Commit 7639b04d authored by Cedric Jourdain's avatar Cedric Jourdain
Browse files

Merge branch 'r2.1-dev' of https://repository.prace-ri.eu/git/UEABS/ueabs into r2.1-dev

parents b0a057ea 19c41863
#!/bin/bash
#SBATCH -N 4
#SBATCH --tasks-per-node=64
#SBATCH --partition=knl
#SBATCH --cpus-per-task=1
#SBATCH --time=2:00:00
exe=$HOME/q-e-qe-6.3/bin/pw.x
export OMP_NUM_THREADS=1
module load intel parastation
module load extoll
numactl -H
srun $exe -npool 2 -ndiag 32 -input ausurf.in > ausurf-4-snc4.out
#!/bin/bash
#SBATCH -N1
#SBATCH --job-name=ausurf-1
#SBATCH --tasks-per-node=48
##SBATCH --cpus-per-task=1
#SBATCH --time=1:00:00
#SBATCH --output=trace-1.out
export OMP_NUM_THREADS=1
QE_HOME=$HOME/q-e-qe-6.3
start_time=$(date +"%s")
srun $QE_HOME/bin/pw.x -npool 2 -ndiag 16 -input ausurf.in
end_time=$(date +"%s")
walltime=$(($end_time-$start_time))
echo "walltime $walltime"
#!/bin/bash
#SBATCH -N1
#SBATCH --job-name=ausurf-1
#SBATCH --tasks-per-node=10
##SBATCH --cpus-per-task=1
#SBATCH --time=30:00
export OMP_NUM_THREADS=1
QE_HOME=$HOME/q-e-qe-6.3
start_time=$(date +"%s")
${EXTRAE_HOME}/bin/mpi2prv -f TRACE.mpits -e $QE_HOME/bin/pw.x -o trace.prv
end_time=$(date +"%s")
walltime=$(($end_time-$start_time))
echo "walltime $walltime"
#!/bin/bash
#SBATCH -N1
#SBATCH --job-name=ausurf-1
#SBATCH --tasks-per-node=48
##SBATCH --cpus-per-task=1
#SBATCH --time=1:00:00
#SBATCH --output=trace-1.out
export OMP_NUM_THREADS=1
QE_HOME=$HOME/q-e-qe-6.3
module load gcc/7.2.0
module load extrae
start_time=$(date +"%s")
srun ./trace.sh $QE_HOME/bin/pw.x -npool 2 -ndiag 16 -input ausurf.in
end_time=$(date +"%s")
walltime=$(($end_time-$start_time))
echo "walltime $walltime"
#!/bin/bash
export EXTRAE_HOME=/apps/BSCTOOLS/extrae/3.6.1/impi_2017_4
export EXTRAE_CONFIG_FILE=extrae.xml
export LD_PRELOAD=${EXTRAE_HOME}/lib/libmpitrace.so
## Run the desired program
$*
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&CONTROL
calculation = 'scf' ,
restart_mode = 'from_scratch' ,
outdir = './save/' ,
pseudo_dir = './',
prefix = 'ta2o5' ,
!disk_io = 'default' ,
!verbosity = 'high' ,
!forc_conv_thr = 1.0D-3
/
&SYSTEM
ibrav = 8,
celldm(1) = 26.9474,
celldm(2) = 0.8457223,
celldm(3) = 1.1,
nosym = .true.
nat = 96,
ntyp = 2,
ecutwfc = 130 ,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
/
&ELECTRONS
conv_thr = 1.0d-8 ,
mixing_beta=0.5D0,
maxiter=200
/
ATOMIC_SPECIES
Ta 180.95 Ta.pbe-mt_fhi.UPF
O 15.999 O.pbe-mt_fhi.UPF
ATOMIC_POSITIONS {bohr}
Ta 0.000000000 11.395009900 0.000000000
Ta 3.368425000 16.591131527 0.000000000
Ta 10.105275001 17.536917899 0.000000000
Ta 6.736849999 11.395009900 0.000000000
Ta 3.368425000 5.196124321 0.000000000
Ta 0.000000000 0.000000000 0.000000000
Ta 6.736849999 0.000000000 0.000000000
Ta 10.105275001 6.141910692 0.000000000
Ta 13.473700000 11.395009900 0.000000000
Ta 16.842125000 16.591131527 0.000000000
Ta 20.210549999 11.395009900 0.000000000
Ta 16.842125000 5.196124321 0.000000000
Ta 13.473700000 0.000000000 0.000000000
Ta 20.210549999 0.000000000 0.000000000
Ta 23.578975001 6.141910692 0.000000000
Ta 23.578975001 17.536917899 0.000000000
Ta 6.736849999 0.000000000 7.218723406
Ta 13.473700000 0.000000000 7.218723406
Ta 20.210549999 0.000000000 7.218723406
Ta 26.947400000 0.000000000 7.218723406
Ta 3.368425000 5.196124321 7.218723406
Ta 0.000000000 11.395009900 7.218723406
Ta 6.736849999 11.395009900 7.218723406
Ta 10.105275001 6.141910692 7.218723406
Ta 16.842125000 5.196124321 7.218723406
Ta 13.473700000 11.395009900 7.218723406
Ta 20.210549999 11.395009900 7.218723406
Ta 23.578975001 6.141910692 7.218723406
Ta 23.578975001 17.536917899 7.218723406
Ta 16.842125000 16.591131527 7.218723406
Ta 10.105275001 17.536917899 7.218723406
Ta 3.368425000 16.591131527 7.218723406
O 0.000000000 11.292453485 3.609364398
O 0.794948301 7.737210245 0.000000000
O 3.381898699 1.333217226 0.000000000
O 3.368425000 4.888457771 3.609364398
O 5.982322799 7.737210245 0.000000000
O 7.599166801 3.509661712 0.000000000
O 10.105275001 6.335624772 3.609364398
O 12.651804300 3.509661712 0.000000000
O 16.855598699 1.333217226 0.000000000
O 16.842125000 4.888457771 3.609364398
O 21.072866801 3.509661712 0.000000000
O 23.578975001 6.335624772 3.609364398
O 26.125504300 3.509661712 0.000000000
O 19.456022800 7.737210245 0.000000000
O 23.592448701 9.936446845 0.000000000
O 20.210549999 11.292453485 3.609364398
O 14.268648299 7.737210245 0.000000000
O 13.473700000 11.292453485 3.609364398
O 10.118748700 9.936446845 0.000000000
O 6.736849999 11.292453485 3.609364398
O 3.381898699 12.728224432 0.000000000
O 7.599166801 14.904671615 0.000000000
O 12.651804300 14.904671615 0.000000000
O 16.855598699 12.728224432 0.000000000
O 21.072866801 14.904671615 0.000000000
O 26.125504300 14.904671615 0.000000000
O 23.578975001 17.730631978 3.609364398
O 23.592448701 21.331456745 0.000000000
O 19.456022800 19.132220148 0.000000000
O 16.842125000 16.283467671 3.609364398
O 14.268648299 19.132220148 0.000000000
O 10.105275001 17.730631978 3.609364398
O 10.118748700 21.331456745 0.000000000
O 5.982322799 19.132220148 0.000000000
O 3.368425000 16.283467671 3.609364398
O 0.794948301 19.132220148 0.000000000
O 0.000000000 22.687460693 3.609364398
O 6.736849999 22.687460693 3.609364398
O 13.473700000 22.687460693 3.609364398
O 20.210549999 22.687460693 3.609364398
O 3.381898699 1.333217226 7.218723406
O 7.599166801 3.509661712 7.218723406
O 12.651804300 3.509661712 7.218723406
O 16.855598699 1.333217226 7.218723406
O 21.072866801 3.509661712 7.218723406
O 26.125504300 3.509661712 7.218723406
O 19.456022800 7.737210245 7.218723406
O 14.268648299 7.737210245 7.218723406
O 10.118748700 9.936446845 7.218723406
O 5.982322799 7.737210245 7.218723406
O 0.794948301 7.737210245 7.218723406
O 3.381898699 12.728224432 7.218723406
O 7.599166801 14.904671615 7.218723406
O 12.651804300 14.904671615 7.218723406
O 16.855598699 12.728224432 7.218723406
O 21.072866801 14.904671615 7.218723406
O 23.592448701 9.936446845 7.218723406
O 26.125504300 14.904671615 7.218723406
O 23.592448701 21.331456745 7.218723406
O 19.456022800 19.132220148 7.218723406
O 14.268648299 19.132220148 7.218723406
O 10.118748700 21.331456745 7.218723406
O 5.982322799 19.132220148 7.218723406
O 0.794948301 19.132220148 7.218723406
K_POINTS automatic
5 5 2 0 0 0
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&CONTROL
title = ' DEISA pw benchmark ',
calculation = 'scf',
restart_mode = 'from_scratch', ! 'restart',
tprnfor = .TRUE.,
etot_conv_thr = 1.d-8,
prefix = 'ausurf'
pseudo_dir = './'
outdir = './out/'
/
&SYSTEM
ibrav = 8,
celldm(1) = 38.7583,
celldm(2) = 0.494393,
celldm(3) = 1.569966,
nat = 112,
ntyp = 1,
nbnd = 800,
ecutwfc = 25.0,
ecutrho = 200.0,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
/
&ELECTRONS
diagonalization='david'
mixing_beta = 0.7
/
&IONS
ion_dynamics = 'none',
/
&CELL
cell_dynamics = 'none',
/
ATOMIC_SPECIES
AU 196.96 Au.pbe-nd-van.UPF
K_POINTS (automatic)
2 2 1 1 1 0
ATOMIC_POSITIONS (angstrom)
AU 29.285000 40.578999 7.173000
AU 29.285000 35.511002 7.173000
AU 32.214001 40.578999 7.173000
AU 32.214001 35.511002 7.173000
AU 35.141998 40.578999 7.173000
AU 35.141998 35.511002 7.173000
AU 38.070999 40.578999 7.173000
AU 38.070999 35.511002 7.173000
AU 40.999001 40.578999 7.173000
AU 40.999001 35.511002 7.173000
AU 43.928001 40.578999 7.173000
AU 43.928001 35.511002 7.173000
AU 46.855999 40.578999 7.173000
AU 46.855999 35.511002 7.173000
AU 29.285000 42.270000 4.782000
AU 29.285000 37.202000 4.782000
AU 32.214001 42.270000 4.782000
AU 32.214001 37.202000 4.782000
AU 35.141998 42.270000 4.782000
AU 35.141998 37.202000 4.782000
AU 38.070999 42.270000 4.782000
AU 38.070999 37.202000 4.782000
AU 40.999001 42.270000 4.782000
AU 40.999001 37.202000 4.782000
AU 43.928001 42.270000 4.782000
AU 43.928001 37.202000 4.782000
AU 46.855999 42.270000 4.782000
AU 46.855999 37.202000 4.782000
AU 30.749001 43.115002 7.173000
AU 30.749001 38.047001 7.173000
AU 33.678001 43.115002 7.173000
AU 33.678001 38.047001 7.173000
AU 36.605999 43.115002 7.173000
AU 36.605999 38.047001 7.173000
AU 39.535000 43.115002 7.173000
AU 39.535000 38.047001 7.173000
AU 42.464001 43.115002 7.173000
AU 42.464001 38.047001 7.173000
AU 45.391998 43.115002 7.173000
AU 45.391998 38.047001 7.173000
AU 48.320999 43.115002 7.173000
AU 48.320999 38.047001 7.173000
AU 30.749001 34.666000 4.782000
AU 30.749001 39.737999 4.782000
AU 33.678001 34.666000 4.782000
AU 33.678001 39.737999 4.782000
AU 36.605999 34.666000 4.782000
AU 36.605999 39.737999 4.782000
AU 39.535000 34.666000 4.782000
AU 39.535000 39.737999 4.782000
AU 42.464001 34.666000 4.782000
AU 42.464001 39.737999 4.782000
AU 45.391998 34.666000 4.782000
AU 45.391998 39.737999 4.782000
AU 48.320999 34.666000 4.782000
AU 48.320999 39.737999 4.782000
AU 29.285000 40.578999 0.000000
AU 29.285000 35.511002 0.000000
AU 32.214001 40.578999 0.000000
AU 32.214001 35.511002 0.000000
AU 35.141998 40.578999 0.000000
AU 35.141998 35.511002 0.000000
AU 38.070999 40.578999 0.000000
AU 38.070999 35.511002 0.000000
AU 40.999001 40.578999 0.000000
AU 40.999001 35.511002 0.000000
AU 43.928001 40.578999 0.000000
AU 43.928001 35.511002 0.000000
AU 46.855999 40.578999 0.000000
AU 46.855999 35.511002 0.000000
AU 30.749001 41.424000 2.391000
AU 30.749001 36.355999 2.391000
AU 33.678001 41.424000 2.391000
AU 33.678001 36.355999 2.391000
AU 36.605999 41.424000 2.391000
AU 36.605999 36.355999 2.391000
AU 39.535000 41.424000 2.391000
AU 39.535000 36.355999 2.391000
AU 42.464001 41.424000 2.391000
AU 42.464001 36.355999 2.391000
AU 45.391998 41.424000 2.391000
AU 45.391998 36.355999 2.391000
AU 48.320999 41.424000 2.391000
AU 48.320999 36.355999 2.391000
AU 29.285000 43.959999 2.391000
AU 29.285000 38.893002 2.391000
AU 32.214001 43.959999 2.391000
AU 32.214001 38.893002 2.391000
AU 35.141998 43.959999 2.391000
AU 35.141998 38.893002 2.391000
AU 38.070999 43.959999 2.391000
AU 38.070999 38.893002 2.391000
AU 40.999001 43.959999 2.391000
AU 40.999001 38.893002 2.391000
AU 43.928001 43.959999 2.391000
AU 43.928001 38.893002 2.391000
AU 46.855999 43.959999 2.391000
AU 46.855999 38.893002 2.391000
AU 30.749001 43.115002 0.000000
AU 30.749001 38.047001 0.000000
AU 33.678001 43.115002 0.000000
AU 33.678001 38.047001 0.000000
AU 36.605999 43.115002 0.000000
AU 36.605999 38.047001 0.000000
AU 39.535000 43.115002 0.000000
AU 39.535000 38.047001 0.000000
AU 42.464001 43.115002 0.000000
AU 42.464001 38.047001 0.000000
AU 45.391998 43.115002 0.000000
AU 45.391998 38.047001 0.000000
AU 48.320999 43.115002 0.000000
AU 48.320999 38.047001 0.000000
......@@ -12,6 +12,8 @@ echo " - irene-skl "
echo " - irene-knl "
echo " - dibona "
echo " - frioul "
echo " - deepsdv "
echo " - hazelhen "
read machine
source ./env/env_${machine}
......@@ -92,6 +94,7 @@ Install(){
# sed -i s/"MEMORY_INSTALLED_PER_CORE_IN_GB = 2.5d0"/"MEMORY_INSTALLED_PER_CORE_IN_GB = 50d0"/g DATA/Par_file
#fi
echo "===> Build"
make clean
time -p make -j 12 all >& make.log &
}
......@@ -123,10 +126,10 @@ Clean(){
Deploy(){
echo "install_dir ="$install_dir
if [ $machine = "occigen" ] || [ $machine = "marenostrum" ] || [ $machine = "marconi-knl" ] || [ $machine = "daint-cpu-only" ] || [ $machine = "daint-gpu" ] || [ $machine = "davide" ] || [ $machine = "juwels" ] || [ $machine = "irene-skl" ] || [ $machine = "irene-knl" ] || [ $machine = "dibona" ] || [ $machine = "frioul" ];then
if [ $machine = "occigen" ] || [ $machine = "marenostrum" ] || [ $machine = "marconi-knl" ] || [ $machine = "daint-cpu-only" ] || [ $machine = "daint-gpu" ] || [ $machine = "davide" ] || [ $machine = "juwels" ] || [ $machine = "irene-skl" ] || [ $machine = "irene-knl" ] || [ $machine = "dibona" ] || [ $machine = "frioul" ] || [ $machine = "deepsdv" ] || [ $machine = "hazelhen" ];then
echo "==> Install on $machine :"
Clean
mkdir -p $install_dir
Clean
export ueabs_dir=`pwd`
Untar
Install
......
#!/bin/bash
module purge
module load intel/18.1 parastation/5.2.0-1-intel
export machine=deepsdv
export software=specfem3d_globe
export version=31octobre
export install_dir=$PROJECT_cprcdeep/prdeep06/benchmarks/$machine/$software/$version/
export CC="mpicc"
export FC="mpifort"
export MPIFC=$FC
export FCFLAGS=" -g -O3 -qopenmp -xCORE-AVX2 -DUSE_FP32 -DOPT_STREAMS -fp-model fast=2 -traceback -mcmodel=medium"
export CFLAGS=" -g -O3 -xCORE-AVX2 "
#!/bin/bash
#module purge
module purge
module load ccc datadir/cines datadir/own dfldatadir/own flavor/buildtarget/x86_64 intel/19.0.0.117 hwloc/1.11.3 mpi/openmpi/2.0.4
export machine=irene-skl
......
#!/bin/bash -l
#SBATCH --job-name=specfem3D_test_case_C
#SBATCH --time=01:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=3
#SBATCH --cpus-per-task=4
#SBATCH --partition=normal
#SBATCH --constraint=gpu
#SBATCH --output=specfem3D_test_case_A_daint-gpu-%j.output
set -e
source ../env/env_daint-gpu
cd $install_dir/TestCaseC/specfem3d_globe
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export CRAY_CUDA_MPS=1
ulimit -s unlimited
MESHER_EXE=./bin/xmeshfem3D
SOLVER_EXE=./bin/xspecfem3D
# backup files used for this simulation
cp DATA/Par_file OUTPUT_FILES/
cp DATA/STATIONS OUTPUT_FILES/
cp DATA/CMTSOLUTION OUTPUT_FILES/
##
## mesh generation
##
sleep 2
echo
echo `date`
echo "starting MPI mesher"
echo
MPI_PROCESS=` echo "$SLURM_NNODES*$SLURM_NTASKS_PER_NODE" | bc -l`
echo "SLURM_NTASKS_PER_NODE = " $SLURM_NTASKS_PER_NODE
echo "SLURM_CPUS_PER_TASKS = " $SLURM_CPUS_PER_TASK
echo "SLURM_NNODES=" $SLURM_NNODES
echo "MPI_PROCESS $MPI_PROCESS"
time srun -n ${MPI_PROCESS} ${MESHER_EXE}
echo " mesher done: `date`"
echo
##
## forward simulation
##
sleep 2
echo
echo `date`
echo starting run in current directory $PWD
echo
#unset FORT_BUFFERED
time srun -n ${MPI_PROCESS} ${SOLVER_EXE}
echo "finished successfully"
echo `date`
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