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Commit b2bde1a3 authored by Van Dung NGUYEN's avatar Van Dung NGUYEN
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Merge branch 'master' into vdg-cm3

parents 8eb16de6 e973116f
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1 merge request!171Vdg cm3
...@@ -9,6 +9,8 @@ ...@@ -9,6 +9,8 @@
#SBATCH --mem-per-cpu=800 #SBATCH --mem-per-cpu=800
#SBATCH --time=0:20:0 #SBATCH --time=0:20:0
module load GCCcore/5.4.0
module load ifort/2016.3.210-GCC-5.4.0-2.26
SUBDIR=$HOME/cm3Libraries/dG3D/benchmarks/taylorMPI SUBDIR=$HOME/cm3Libraries/dG3D/benchmarks/taylorMPI
echo "subdir=" $SUBDIR echo "subdir=" $SUBDIR
...@@ -29,7 +31,7 @@ cp -f $SUBDIR/$mshfile $SCRATCH/ || exit $? ...@@ -29,7 +31,7 @@ cp -f $SUBDIR/$mshfile $SCRATCH/ || exit $?
cd $SCRATCH # needed to work in the tmpscrach dir otherwise work on home !! cd $SCRATCH # needed to work in the tmpscrach dir otherwise work on home !!
#ls -artl #ls -artl
export PETSC_DIR=$HOME/local/petsc-3.4.3 export PETSC_DIR=$HOME/local/petsc-3.10.5
export PETSC_ARCH=linux-gnu-c-opt export PETSC_ARCH=linux-gnu-c-opt
export PATH=$HOME/local/bin:$PATH export PATH=$HOME/local/bin:$PATH
...@@ -37,9 +39,7 @@ export PATH=$PATH:$HOME/cm3Libraries/dG3D/release ...@@ -37,9 +39,7 @@ export PATH=$PATH:$HOME/cm3Libraries/dG3D/release
export PATH=$PATH:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh export PATH=$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:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers:$HOME/cm3Libraries/dG3D/release/NonLinearSolver/gmsh/utils/wrappers/gmshpy
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
mpirun python $SCRATCH/$pyfile > $SCRATCH/output.txt 2>&1 mpirun python $SCRATCH/$pyfile > $SCRATCH/output.txt 2>&1
......
...@@ -29,9 +29,9 @@ else: ...@@ -29,9 +29,9 @@ else:
else: else:
if tmpo not in lnodes: if tmpo not in lnodes:
lnodes.append(tmpo) lnodes.append(tmpo)
system("ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)) # nic3 system("ssh %s rm -r /workdir/lnoels/%d"%(tmpo,simnum)) # hercules
#system("ssh %s rm -r /scratch/gbecker_%d"%(tmpo,simnum)) # dragon #system("ssh %s rm -r /scratch/lnoels_%d"%(tmpo,simnum)) # dragon
#system("ssh %s rm -r /tmp/lnoels_%d"%(tmpo,simnum)) # vega #system("ssh %s rm -r /tmp/lnoels_%d"%(tmpo,simnum)) # vega
#print "ssh %s rm -r /tmpscratch/gbecker_%d"%(tmpo,simnum) #print "ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)
print "clear scratch OK" print "clear scratch OK"
...@@ -29,9 +29,9 @@ else: ...@@ -29,9 +29,9 @@ else:
else: else:
if tmpo not in lnodes: if tmpo not in lnodes:
lnodes.append(tmpo) lnodes.append(tmpo)
system("scp %s:/tmpscratch/lnoels_%d/* ."%(tmpo,simnum)) # nic3 system("scp %s:/workdir/lnoels/%d/* ."%(tmpo,simnum)) # hercules
#system("scp %s:/scratch/lnoels_%d/* ."%(tmpo,simnum)) # dragon #system("scp %s:/scratch/lnoels_%d/* ."%(tmpo,simnum)) # dragon
system("scp %s:/tmp/lnoels_%d/* ."%(tmpo,simnum)) # vega` #system("scp %s:/tmp/lnoels_%d/* ."%(tmpo,simnum)) # vega`
#print "ssh %s rm -r /tmpscratch/gbecker_%d"%(tmpo,simnum) #print "ssh %s rm -r /tmpscratch/lnoels_%d"%(tmpo,simnum)
print "copy scratch OK" print "copy scratch OK"
...@@ -261,16 +261,28 @@ Then wait until the job end (the last line of the created file "petsc-install.ou ...@@ -261,16 +261,28 @@ Then wait until the job end (the last line of the created file "petsc-install.ou
- hercules: - hercules:
function load_module() function load_module()
{ {
#module purge module load GCCcore/5.4.0
module load openmpi/1.4.5/gcc/4.7.2 module load ifort/2016.3.210-GCC-5.4.0-2.26
export LAPACKDIR=/usr/lib
export LAPACKLIB=lapack
export BLASDIR=/usr/lib
export BLASLIB=blas
export MPI_HOME=$OPENMPI
export MPI_INC=$OPENMPI_INC
module list module list
} }
in .bashrc:
export PATH=$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): - 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 alredy in your .bashrc
......
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