Added Running Jobs

pages/merlin6/merlin6-slurm/running-jobs.md

@@ -2,7 +2,7 @@
 title: Running Jobs 
 #tags:
 #keywords:
-last_updated: 13 June 2019
+last_updated: 18 June 2019
 #summary: ""
 sidebar: merlin6_sidebar
 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`` 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
 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
 ```
 
-### Output and Errors
+## Output and Errors
 
 By default, Slurm script will generate standard output and errors files in the directory from where
 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**.
 
-### Partitions
+## Partitions
 
 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:
@@ -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. 
 
-### 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
 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:
 
@@ -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.
 ```
 
-#### 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:
 
@@ -86,13 +84,13 @@ shorter times. This may affect scheduling priorities.
    #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
 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.
 
-#### Slurm CPU Mandatory Settings
+### Slurm CPU Mandatory Settings
 
 The following options are mandatory settings that **must be included** in your batch scripts:
 
@@ -101,7 +99,7 @@ The following options are mandatory settings that **must be included** in your b
 #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 
 must be used. Users can define which GPUs resources they need with the ``--gres`` option.