pwd`
-#not copy or remove if cd didn't work 
 if [ "​${Zpwd}"​ -ne "​${Zdir}"​ ];then if [ "​${Zpwd}"​ -ne "​${Zdir}"​ ];then
 rsync -av --remove-source-files "​${Zbas}"​ "​${Zdir}/"​ rsync -av --remove-source-files "​${Zbas}"​ "​${Zdir}/"​
scratch_output.txt · Last modified: 2017/06/29 15:53 by root