Merge branch 'master' into vdg-cm3

NonLinearSolver/clusterScript/herculestaylor.sh

@@ -9,6 +9,8 @@
 #SBATCH --mem-per-cpu=800
 #SBATCH --time=0:20:0
 
+module load GCCcore/5.4.0
+module load ifort/2016.3.210-GCC-5.4.0-2.26
 SUBDIR=$HOME/cm3Libraries/dG3D/benchmarks/taylorMPI
 echo "subdir=" $SUBDIR
 
@@ -29,7 +31,7 @@ cp -f $SUBDIR/$mshfile $SCRATCH/ || exit $?
 cd $SCRATCH # needed to work in the tmpscrach dir otherwise work on home !!
 #ls -artl
 
-export PETSC_DIR=$HOME/local/petsc-3.4.3
+export PETSC_DIR=$HOME/local/petsc-3.10.5
 export PETSC_ARCH=linux-gnu-c-opt
 
 export PATH=$HOME/local/bin:$PATH
@@ -37,9 +39,7 @@ export PATH=$PATH:$HOME/cm3Libraries/dG3D/release
 export PATH=$PATH:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh
 
 
-export PYTHONPATH=$PYTHONPATH:$HOME/cm3Libraries/dG3D/release:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/wrappers
-export PYTHONPATH=$PYTHONPATH:$HOME/cm3Libraries/dG3D/release:$HOME/cm3Libraries/dG3D/debug:$HOME/cm3Libraries/dG3D/debug/NonLinearSolver/gmsh/utils/wrappers:$HOME/cm3Libraries/dG3D/debug/NonLinearSolver/gmsh/utils/wrappers/gmshpy:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers/gmshpy
-
+export PYTHONPATH=$PYTHONPATH:$HOME/cm3Libraries/dG3D/release:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers/gmshpy
 
 mpirun python  $SCRATCH/$pyfile > $SCRATCH/output.txt 2>&1
 

NonLinearSolver/clusterScript/scratchclear.py

@@ -29,9 +29,9 @@ else:
         else:
             if tmpo not in lnodes:
                 lnodes.append(tmpo)
-	        system("ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)) # nic3
-		#system("ssh %s rm -r /scratch/gbecker_%d"%(tmpo,simnum)) # dragon
+	        system("ssh %s rm -r /workdir/lnoels/%d"%(tmpo,simnum)) # hercules
+		#system("ssh %s rm -r /scratch/lnoels_%d"%(tmpo,simnum)) # dragon
                 #system("ssh %s rm -r /tmp/lnoels_%d"%(tmpo,simnum)) # vega
-	        #print "ssh %s rm -r /tmpscratch/gbecker_%d"%(tmpo,simnum)
+	        #print "ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)
 
     print "clear scratch OK"

NonLinearSolver/clusterScript/scratchcopy.py

@@ -29,9 +29,9 @@ else:
         else:
             if tmpo not in lnodes:
                 lnodes.append(tmpo)
-	        system("scp %s:/tmpscratch/lnoels_%d/* ."%(tmpo,simnum)) # nic3
+	        system("scp %s:/workdir/lnoels/%d/* ."%(tmpo,simnum)) # hercules
 		#system("scp %s:/scratch/lnoels_%d/* ."%(tmpo,simnum)) # dragon
-                system("scp %s:/tmp/lnoels_%d/* ."%(tmpo,simnum)) # vega`
-	        #print "ssh %s rm -r /tmpscratch/gbecker_%d"%(tmpo,simnum)
+                #system("scp %s:/tmp/lnoels_%d/* ."%(tmpo,simnum)) # vega`
+	        #print "ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)
 
     print "copy scratch OK"

cm3apps/install.txt

@@ -261,16 +261,28 @@ Then wait until the job end (the last line of the created file "petsc-install.ou
 	- hercules:
 	function load_module()
 	{
-	        #module purge
-	        module load openmpi/1.4.5/gcc/4.7.2
-		export LAPACKDIR=/usr/lib
-        	export LAPACKLIB=lapack
-        	export BLASDIR=/usr/lib
-        	export BLASLIB=blas
-		export MPI_HOME=$OPENMPI
-		export MPI_INC=$OPENMPI_INC
+                module load GCCcore/5.4.0
+                module load ifort/2016.3.210-GCC-5.4.0-2.26
 	        module list
 	}
+        in .bashrc:
+	export PATH=$HOME/local/cvs/bin:$HOME/local/cmake/bin:$HOME/local/swig/bin:$PATH
+	export PETSC_DIR=$HOME/local/petsc-3.10.5
+	export PETSC_ARCH=linux-gnu-c-opt
+	export SLEPC_DIR=$HOME/local/slepc-3.10.2
+	export SLEPC_ARCH=linux-gnu-c-opt
+	export LD_LIBRARY_PATH=$PETSC_DIR/$PETSC_ARCH/lib:$LD_LIBRARY_PATH
+	export PATH=$PETSC_DIR/$PETSC_ARCH/bin:$PATH
+	export MPI_HOME=$PETSC_DIR/$PETSC_ARCH/
+	export MPI_RUN=$MPI_HOME/bin/mpirun
+
+	export PATH=$PATH:$HOME/cm3Libraries/cm3apps/release/NonLinearSolver/gmsh
+	export PATH=$PATH:$HOME/cm3Libraries/dG3D/debug/NonLinearSolver/gmsh
+	export PATH=$PATH:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh
+	export PYTHONPATH=$PYTHONPATH:$HOME/cm3Libraries/dG3D/release:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers/gmshpy
+
+
+
 
         - vega: (this cluster load common module in the user .bashrc so I do not define a function but I add the module directly in the .bashrc):
 alredy in your .bashrc