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Commit ff22c937 authored by Guilherme Calandrini's avatar Guilherme Calandrini
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2 merge requests!990Automated merge from preview to main,!982fix for using clusters not partitions
...@@ -211,13 +211,13 @@ inside the python code and scale computations over the jobs. ...@@ -211,13 +211,13 @@ inside the python code and scale computations over the jobs.
creates a Dask Scheduler in the Python process creates a Dask Scheduler in the Python process
where the cluster object is instantiated. where the cluster object is instantiated.
Please check the example of a definition of the cluster object Please check the example of a definition of the cluster object
for the partition `alpha` (queue at the dask terms) on the ZIH system: for the cluster `Alpha` (queue at the dask terms) on the ZIH system:
```python ```python
from dask_jobqueue import SLURMCluster from dask_jobqueue import SLURMCluster
cluster = SLURMCluster(queue='alpha', cluster = SLURMCluster(queue='alpha',
cores=8, cores=4,
processes=2, processes=2,
project='p_number_crunch', project='p_number_crunch',
memory="8GB", memory="8GB",
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...@@ -65,9 +65,9 @@ marie@compute$ R -e 'install.packages("ggplot2")' ...@@ -65,9 +65,9 @@ marie@compute$ R -e 'install.packages("ggplot2")'
## Deep Learning with R ## Deep Learning with R
The deep learning frameworks perform extremely fast when run on accelerators such as GPU. The deep learning frameworks perform extremely fast when run on accelerators such as GPU.
Therefore, using nodes with built-in GPUs, e.g., partitions Therefore, using nodes with built-in GPUs, e.g., clusters
[ml](../jobs_and_resources/hardware_overview.md) [Power9](../jobs_and_resources/hardware_overview.md)
and [alpha](../jobs_and_resources/alpha_centauri.md), is beneficial for the examples here. and [Alpha](../jobs_and_resources/alpha_centauri.md), is beneficial for the examples here.
### R Interface to TensorFlow ### R Interface to TensorFlow
...@@ -399,7 +399,7 @@ Another example: ...@@ -399,7 +399,7 @@ Another example:
#snow::stopCluster(cl) # usually it hangs over here with Open MPI > 2.0. In this case this command may be avoided, Slurm will clean up after the job finishes #snow::stopCluster(cl) # usually it hangs over here with Open MPI > 2.0. In this case this command may be avoided, Slurm will clean up after the job finishes
``` ```
To use Rmpi and MPI please use one of these partitions: `haswell`, `broadwell` or `rome`. To use Rmpi and MPI please use one of these clusters: `Alpha`, `Barnard` or `Romeo`.
Use `mpirun` command to start the R script. It is a wrapper that enables the communication Use `mpirun` command to start the R script. It is a wrapper that enables the communication
between processes running on different nodes. It is important to use `-np 1` (the number of spawned between processes running on different nodes. It is important to use `-np 1` (the number of spawned
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...@@ -180,7 +180,7 @@ can deactivate the conda environment as follows: ...@@ -180,7 +180,7 @@ can deactivate the conda environment as follows:
??? example ??? example
This is an example on partition `alpha`. The example creates a conda virtual environment, and This is an example on cluster `Alpha`. The example creates a conda virtual environment, and
installs the package `torchvision` with conda. installs the package `torchvision` with conda.
```console ```console
marie@login.alpha$ srun --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash marie@login.alpha$ srun --nodes=1 --gres=gpu:1 --time=01:00:00 --pty bash
......
...@@ -12,7 +12,7 @@ marie@compute$ module spider TensorFlow ...@@ -12,7 +12,7 @@ marie@compute$ module spider TensorFlow
[...] [...]
``` ```
to find out, which TensorFlow modules are available on your partition. to find out, which TensorFlow modules are available on your cluster.
On ZIH systems, TensorFlow 2 is the default module version. For compatibility hints between On ZIH systems, TensorFlow 2 is the default module version. For compatibility hints between
TensorFlow 2 and TensorFlow 1, see the corresponding [section below](#compatibility-tf2-and-tf1). TensorFlow 2 and TensorFlow 1, see the corresponding [section below](#compatibility-tf2-and-tf1).
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