Differences

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--- doku:lammps [2014/10/29 13:58] – sh
+++ doku:lammps [2014/11/04 09:46] (current) – sh
@@ Line 174: / Line 174: @@
 cp ./lmp_vsc1   /opt/sw/lammps/lmp_vsc1
 </code>
+NOTE: To get information about included packages
+<code>
+make package-status
+</code>
 ===== LAMMPS on GPUs ======
@@ Line 197: / Line 203: @@
 make clean-vsc1
 make vsc1
-cp ./lmp_vsc1   /opt/sw/lammps/lmp_fermi_vsc1
+cp ./lmp_vsc1   /opt/sw/lammps/lmp_fermi[kepler]_vsc1
 </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
-NOTE2: To get information about packages that will be used
 <code>
-make package-status
+      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
+      cd ../../src
+      ... continue with the above block to build lmp_vsc1
 </code>
@@ Line 242: / Line 254: @@
 === For example /opt/sw/lammps/examples/kokkos/ on VSC-1 ===
-. Change into some temporary directory and prepare the submit script for SGE (fermi queue) using 1 GPU or 2 GPUs per node.
+. 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
@@ Line 261: / Line 273: @@
 # single GPU
 /opt/sw/lammps/lmp_fermi_vsc1 -k on t 6  -sf kk -in ./in.kokkos
-mv ./log.lammps ./log.lammps_fermi.1_gpu.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.2_gpu.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.
+==== GPU kepler ====
+=== For example /opt/sw/lammps/examples/kokkos/ on VSC-1 ===
+. Change into some temporary directory and prepare the submit script for SGE (kepler queue). The test is analogous to the one for fermi, hence two consecutive short runs employing 1 GPU or 2 GPUs per node.
+vi ./sge_lammps_kepler_kokkos.scrpt
+<code>
+#$ -N lammps_kokkos
+#$ -S /bin/bash
+#$ -cwd
+#$ -pe smp 12
+#$ -V
+#$ -q kepler
+#$ -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_kepler_vsc1 -k on t 6  -sf kk -in ./in.kokkos
+mv ./log.lammps ./log.lammps_kepler.1gpu.kokkos
+# 2 x GPU
+mpirun -np 2 /opt/sw/lammps/lmp_kepler_vsc1 -k on t 6 -sf kk -in ./in.kokkos
+mv ./log.lammps ./log.lammps_kepler.2gpu.kokkos
+</code>
+. Change into the fermi group and submit it to the appropriate --- kepler --- queue.
+<code>
+sg fermi
+qsub.py ./sge_lammps_kepler_kokkos.scrpt
 </code>
+. Compare the results - ./log.lammps_kepler.[1,2]gpu.kokkos - to the reference log files in /opt/sw/lammps/examples/kokkos.