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Added Running Jobs

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2019-06-18 14:53:39 +02:00
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pages/merlin6/merlin6-slurm/running-jobs.md
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title: Running Jobs title: Running Jobs
#tags: #tags:
#keywords: #keywords:
last_updated: 13 June 2019 last_updated: 18 June 2019
#summary: "" #summary: ""
sidebar: merlin6_sidebar sidebar: merlin6_sidebar
permalink: /merlin6/running-jobs.html permalink: /merlin6/running-jobs.html
@ -17,9 +17,7 @@ permalink: /merlin6/running-jobs.html
* ``salloc``: to obtain a Slurm job allocation (a set of nodes), execute command(s), and then release the allocation when the command is finished. * ``salloc``: to obtain a Slurm job allocation (a set of nodes), execute command(s), and then release the allocation when the command is finished.
* ``salloc`` is equivalent to an interactive run * ``salloc`` is equivalent to an interactive run
## Slurm settings ## Shared nodes and exclusivity
### Shared nodes and exclusivity
The **Merlin6** cluster has been designed in a way that should allow running MPI/OpenMP processes as well as single core based jobs. For allowing The **Merlin6** cluster has been designed in a way that should allow running MPI/OpenMP processes as well as single core based jobs. For allowing
co-existence, nodes are configured by default in a shared mode. It means, that multiple jobs from multiple users may land in the same node. This co-existence, nodes are configured by default in a shared mode. It means, that multiple jobs from multiple users may land in the same node. This
@ -34,7 +32,7 @@ Exclusivity of a node can be setup by specific the ``--exclusive`` option as fol
#SBATCH --exclusive #SBATCH --exclusive
``` ```
### Output and Errors ## Output and Errors
By default, Slurm script will generate standard output and errors files in the directory from where By default, Slurm script will generate standard output and errors files in the directory from where
you submit the batch script: you submit the batch script:
@ -51,7 +49,7 @@ If you want to the default names it can be done with the options ``--output`` an
Use **man sbatch** (``man sbatch | grep -A36 '^filename pattern'``) for getting a list specification of **filename patterns**. Use **man sbatch** (``man sbatch | grep -A36 '^filename pattern'``) for getting a list specification of **filename patterns**.
### Partitions ## Partitions
Merlin6 contains 3 partitions for general purpose. These are ``general``, ``daily`` and ``hourly``. If no partition is defined, Merlin6 contains 3 partitions for general purpose. These are ``general``, ``daily`` and ``hourly``. If no partition is defined,
``general`` will be the default. Partition can be defined with the ``--partition`` option as follows: ``general`` will be the default. Partition can be defined with the ``--partition`` option as follows:
@ -62,12 +60,12 @@ Merlin6 contains 3 partitions for general purpose. These are ``general``, ``dail
Please check the section [Slurm Configuration#Merlin6 Slurm Partitions] for more information about Merlin6 partition setup. Please check the section [Slurm Configuration#Merlin6 Slurm Partitions] for more information about Merlin6 partition setup.
### CPU-based Jobs Settings ## CPU-based Jobs Settings
CPU-based jobs are available for all PSI users. Users must belong to the ``merlin6`` Slurm ``Account`` in order to be able CPU-based jobs are available for all PSI users. Users must belong to the ``merlin6`` Slurm ``Account`` in order to be able
to run on CPU-based nodes. All users registered in Merlin6 are automatically included in the ``Account``. to run on CPU-based nodes. All users registered in Merlin6 are automatically included in the ``Account``.
#### Slurm CPU Mandatory Settings ### Slurm CPU Mandatory Settings
The following options are mandatory settings that **must be included** in your batch scripts: The following options are mandatory settings that **must be included** in your batch scripts:
@ -75,7 +73,7 @@ The following options are mandatory settings that **must be included** in your b
#SBATCH --constraint=mc # Always set it to 'mc' for CPU jobs. #SBATCH --constraint=mc # Always set it to 'mc' for CPU jobs.
``` ```
#### Slurm CPU Recommended Settings ### Slurm CPU Recommended Settings
There are some settings that are not mandatory but would be needed or useful to specify. These are the following: There are some settings that are not mandatory but would be needed or useful to specify. These are the following:
@ -86,13 +84,13 @@ shorter times. This may affect scheduling priorities.
#SBATCH --time=<D-HH:MM:SS> # Time job needs to run #SBATCH --time=<D-HH:MM:SS> # Time job needs to run
``` ```
### GPU-based Jobs Settings ## GPU-based Jobs Settings
GPU-base jobs are restricted to BIO users, however access for PSI users can be requested on demand. Users must belong to GPU-base jobs are restricted to BIO users, however access for PSI users can be requested on demand. Users must belong to
the ``merlin6-gpu`` Slurm ``Account`` in order to be able to run GPU-based nodes. BIO users belonging to any BIO group the ``merlin6-gpu`` Slurm ``Account`` in order to be able to run GPU-based nodes. BIO users belonging to any BIO group
are automatically registered to the ``merlin6-gpu`` account. Other users should request access to the Merlin6 administrators. are automatically registered to the ``merlin6-gpu`` account. Other users should request access to the Merlin6 administrators.
#### Slurm CPU Mandatory Settings ### Slurm CPU Mandatory Settings
The following options are mandatory settings that **must be included** in your batch scripts: The following options are mandatory settings that **must be included** in your batch scripts:
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#SBATCH --gres=gpu # Always set at least this option when using GPUs #SBATCH --gres=gpu # Always set at least this option when using GPUs
``` ```
### Slurm GPU Recommended Settings ## Slurm GPU Recommended Settings
GPUs are also a shared resource. Hence, multiple users can run jobs on a single node, but only one GPU per user process GPUs are also a shared resource. Hence, multiple users can run jobs on a single node, but only one GPU per user process
must be used. Users can define which GPUs resources they need with the ``--gres`` option. must be used. Users can define which GPUs resources they need with the ``--gres`` option.