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fluiddyn
fluidsim
Commits
6ba2201526c3
Commit
997d2595
authored
Jan 22, 2022
by
vlabarre
Browse files
Install pythran with conda rather than with pip fixes problems
parent
b52d62843afa
Pipeline
#31390
passed with stage
in 16 minutes and 58 seconds
Changes
7
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1
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doc/examples/clusters/jean_zay/install/2_create_conda_env.sh
View file @
6ba22015
#!/bin/bash
source
../setup_env_base.sh
set
-e
conda
env
remove
--name
env_fluidsim
-y
conda
env
remove
--name
env_fluidsim
#-y
# Note: The python version is important for packages compatibility
conda create
-n
env_fluidsim
# python=3.8 #mamba
conda create
-y
-n
env_fluidsim mamba
conda activate env_fluidsim
mamba
install
-y
\
ipython scipy
"blas-devel[build=*openblas]"
\
matplotlib pandas psutil pillow scikit-image
\
mako clangdev
\
# you can also use mamba
conda
install
ipython
python
=
3.8.8 scipy
"blas-devel[build=*openblas]"
\
matplotlib pandas psutil pillow scikit-image mako clangdev
\
mercurial hg-git hg-evolve
# Using Pythran master > 0.11.0 (possible performance boost)
pip
install
git+https://github.com/serge-sans-paille/pythran#egg
=
pythran
#pip install git+https://github.com/serge-sans-paille/pythran#egg=pythran
#pip install pythran
conda
install
pythran
# (Vincent) I don't know why, but it is important to install with conda (and not pip)
#pip install hg-fluiddyn transonic setuptools cython pytest
pip
install
hg-fluiddyn transonic setuptools cython pytest
# Better than with conda install because we don't want the fftw conda package
pip
install
pyfftw
pip
install
mpi4py
--no-binary
mpi4py
# to install hdf5 and h5py parallel
export
HDF5_DIR
=
/gpfslocalsup/spack_soft/hdf5/1.12.0/gcc-8.3.1-qj43pa5rathksrgn4sx2ici42tg75nun
CC
=
"mpicc"
HDF5_MPI
=
"ON"
pip
install
--no-deps
--no-binary
=
h5py h5py
# Install hdf5 and h5py parallel
# (Check the HDF5_DIR with module show)
HDF5_DIR
=
/gpfslocalsup/spack_soft/hdf5/1.12.0/gcc-8.3.1-qj43pa5rathksrgn4sx2ici42tg75nun
CC
=
"mpicc"
HDF5_MPI
=
"ON"
HDF5_DIR
=
/gpfslocalsup/spack_soft/hdf5/1.12.0/gcc-8.3.1-qj43pa5rathksrgn4sx2ici42tg75nun pip
install
--no-deps
--no-binary
=
h5py h5py
python
-c
"import h5py; assert h5py.h5.get_config().mpi, 'h5py not built with MPI support'"
doc/examples/clusters/jean_zay/install/4_clone_fluid.sh
View file @
6ba22015
...
...
@@ -3,7 +3,6 @@ rm -rf fluiddyn fluidfft
hg clone https://foss.heptapod.net/fluiddyn/fluiddyn
hg clone https://foss.heptapod.net/fluiddyn/fluidfft
hg clone https://foss.heptapod.net/fluiddyn/transonic
# TODO: remove this line when topic fix-bug-mpi-barrier-jean-zay is merged
hg clone https://foss.heptapod.net/fluiddyn/transonic
cd
$WORK
/Dev/fluidsim/doc/examples/clusters/jean_zay/install
doc/examples/clusters/jean_zay/install/5_update_install_fluid.sh
View file @
6ba22015
...
...
@@ -7,20 +7,21 @@ hg up cluster-jean-zay # cluster-jean-zay should be replaced by default when mer
make clean
pip
install
-e
.
# TODO: Remove the line with transonic when fix-bug-mpi-barrier-jean-zay is merged
cd
$WORK
/Dev/transonic
hg pull
hg up
fix-bug-mpi-barrier-jean-zay
hg up
default
make clean
pip
install
-e
.
cd
$WORK
/Dev/fluidfft
hg pull
hg up default
# pip install -e . seems to run something with mpi, which is forbidden
python setup.py develop
# TODO: QUESTION for Vincent: does this work for fluidfft?
# pip install -e . --no-build-isolation
# Vincent: No
cd
$WORK
/Dev/fluidsim
make cleanall
...
...
doc/examples/clusters/jean_zay/install/install_p3dfft.sh
View file @
6ba22015
...
...
@@ -13,7 +13,7 @@ pkgdir="${WORK}/.local/${pkgname}/${pkgver}"
# C and Fortran 90 MPI compilers
CC
=
mpicc
#FC=mpif90
FC
=
'mpif90 -nofor_main'
#
FC='mpif90 -nofor_main'
# FFTW
# ----
...
...
@@ -54,7 +54,7 @@ build() {
LDFLAGS
=
"-lm"
./configure
--enable-gnu
--enable-openmpi
--enable-fftw
\
--with-fftw
=
/gpfslocalsup/spack_soft/fftw/3.3.8/gcc-8.3.1-yancwmvy7k2qaxtswmzlvyda5bsahmoh/
\
--prefix
=
${
pkgdir
}
CC
=
${
CC
}
CCLD
=
${
FC
}
--prefix
=
${
pkgdir
}
CC
=
${
CC
}
CCLD
=
'mpif90 -nofor_main'
make
}
...
...
doc/examples/clusters/jean_zay/scripts/run_simul.py
View file @
6ba22015
...
...
@@ -6,7 +6,7 @@ with the forcing tcrandom_anisotropic
from
fluiddyn.util
import
mpi
#mpi.comm.barrier()
mpi
.
print_sorted
(
"starting"
)
#
mpi.print_sorted("starting")
import
numpy
as
np
...
...
@@ -28,7 +28,7 @@ params.output.sub_directory = "Fluidsim_Data/examples"
params
.
short_name_type_run
=
"aniso_"
+
kind
#params.projection = "poloidal"
nx
=
ny
=
nz
=
320
*
2
nx
=
ny
=
nz
=
160
Lx
=
2.0
*
np
.
pi
params
.
oper
.
nx
=
nx
params
.
oper
.
ny
=
ny
...
...
@@ -39,12 +39,12 @@ params.oper.Lz = Lz = Lx / nx * nz
params
.
time_stepping
.
USE_T_END
=
True
params
.
time_stepping
.
cfl_coef
=
0.2
params
.
time_stepping
.
t_end
=
0.2
params
.
time_stepping
.
t_end
=
2.0
# Brunt Vaisala frequency
params
.
N
=
2.0
# Viscosity
params
.
nu_2
=
1e-
3
params
.
nu_2
=
1e-
2
mpi
.
printby0
(
f
"N =
{
params
.
N
:.
3
e
}
, nu_2 =
{
params
.
nu_2
:.
3
e
}
"
)
...
...
doc/examples/clusters/jean_zay/scripts/submit_simul.py
View file @
6ba22015
...
...
@@ -4,11 +4,11 @@ from fluiddyn.clusters.idris import JeanZay as Cluster
cluster
=
Cluster
()
nb_nodes
=
8
nb_nodes
=
1
nb_cores_per_node
=
cluster
.
nb_cores_per_node
nb_procs
=
nb_mpi_processes
=
nb_nodes
*
nb_cores_per_node
walltime
=
"00:
2
0:00"
walltime
=
"00:
1
0:00"
cluster
.
commands_setting_env
.
append
(
"export TRANSONIC_MPI_TIMEOUT=100"
...
...
@@ -22,7 +22,7 @@ cluster.submit_script(
"run_simul.py"
,
name_run
=
f
"ns3d.strat"
,
nb_nodes
=
nb_nodes
,
nb_cores_per_node
=
nb_cores_per_node
,
# it is computed automatically I think
nb_cores_per_node
=
nb_cores_per_node
,
nb_mpi_processes
=
nb_mpi_processes
,
omp_num_threads
=
1
,
ask
=
True
,
...
...
doc/examples/clusters/jean_zay/setup_env_base.sh
View file @
6ba22015
...
...
@@ -4,10 +4,14 @@ alias duh1='du -h --max-depth=1'
module load python/3.8.8 gcc/8.3.1 openmpi/4.1.1 hdf5/1.12.0-mpi
module load fftw/3.3.8-mpi pfft/1.0.8-alpha-mpi
#module load mercurial/6.0
conda init bash
source
$HOME
/.bashrc
conda activate base
# needed to use clang for Pythran
unset
CC
unset
CXX
...
...
@@ -16,4 +20,4 @@ export FLUIDSIM_PATH=$WORK
export
LD_LIBRARY_PATH
=
$LD_LIBRARY_PATH
:
$WORK
/.local/p3dfft/2.7.6/lib
conda activate base
#
conda activate base
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