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--- strutture:cnaf:clusterhpc:using_the_cnaf_hpc_cluster [2021/02/16 14:17]
dcesini@infn.it [An MPI submission script]
+++ strutture:cnaf:clusterhpc:using_the_cnaf_hpc_cluster [2021/03/05 14:54]
dcesini@infn.it [Alternative MPI multinode submission]
@@ Line 126: / Line 126: @@
 </code>
-==== Submitting MPI Jobs ====
+==== Submitting MPI Jobs via mpirun.lsf (obsolete)====
 Currently only **OpenMPI** jobs have been tested on the HPC cluster. \\
@@ Line 193: / Line 193: @@
 ) Create automatically the machine file to be using in the mpirun:
-    echo $LSB_HOSTS | awk '{split($0,array," ")} END {for (i in array) printf ("%s\n",array[i])}' | awk '{count[$0]++} END {for (word in count) print word,"slots=" count[word]}' > /home/HPC/tandric/specfem3d/mymachine.txt
+    echo $LSB_HOSTS | awk '{split($0,array," ")} END {for (i in array) printf ("%s\n",array[i])}' | awk '{count[$0]++} END {for (word in count) print word,"slots=" count[word]}' > /home/HPC/username/mymachine.txt
 ) Use this command to launch mpirun:
-    mpirun --machinefile /home/HPC/tandric/specfem3d/machinefile.txt -x PSM_SHAREDCONTEXTS_MAX=8 -np $NPROC /home/HPC/tandric/specfem3d/bin/xspecfem3D
+    mpirun --machinefile /home/HPC/username/machinefile.txt -x PSM_SHAREDCONTEXTS_MAX=8 -np $LSB_DJOB_NUMPROC /home/HPC/username/executablename
-All together this became) Submit a script with:
+A possible bsub submission is:
-    bsub -q hpc_inf_SL7  -n 16 -R "span[ptile=8]" -o testmpimy.out -e testmpimy.err /home/HPC/tandric/specfem3d/run_this_example.sh
+    bsub -q hpc_inf_SL7  -n 16 -R "span[ptile=8]" -o testmpimy.out -e testmpimy.err /home/HPC/username/run_this_example.sh
-where in the run_this_example.sh script you have the previous commands. So in this case:
+where in the run_this_example.sh script you launch the previous commands:
 ----run_this_example.sh----
@@ Line 209: / Line 209: @@
     #!/bin/bash
-    echo $LSB_HOSTS | awk '{split($0,array," ")} END {for (i in array) printf ("%s\n",array[i])}' | awk '{count[$0]++} END {for (word in count) print word,"slots=" count[word]}' > /home/HPC/tandric/specfem3d/mymachine.txt
+    echo $LSB_HOSTS | awk '{split($0,array," ")} END {for (i in array) printf ("%s\n",array[i])}' | awk '{count[$0]++} END {for (word in count) print word,"slots=" count[word]}' > /home/HPC/username/mymachine.txt
-    mpirun --machinefile /home/HPC/tandric/specfem3d/machinefile.txt -x PSM_SHAREDCONTEXTS_MAX=8 -np $NPROC /home/HPC/tandric/specfem3d/bin/xspecfem3D
+    mpirun --machinefile /home/HPC/username/machinefile.txt -x PSM_SHAREDCONTEXTS_MAX=8 -np $LSB_DJOB_NUMPROC /home/HPC/username/executablename
 ==== Submitting GPU Jobs ====

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