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Commit 8565fb74 authored by jourdain's avatar jourdain
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Merge branch 'develop' of https://dci-gitlab.cines.fr/dci/abs into develop

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variables:
GIT_CLONE_PATH: $SCRATCHDIR/abs/$CI_CONCURRENT_PROJECT_ID
stages:
- download
- compile
- run-small
- run
.runner: &runner
tags:
- alfred, occigen
.variables: &smilei
<<: *runner
variables:
APP_NAME: "SMILEI"
.download-app: &download-app
stage: download
script:
- cd ${APP_NAME}
- ./download.sh
#GLOBAL WORKFLOW
dl-smilei:
<<: *smilei
<<: *download-app
Abinit/compile.sh 100644 → 100755
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#!/bin/bash
cd /tmp/abinit-8.10.3
make distclean
module load intel/19.4 intelmpi/2019.4.243
export CPATH=${MKLROOT}/include:$CPATH
export FCFLAGS_OPENMP="-fopenmp"
export FCFLAGS=' -extend-source -noaltparam -nofpscomp -fopenmp'
env CC="mpicc -fopenmp -fPIC" CXX="mpiCC -fopenmp -fPIC" F77="mpif90 -fopenmp -fPIC" F90="mpif90 -fopenmp -fPIC" FC="mpif90 -fopenmp -fPIC" ./configure --disable-debug --enable-mpi --disable-xml --with-linalg-flavor="mkl+scalapack" --with-linalg-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -mkl" --with-fft-flavor=fftw3 --with-fft-libs="-lfftw3xf_intel_pic -mkl" --with-dft-flavor="libxc+atompaw+wannier90" --enable-mpi-io --with-trio-flavor="netcdf" --enable-gw-dpc="no" --with-tardir=/tmp/tardir --prefix=$HOME/ABINIT --enable-openmp --enable-optim
export FCFLAGS='-mtune=native -march=native -fPIC -extend-source -noaltparam -nofpscomp -fopenmp'
env CC="mpicc" CXX="mpicxx" F77="mpif90" F90="mpif90" FC="mpif90" ./configure --disable-debug --enable-mpi --disable-xml --with-linalg-flavor="mkl+scalapack" --with-linalg-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -mkl" --with-fft-flavor=fftw3 --with-fft-libs="-lfftw3xf_intel -mkl" --with-dft-flavor="libxc+atompaw+wannier90" --enable-mpi-io --with-trio-flavor="netcdf" --enable-gw-dpc="no" --with-tardir=/tmp/tardir --prefix=$HOME/ABINIT --enable-openmp --enable-optim
make -j 40
make install
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......@@ -2,14 +2,13 @@
mkdir -p /tmp/tardir
cd /tmp/tardir
wget http://forge.abinit.org/fallbacks/atompaw-4.0.1.0.tar.gz
wget http://forge.abinit.org/fallbacks/libxc-3.0.0.tar.gz
wget http://forge.abinit.org/fallbacks/netcdf-4.1.1.tar.gz
wget http://forge.abinit.org/fallbacks/wannier90-2.0.1.1.tar.gz
wget -nc http://forge.abinit.org/fallbacks/atompaw-4.0.1.0.tar.gz
wget -nc http://forge.abinit.org/fallbacks/libxc-3.0.0.tar.gz
wget -nc http://forge.abinit.org/fallbacks/netcdf-4.1.1.tar.gz
wget -nc http://forge.abinit.org/fallbacks/wannier90-2.0.1.1.tar.gz
cd ..
mkdir tarballs
wget https://www.abinit.org/sites/default/files/packages/abinit-8.10.3.tar.gz
cd /tmp
wget -nc --no-check-certificate https://www.abinit.org/sites/default/files/packages/abinit-8.10.3.tar.gz
tar xf abinit-8.10.3.tar.gz
cd abinit-8.10.3
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#!/bin/bash
#MSUB -n 128 # Number of MPI processes
#MSUB -c 16 # Number of threads
#MSUB -T 19000 # Time requested in seconds
#MSUB -r abinit_test_ti255 # Name of the job
#MSUB -m work,scratch
#MSUB -q rome # Partition
#MSUB -A tgcc0090 # Project id
# M S U B -Q test # TEST QoS
module purge
module load datadir/own
module load datadir/cines
module load dfldatadir/own
module load flavor/buildmpi/openmpi/4.0
module load flavor/openmpi/standard
module load flavor/buildcompiler/intel/19
module load feature/mkl/lp64
module load feature/mkl/sequential
module load mkl/19.0.5.281
module load licsrv/intel
module load c/intel/19.0.5.281
module load c++/intel/19.0.5.281
module load fortran/intel/19.0.5.281
module load intel/19.0.5.281
module load feature/openmpi/net/auto
module load hwloc/2.0.4
module load sharp/2.0
module load hcoll/4.4.2938
module load ucx/1.7.0
module load mpi/openmpi/4.0.2
# set max 2GB stack
ulimit -s 2000000
#export KMP_DETERMINISTIC_REDUCTION=1
# IRENE SKYLAKE OMP_NUM_THREADS=12 Proc. 0 individual time (sec): cpu= 28702.0 wall= 3602.4
# OCCIGEN OMP_NUM_THREADS=1 - Proc. 0 individual time (sec): cpu= 18945.1 wall= 18962.5
# OCCIGEN OMP_NUM_THREADS=2 - Proc. 0 individual time (sec): cpu= 36255.7 wall= 18135.0
# IRENE OMP_NUM_THREADS=1 - Proc. 0 individual time (sec): cpu= 17933.7 wall= 17980.9
# IRENE OMP_NUM_THREADS=11 Proc. 0 individual time (sec): cpu= 59060.5 wall= 5376.3
# IRENE OMP_NUM_THREADS=12 Proc. 0 individual time (sec): cpu= 61102.7 wall= 5096.8
export OMP_STACKSIZE=200M
export KMP_LIBRARY=turnaround
export KMP_BLOCKTIME=infinite
#export KMP_AFFINITY=verbose,granularity=fine,compact,1,0
export KMP_AFFINITY=disabled
export OMP_NUM_THREADS=12
export MKL_NUM_THREADS=12
export PATH=$CCCSCRATCHDIR/AO2020/ABINIT/bin:$PATH
export LD_LIBRARY_PATH=$CCCSCRATCHDIR/AO2020/ABINIT/lib:$LD_LIBRARY_PATH
export MKL_DEBUG_CPU_TYPE=5
#export MKL_CBWR=AVX2
export OMP_NESTED=TRUE
export MKL_DYNAMIC=FALSE
export OMP_DYNAMIC=FALSE
ccc_mprun abinit -i abinit_test_ti255.files > abinit_test_ti255.log 2>&1
# top - 17:04:29 up 1 day, 21:26, 1 user, load average: 8.00, 8.01, 8.05
# Tasks: 2523 total, 9 running, 2514 sleeping, 0 stopped, 0 zombie
# %Cpu(s): 3.2 us, 0.1 sy, 0.0 ni, 96.7 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
# KiB Mem : 26324713+total, 23950019+free, 20492052 used, 3254892 buff/cache
# KiB Swap: 0 total, 0 free, 0 used. 23936841+avail Mem
# PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ P COMMAND
# 171622 ciroube 20 0 6489408 1.5g 64312 R 94.7 0.6 129:48.17 0 abinit
# 171623 ciroube 20 0 6555448 1.5g 65416 R 94.7 0.6 129:48.28 16 abinit
# 171624 ciroube 20 0 6507224 1.6g 63840 R 94.7 0.6 129:48.18 32 abinit
# 171625 ciroube 20 0 6468896 1.5g 63660 R 94.7 0.6 129:48.29 48 abinit
# 171626 ciroube 20 0 6524128 1.5g 63688 R 94.7 0.6 129:47.53 64 abinit
# 171627 ciroube 20 0 6468332 1.5g 64804 R 94.7 0.6 129:47.01 80 abinit
# 171628 ciroube 20 0 6470816 1.5g 61000 R 94.7 0.6 129:47.28 96 abinit
# 171629 ciroube 20 0 6384584 1.5g 59800 R 94.7 0.6 129:51.65 112 abinit
# 179634 ciroube 20 0 174836 4704 1568 R 21.1 0.0 0:00.07 70 top
# Mem[|||||||||||||* 21.5G/251G] Tasks: 52, 36 thr; 9 running
# Swp[ 0K/0K] Load average: 8.04 8.03 8.05
# Avg[#####* 3.6%] Uptime: 1 day, 21:49:39
# Loa[|||||||||||| 8.04]
# Loa[||||||||||||############************ 8.04/8.03/8.05]
# PID USER PRI NI VIRT RES SHR S CPU% MEM% TIME+ Command
# 171623 ciroube 20 0 6658M 1812M 67328 R 114. 0.7 2h32:36 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171625 ciroube 20 0 6574M 1809M 65524 R 114. 0.7 2h32:37 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171627 ciroube 20 0 6573M 1819M 66672 R 114. 0.7 2h32:35 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171629 ciroube 20 0 6491M 1808M 61840 R 114. 0.7 2h32:40 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171622 ciroube 20 0 6594M 1810M 65920 R 85.5 0.7 2h32:36 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171624 ciroube 20 0 6613M 1846M 65376 R 85.5 0.7 2h32:36 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171626 ciroube 20 0 6628M 1828M 65252 R 85.5 0.7 2h32:36 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
# 171628 ciroube 20 0 6574M 1829M 62536 R 85.5 0.7 2h32:35 /ccc/scratch/cont003/cines/ciroube/AO2020/ABINIT/bin/abinit -i abinit_test_ti255.files
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#!/bin/bash
#SBATCH -J abinit_test_ti255
#SBATCH --nodes=43
#SBATCH --ntasks=128
#SBATCH --cpus-per-task=12
#SBATCH --time=02:00:00
#SBATCH --hint=nomultithread
#SBATCH --qos=qos_cpu-dev
#SBATCH -A qbg@cpu
cd $SLURM_SUBMIT_DIR
module purge
module load abinit/8.10.3-mpi
#module load intel-compilers/19.0.5
#module load intel-mkl/19.0.5
#module load intel-mpi/19.0.5
#export PATH=/gpfslocalsup/spack_soft/abinit/8.10.3/intel-18.0.5-iodjoowmaestj5t7u72wvzvmxuaxrtym/bin:$PATH
#export LD_LIBRARY_PATH=/gpfslocalsup/spack_soft/fftw/3.3.8/intel-19.0.5-uitqxse2pwj6xndjihgo54lmo5zpv7wy/lib:/gpfslocalsup/spack_soft/netcdf-fortran/4.4.5/intel-19.0.4-nm7vlsr6edc7yqkb2v7l4p6mu4dcgkoy/lib:/gpfslocalsup/spack_soft/hdf5/1.10.5/intel-19.0.5-v4d6fdbpytf2in7bzykz6hbv4domjs7b/lib:/gpfslocalsup/spack_soft/libxc/3.0.1/intel-19.0.5-2wxuz66qzbvv2xl4ztjzloxtmb5nkgo3/lib:$LD_LIBRARY_PATH
# set max 1GB stack
ulimit -s 1000000
#export KMP_DETERMINISTIC_REDUCTION=1
export OMP_STACKSIZE=1000M
export KMP_LIBRARY=turnaround
export KMP_BLOCKTIME=infinite
export KMP_AFFINITY=granularity=fine,compact,1,0
export OMP_NUM_THREADS=12
#export MKL_NUM_THREADS=12
#export MKL_DEBUG_CPU_TYPE=5
#export MKL_CBWR=AVX2
export OMP_NESTED=TRUE
export MKL_DYNAMIC=TRUE
export OMP_DYNAMIC=FALSE
srun abinit -i abinit_test_ti255.files > abinit_test_ti255.log 2>&1
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#!/bin/bash
#SBATCH -N 64
#SBATCH -n 128 # Number of MPI processes
#SBATCH -c 14 # Number of threads
#SBATCH -t 2:0:0
#SBATCH -J abinit_test_ti255
#SBATCH -C BDW28
#SBATCH --cpu-freq=2600000 # fixed CPU frequency at 2.6GHz
cd $SLURM_SUBMIT_DIR
module purge
module load intel/19.4 intelmpi/2019.4.243
unset I_MPI_DAPL_DIRECT_COPY_THRESHOLD
export MLX5_SINGLE_THREADED=0
export MLX4_SINGLE_THREADED=0
# set max 2GB stack
ulimit -s 2000000
export OMP_STACKSIZE=500M
#export KMP_DETERMINISTIC_REDUCTION=1
export KMP_LIBRARY=turnaround
export KMP_BLOCKTIME=infinite
export KMP_AFFINITY=verbose,granularity=fine,compact,1,0
export OMP_NUM_THREADS=12
export MKL_NUM_THREADS=12
#source /opt/software/common/intel/vtune_amplifier_2019/apsvars.sh
#srun --cpu-freq=2600000 aps abinit -i abinit_test_ti255.files > abinit_test_ti255.log.$SLURM_JOBID 2>&1
srun --cpu-freq=2600000 $HOME/ABINIT/bin/abinit -i abinit_test_ti255.files > abinit_test_ti255.log 2>&1
#aps --report=aps_result_*
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#!/bin/bash
#SBATCH -N 2
#SBATCH -n 8 # Number of MPI processes
#SBATCH -c 7 # Number of threads
#SBATCH -t 2:0:0
#SBATCH -J abinit_test_au31
#SBATCH -C BDW28
#SBATCH --cpu-freq=2600000 # fixed CPU frequency at 2.6GHz
cd $SLURM_SUBMIT_DIR
module purge
module load intel/19.4 intelmpi/2019.4.243
unset I_MPI_DAPL_DIRECT_COPY_THRESHOLD
export MLX5_SINGLE_THREADED=0
export MLX4_SINGLE_THREADED=0
# set max 2GB stack
ulimit -s 2000000
#export KMP_DETERMINISTIC_REDUCTION=1
export KMP_LIBRARY=turnaround
export KMP_BLOCKTIME=infinite
export KMP_AFFINITY=granularity=fine,compact,1,0
export OMP_NUM_THREADS=4
export MKL_NUM_THREADS=4
#source /opt/software/common/intel/vtune_amplifier_2019/apsvars.sh
#srun --cpu-freq=2600000 aps abinit -i abinit_test_au31.files > abinit_test_au31.log.$SLURM_JOBID 2>&1
srun --cpu-freq=2600000 $HOME/ABINIT/bin/abinit -i abinit_test_au31.files > abinit_test_au31.log 2>&1
#aps --report=aps_result_*
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abinit_test_au31.in
abinit_test_au31.out
abinit_test_au31_i
abinit_test_au31_o
abinit_test_au31_t
au.hpc.paw
\ No newline at end of file
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# ================================================== #
# ABINIT - INPUT FILE - GOLD 31 ATOMS (one vacancy) #
# Small test to be run on 8 MPI x 4 openMP threads #
# #
# MT 01/2020 #
# ================================================== #
#Process distribution (parallelism)
npband 8 bandpp 16 npfft 1 npkpt 1 # 8 MPI x 4 threads
#Self-consistent cycle parameters
wfoptalg 114 ! This is the default
toldfe 1.d-10
nstep 20
#Plane wave basis
ecut 5.
pawecutdg 8.
#K-points and symetries
nkpt 1
kpt 3*0.
kptopt 0
istwfk *1
nsym 0
chksymbreak 0
#Electronic configuration
nband 256
occopt 3
tsmear 0.001 hartree
#Activation/deactivation of I/O
optforces 2
optstress 1
prtwf 0
prtden 0
prteig 0
timopt 0
#Simulation cell
acell 3*15.34
rprim 1. 0. 0. 0. 1. 0. 0. 0. 1.
natom 31
ntypat 1
typat 31*1
znucl 79.
chkprim 0
#Atomic positions
xred
2.50000000000000e-01 2.50000000000000e-01 0.00000000000000e+00
2.50000000000000e-01 0.00000000000000e+00 2.50000000000000e-01
0.00000000000000e+00 2.50000000000000e-01 2.50000000000000e-01
0.00000000000000e+00 0.00000000000000e+00 5.00000000000000e-01
2.50000000000000e-01 2.50000000000000e-01 5.00000000000000e-01
2.50000000000000e-01 0.00000000000000e+00 7.50000000000000e-01
0.00000000000000e+00 2.50000000000000e-01 7.50000000000000e-01
0.00000000000000e+00 5.00000000000000e-01 0.00000000000000e+00
2.50000000000000e-01 7.50000000000000e-01 0.00000000000000e+00
2.50000000000000e-01 5.00000000000000e-01 2.50000000000000e-01
0.00000000000000e+00 7.50000000000000e-01 2.50000000000000e-01
0.00000000000000e+00 5.00000000000000e-01 5.00000000000000e-01
2.50000000000000e-01 7.50000000000000e-01 5.00000000000000e-01
2.50000000000000e-01 5.00000000000000e-01 7.50000000000000e-01
0.00000000000000e+00 7.50000000000000e-01 7.50000000000000e-01
5.00000000000000e-01 0.00000000000000e+00 0.00000000000000e+00
7.50000000000000e-01 2.50000000000000e-01 0.00000000000000e+00
7.50000000000000e-01 0.00000000000000e+00 2.50000000000000e-01
5.00000000000000e-01 2.50000000000000e-01 2.50000000000000e-01
5.00000000000000e-01 0.00000000000000e+00 5.00000000000000e-01
7.50000000000000e-01 2.50000000000000e-01 5.00000000000000e-01
7.50000000000000e-01 0.00000000000000e+00 7.50000000000000e-01
5.00000000000000e-01 2.50000000000000e-01 7.50000000000000e-01
5.00000000000000e-01 5.00000000000000e-01 0.00000000000000e+00
7.50000000000000e-01 7.50000000000000e-01 0.00000000000000e+00
7.50000000000000e-01 5.00000000000000e-01 2.50000000000000e-01
5.00000000000000e-01 7.50000000000000e-01 2.50000000000000e-01
5.00000000000000e-01 5.00000000000000e-01 5.00000000000000e-01
7.50000000000000e-01 7.50000000000000e-01 5.00000000000000e-01
7.50000000000000e-01 5.00000000000000e-01 7.50000000000000e-01
5.00000000000000e-01 7.50000000000000e-01 7.50000000000000e-01
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#!/bin/bash
rm -f abinit_test_au31_i* abinit_test_au31_o* abinit_test_au31_t*
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#!/bin/bash
sbatch ../machines/occigen-bdw/batch_small_au31.slurm
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abinit_test_ti255.in
abinit_test_ti255.out
abinit_test_ti255_i
abinit_test_ti255_o
abinit_test_ti255_t
ti.hpc.paw
\ No newline at end of file
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# ======================================================== #
# ABINIT - INPUT FILE - TITANIUM 255 ATOMS #
# LOBPCG algorithm #
# #
# HOWTO: #
# - select one of the datasets (change 'jdtset' below) #
# - run ABINIT with the corresponding MPI/openMP distrib. #
# #
# MT 01/2020 #
# ======================================================== #
#Processes/threads distribution (parallelism)
# ===> SELECT one of the following datasets
ndtset 1 jdtset 2
#npband1 256 bandpp1 12 npfft1 1 npkpt1 1 # 256 MPI x 12 thread(s)
npband2 128 bandpp2 12 npfft2 1 npkpt2 1 # 128 MPI x 12 thread(s)
#npband3 256 bandpp3 12 npfft3 1 npkpt3 1 # 256 MPI x 6 thread(s)
#npband4 512 bandpp4 12 npfft4 8 npkpt4 1 # 512 MPI x 3 thread(s)
#npband5 256 bandpp5 16 npfft5 6 npkpt5 1 # 1536 MPI x 1 thread(s)
#Self-consistent cycle parameters
wfoptalg 114
tolvrs 1.d-5
nstep 20
#Plane wave basis
ecut 8.
pawecutdg 20.
#K-points and symetries
nkpt 1
kpt 3*0.5
kptopt 0
istwfk *1
nsym 0
chksymbreak 0
#Electronic configuration
nband 3072
occopt 3
tsmear 1800. K
#Activation/deactivation of I/O
optforces 2
optstress 1
prtwf 0
prtden 0
prteig 0
timopt 0
#Simulation cell
acell 50.4 25.2 25.2
rprim 1. 0. 0. 0. 1. 0. 0. 0. 1.
natom 255
ntypat 1
typat 256*1
znucl 22.
chkprim 0
pawovlp -1
#Atomic positions
xred
!0.00000000000000 0.00000000000000 0.00000000000000
0.06250000000000 0.12500000000000 0.12500000000000
0.00000000000000 0.00000000000000 0.25000000000000
0.06250000000000 0.12500000000000 0.37500000000000
0.00000000000000 0.00000000000000 0.50000000000000
0.06250000000000 0.12500000000000 0.62500000000000
0.00000000000000 0.00000000000000 0.75000000000000
0.06250000000000 0.12500000000000 0.87500000000000
0.00000000000000 0.25000000000000 0.00000000000000
0.06250000000000 0.37500000000000 0.12500000000000
0.00000000000000 0.25000000000000 0.25000000000000
0.06250000000000 0.37500000000000 0.37500000000000
0.00000000000000 0.25000000000000 0.50000000000000
0.06250000000000 0.37500000000000 0.62500000000000
0.00000000000000 0.25000000000000 0.75000000000000
0.06250000000000 0.37500000000000 0.87500000000000
0.00000000000000 0.50000000000000 0.00000000000000
0.06250000000000 0.62500000000000 0.12500000000000
0.00000000000000 0.50000000000000 0.25000000000000
0.06250000000000 0.62500000000000 0.37500000000000
0.00000000000000 0.50000000000000 0.50000000000000
0.06250000000000 0.62500000000000 0.62500000000000
0.00000000000000 0.50000000000000 0.75000000000000
0.06250000000000 0.62500000000000 0.87500000000000
0.00000000000000 0.75000000000000 0.00000000000000
0.06250000000000 0.87500000000000 0.12500000000000
0.00000000000000 0.75000000000000 0.25000000000000
0.06250000000000 0.87500000000000 0.37500000000000
0.00000000000000 0.75000000000000 0.50000000000000
0.06250000000000 0.87500000000000 0.62500000000000
0.00000000000000 0.75000000000000 0.75000000000000
0.06250000000000 0.87500000000000 0.87500000000000
0.12500000000000 0.00000000000000 0.00000000000000
0.18750000000000 0.12500000000000 0.12500000000000
0.12500000000000 0.00000000000000 0.25000000000000
0.18750000000000 0.12500000000000 0.37500000000000
0.12500000000000 0.00000000000000 0.50000000000000
0.18750000000000 0.12500000000000 0.62500000000000
0.12500000000000 0.00000000000000 0.75000000000000
0.18750000000000 0.12500000000000 0.87500000000000
0.12500000000000 0.25000000000000 0.00000000000000
0.18750000000000 0.37500000000000 0.12500000000000
0.12500000000000 0.25000000000000 0.25000000000000
0.18750000000000 0.37500000000000 0.37500000000000
0.12500000000000 0.25000000000000 0.50000000000000
0.18750000000000 0.37500000000000 0.62500000000000
0.12500000000000 0.25000000000000 0.75000000000000
0.18750000000000 0.37500000000000 0.87500000000000
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Abinit/testcase_ti255_big/prepare.sh 0 → 100755
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#!/bin/bash
rm -f abinit_test_ti255_i* abinit_test_ti255_o* abinit_test_ti255_t*
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#!/bin/bash
sbatch ../machines/occigen-bdw/batch_large_ti255.slurm
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source diff could not be displayed: it is too large. Options to address this: view the blob.
GYSELAX/README.md
+ 11
− 17
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......@@ -4,19 +4,21 @@ Description:
Presentation
------------
YALES2BIO is a red blood flow solver. It is used for the analysis of medical devices in contact with blood such as flow diverters, Ventricular Assist Devices, extra corporal circulation, artificial heart and valves, cytometers among others. Optimizing such devices requires dealing with both macroscopic (pressure loss, residence time, wall shear stress, turbulence) and microscopic (blood cells deformation and interaction with other cells or solid boundaries) features.
The Gysela 5D code models the electrostatic branch of the Ion Temperature Gradient turbulence in tokamak plasmas.
Gysela is a 5D full-f and flux-driven gyrokinetic code. As such, it evolves in time the five-dimensional (3D in configuration space, 2D in velocity space) ion distribution function. For now, Gysela assumes electrons to be adiabatic and considers a global simplified magnetic geometry (concentric toroidal magnetic flux surfaces with circular cross-sections). The code simulates the full ion distribution function without any scale separation between equilibrium and fluctuations (”full-f”).
From the physics point of view, the other peculiarities of the Gysela code are the presence of an ion-ion collision operator accounting for neoclassical transport, and the existence of versatile sources (heat, momentum, …) which sustain the mean profiles on confinement times (“flux-driven”).
From the numerical point of view, Gysela is based on a semi-lagrangian scheme, hence is name: GYSELA 5D is an acronym for GYrokinetic SEmi-LAgrangian in 5 Dimensions. Two solvers are at the heart of Gysela: a Vlasov solver for computing ions advections and a Poisson solver for computing the magnetic field.
Technical information:
----------------------
* website : https://imag.umontpellier.fr/~yales2bio/index.html
* Scientific domain : haemodynamics
* website : http://gyseladoc.gforge.inria.fr/
* Scientific domain : Fusion
* Language : Fortran
* Parallelism : MPI + OpenMP
* GPU acceleration : No
* Scalability : good
* Vectorization: poor
* Vectorization: good
Compilation and simulation:
......@@ -30,26 +32,22 @@ Download:
The sources are available in a tarball and correspond to a stable release. To un-tar this release, run
```
export TARBALL_PATH=path/to/gysela/tarball (for occigen: export TARBALL_PATH=$SCRATCHDIR/abs_porjects/)
./download.sh
```
Compile:
--------
To compile the code, several librairies are needed:
* hdf5 in sequential (works with the 1.8.17 version)
* parmetis
* scotch
Then, a Makefile.in is needed. For IRENE, OCCIGEN and JEAN-ZAY platforms, this file is already made. For another platform one has to write it. An example can be found in...
Compile the code using:
```
source machines/occigen-bdw/env
source machines/occigen-bdw/env_bench
./compile.sh
```
`machines/occigen-bdw/env` contains the information for compilation (module load gcc openmpi lapack hdf5 ...)
In `source machines/occigen-bdw/env_bench` **occigen-bdw** is to be replaced with the proper machine name (jean-zay-cpu, irene-amd...). It the directory does not exist fo a machine, please add it.
`machines/occigen-bdw/env` contains the information for compilation. To use GYSELAX, you need to export the ARCH environment variables (export ARCH=occigen2). Then, the user needs to source the gysela environement variable setting file `gysela/scripts/lib/setup_path.sh`. This is done in the env file.
Run and validate the simulation:
--------------------------------
......@@ -67,9 +65,5 @@ cd testcase_XXX
./run.sh
./validate.sh
```
And getting no error code returned.
Those steps can also be used in a batch file for running the simulation using a job scheduler.
GYSELAX/compile.sh
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####################################
# TEST THE ENVIRONMENT
####################################
echo "################################"
####################################
# GO TO GYSELAX DIRECTORY
####################################
......
GYSELAX/download.sh
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#####################################
## CLONE THE GYSELAX REPO
#####################################
#git clone https://gitlab.maisondelasimulation.fr/gysela-developpers/gysela.git 1>/dev/null 2>/dev/null
####################################
# CLONE THE GYSELAX REPO
####################################
git clone https://gitlab.maisondelasimulation.fr/gysela-developpers/gysela.git 1>/dev/null 2>/dev/null
tar xvf $TARBALL_PATH/gysela.tar.gz -C ./ 1>/dev/null 2>/dev/null
####################################
# TEST THE DOWNLOAD
......
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