-
Notifications
You must be signed in to change notification settings - Fork 9
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
6 changed files
with
135 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,36 @@ | ||
# Install fluidsim with Miniforge on Dahu | ||
|
||
We show in this directory | ||
(<https://foss.heptapod.net/fluiddyn/fluidsim/-/tree/branch/default/doc/examples/clusters/gricad_miniforge>) | ||
how to use Fluidsim with Miniforge on Gricad clusters. The main documentation | ||
for this HPC platform is [here](https://gricad-doc.univ-grenoble-alpes.fr/hpc/). | ||
|
||
## Install Miniforge | ||
|
||
```sh | ||
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" | ||
bash Miniforge3-$(uname)-$(uname -m).sh -b | ||
$HOME/miniforge3/bin/conda init | ||
. .bashrc | ||
conda config --set auto_activate_base false | ||
``` | ||
|
||
## Install Fluidsim in a conda env | ||
|
||
```sh | ||
conda env create --file https://foss.heptapod.net/fluiddyn/fluidsim/-/raw/branch/default/doc/examples/clusters/gricad_miniforge/env-fluidsim-mpi.yml | ||
``` | ||
|
||
## Submit jobs | ||
|
||
```sh | ||
./submit_bench_fluidfft.py | ||
./submit_bench_fluidsim.py | ||
``` | ||
|
||
For the devel script `submit_devel_bench_fluidsim.py`, one needs to be connected | ||
to a devel login node (`ssh dahu-oar3`). | ||
|
||
```sh | ||
./submit_devel_bench_fluidsim.py | ||
``` |
10 changes: 10 additions & 0 deletions
10
doc/examples/clusters/gricad_miniforge/env-fluidsim-mpi.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,10 @@ | ||
name: env-fluidsim-mpi | ||
dependencies: | ||
- fluidsim | ||
- openmpi | ||
- h5py=*=mpi* | ||
- fluidfft-fftw | ||
- fluidfft-fftwmpi | ||
- fluidfft-mpi_with_fftw | ||
- ipython | ||
- matplotlib |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,49 @@ | ||
from pathlib import Path | ||
|
||
from fluiddyn.clusters.oar import ClusterOAR | ||
|
||
|
||
path_miniforge = Path.home() / "miniforge3" | ||
|
||
|
||
class Dahu(ClusterOAR): | ||
name_cluster = "dahu" | ||
has_to_add_name_cluster = False | ||
frontends = ["dahu", "dahu-oar3"] | ||
use_oar_envsh = False | ||
|
||
commands_setting_env = [ | ||
"source /etc/profile", | ||
f"source {path_miniforge / 'etc/profile.d/conda.sh'}", | ||
"conda activate env-fluidsim-mpi", | ||
] | ||
|
||
|
||
class DahuDevel(Dahu): | ||
devel = True | ||
frontends = ["dahu-oar3"] | ||
|
||
|
||
class Dahu16_6130(Dahu): | ||
nb_cores_per_node = 16 | ||
resource_conditions = "cpumodel='Gold 6130' and n_cores=16" | ||
|
||
|
||
class Dahu32_6130(Dahu): | ||
nb_cores_per_node = 32 | ||
resource_conditions = "cpumodel='Gold 6130' and n_cores=32" | ||
|
||
|
||
class Dahu24_6126(Dahu): | ||
nb_cores_per_node = 24 | ||
resource_conditions = "cpumodel='Gold 6126' and n_cores=24" | ||
|
||
|
||
class Dahu32_5218(Dahu): | ||
nb_cores_per_node = 32 | ||
resource_conditions = "cpumodel='Gold 5218' and n_cores=32" | ||
|
||
|
||
class Dahu16_6244(Dahu): | ||
nb_cores_per_node = 16 | ||
resource_conditions = "cpumodel='Gold 6244' and n_cores=16" |
14 changes: 14 additions & 0 deletions
14
doc/examples/clusters/gricad_miniforge/submit_bench_fluidfft.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,14 @@ | ||
#!/usr/bin/env python3 | ||
from gricad_simple import Dahu32_6130 as Cluster | ||
|
||
cluster = Cluster() | ||
|
||
for nb_nodes in [1]: | ||
cluster.submit_command( | ||
command="fluidfft-bench 1024 -d 3", | ||
name_run=f"bench_fluidfft_{nb_nodes}nodes", | ||
nb_nodes=nb_nodes, | ||
nb_mpi_processes="auto", | ||
walltime="01:00:00", | ||
project="pr-strat-turb", | ||
) |
13 changes: 13 additions & 0 deletions
13
doc/examples/clusters/gricad_miniforge/submit_bench_fluidsim.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,13 @@ | ||
#!/usr/bin/env python3 | ||
from gricad_simple import Dahu32_6130 as Cluster | ||
|
||
cluster = Cluster() | ||
|
||
cluster.submit_command( | ||
command="fluidsim-bench 1024 -d 3 -s ns3d -o .", | ||
name_run="bench_fluidsim", | ||
nb_nodes=1, | ||
nb_mpi_processes="auto", | ||
walltime="00:30:00", | ||
project="pr-strat-turb", | ||
) |
13 changes: 13 additions & 0 deletions
13
doc/examples/clusters/gricad_miniforge/submit_devel_bench_fluidsim.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,13 @@ | ||
#!/usr/bin/env python3 | ||
from gricad_simple import DahuDevel as Cluster | ||
|
||
cluster = Cluster() | ||
|
||
cluster.submit_command( | ||
command="fluidsim-bench 256 -d 3 -s ns3d -o .", | ||
name_run="bench_fluidsim", | ||
nb_nodes=1, | ||
nb_mpi_processes=2, | ||
walltime="00:30:00", | ||
project="pr-strat-turb", | ||
) |