Differences

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--- doku:lammps [2014/10/29 13:32] – sh
+++ doku:lammps [2014/11/04 09:36] – sh
@@ Line 200: / Line 200: @@
 </code>
-NOTE: for the fermi nodes use ''CUDA_ARCH = -arch=sm_20'', and for the kepler nodes use ''CUDA_ARCH = -arch=sm_35''
+NOTE: for the fermi nodes use ''CUDA_ARCH = -arch=sm_20'', and for the kepler nodes use ''CUDA_ARCH = -arch=sm_35''; so switching from building for 'fermi' to building for 'kepler' requires re-compilation of package ''gpu'', ie
+<code>
+      cd .../wherever/it/is/lammps-28Jun14/lib/gpu
+      cp Makefile.fermi Makefile.kepler
+      vi Makefile.kepler   ( set CUDA_ARCH = -arch=sm_35 )
+      make -f Makefile.kepler clean
+      make -f Makefile.kepler
+</code>
-NOTE2: To get information about packages that will be used
+NOTE_2: To get information about included packages
 <code>
 make package-status
@@ Line 214: / Line 221: @@
 === For example /opt/sw/lammps/examples/peptide/ on VSC-1 ===
-. Change into some temporary directory and prepare the submit script for SGE;
+. Change into some temporary directory and prepare the submit script for SGE.
+vi ./sge_lammps_peptide.scrpt
 <code>
 #$ -N lammps_peptide
@@ Line 228: / Line 237: @@
 mpirun -machinefile $TMPDIR/machines -np $NSLOTS /opt/sw/lammps/lmp_vsc1  -in  ./in.peptide
+</code>
+. Submit it and compare the results - log.lammps - to the reference log files in /opt/sw/lammps/examples/peptide.
+<code>
+qsub ./sge_lammps_peptide.scrpt
 </code>
+==== GPU fermi ====
+=== For example /opt/sw/lammps/examples/kokkos/ on VSC-1 ===
+. Change into some temporary directory and prepare the submit script for SGE (fermi queue). Two consecutive short test runs will employ 1 GPU and 2 GPUs per node.
+vi ./sge_lammps_fermi_kokkos.scrpt
+<code>
+#$ -N lammps_kokkos
+#$ -S /bin/bash
+#$ -cwd
+#$ -pe smp 12
+#$ -V
+#$ -q fermi
+#$ -P fermi
+export LD_LIBRARY_PATH=/opt/sw/openkim-api/1.6.3/lib/libkim-api-v1.so:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64:$LD_LIBRARY_PATH
+export I_MPI_FABRICS=shm:dapl
+# single GPU
+/opt/sw/lammps/lmp_fermi_vsc1 -k on t 6  -sf kk -in ./in.kokkos
+mv ./log.lammps ./log.lammps_fermi.1gpu.kokkos
+# 2 x GPU
+mpirun -np 2 /opt/sw/lammps/lmp_fermi_vsc1 -k on t 6 -sf kk -in ./in.kokkos
+mv ./log.lammps ./log.lammps_fermi.2gpu.kokkos
+</code>
+. Change into the fermi group and submit it to the appropriate queue.
+<code>
+sg fermi
+qsub.py ./sge_lammps_fermi_kokkos.scrpt
+</code>
+. Compare the results - ./log.lammps_fermi.[1,2]gpu.kokkos - to the reference log files in /opt/sw/lammps/examples/kokkos.