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en:centro:servizos:hpc [2023/03/03 13:57] – [Queue system (QOS)] fernando.guillenen:centro:servizos:hpc [2024/03/13 10:37] (current) – [Sending a job to the queue system] fernando.guillen
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 # Install  # Install 
 sh Miniconda3-py39_4.11.0-Linux-x86_64.sh sh Miniconda3-py39_4.11.0-Linux-x86_64.sh
 +#  Initialize for bash shell
 +~/miniconda3/bin/conda init bash
 </code> </code>
  
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 ==== Sending a job to the queue system ==== ==== Sending a job to the queue system ====
 == Requesting resources == == Requesting resources ==
-By default, if you submit a job without specifying anything, the system submits it to the default (regular) QOS and assigns it a node, a CPU and all available memory. The time limit for job execution is that of the queue (4 days and 4 hours). +By default, if you submit a job without specifying anything, the system submits it to the default (regular) QOS and assigns it a node, a CPU and 4 GB. The time limit for job execution is that of the queue (4 days and 4 hours). 
 This is very inefficient, the ideal is to specify as much as possible at least three parameters when submitting jobs: This is very inefficient, the ideal is to specify as much as possible at least three parameters when submitting jobs:
   -  %%Node number (-N or --nodes), tasks (-n or --ntasks) and/or CPUs per task (-c or --cpus-per-task).%%   -  %%Node number (-N or --nodes), tasks (-n or --ntasks) and/or CPUs per task (-c or --cpus-per-task).%%
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 == Job submission == == Job submission ==
 +  - sbatch
   - salloc   - salloc
   - srun   - srun
-  - sbatch 
  
-1. SALLOC \\ +1. SBATCH \\
-It is used to immediately obtain an allocation of resources (nodes). As soon as it is obtained, the specified command or a shell is executed.  +
-<code bash> +
-# Get 5 nodes and launch a job. +
-hpc-login2 ~]$ salloc -N5 myprogram +
-# Get interactive access to a node (Press Ctrl+D to exit): +
-hpc-login2 ~]$ salloc -N1  +
-</code> +
-2. SRUN \\ +
-It is used to launch a parallel job (preferable to using mpirun). It is interactive and blocking. +
-<code bash> +
-# Launch the hostname command on 2 nodes +
-hpc-login2 ~]$ srun -N2 hostname +
-hpc-node1 +
-hpc-node2 +
-</code> +
-3. SBATCH \\+
 Used to send a script to the queuing system. It is batch-processing and non-blocking. Used to send a script to the queuing system. It is batch-processing and non-blocking.
 <code bash> <code bash>
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 hpc-login2 ~]$ sbatch test_job.sh  hpc-login2 ~]$ sbatch test_job.sh 
 </code> </code>
 +2. SALLOC \\
 +It is used to immediately obtain an allocation of resources (nodes). As soon as it is obtained, the specified command or a shell is executed. 
 +<code bash>
 +# Get 5 nodes and launch a job.
 +hpc-login2 ~]$ salloc -N5 myprogram
 +# Get interactive access to a node (Press Ctrl+D to exit):
 +hpc-login2 ~]$ salloc -N1 
 +# Get interactive EXCLUSIVE access to a node
 +hpc-login2 ~]$ salloc -N1 --exclusive
 +</code>
 +3. SRUN \\
 +It is used to launch a parallel job (preferable to using mpirun). It is interactive and blocking.
 +<code bash>
 +# Launch the hostname command on 2 nodes
 +hpc-login2 ~]$ srun -N2 hostname
 +hpc-node1
 +hpc-node2
 +</code>
 +
  
 ==== GPU use ==== ==== GPU use ====
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 JOBID PARTITION     NAME     USER      STATE       TIME  NODES NODELIST(REASON) JOBID PARTITION     NAME     USER      STATE       TIME  NODES NODELIST(REASON)
 6547  defaultPa  example <username>  RUNNING   22:54:55      1 hpc-fat1 6547  defaultPa  example <username>  RUNNING   22:54:55      1 hpc-fat1
 +
 +## Check status of queue use:
 +hpc-login2 ~]$ estado_colas.sh
 +JOBS PER USER:
 +--------------
 +       usuario.uno:  3
 +       usuario.dos:  1
 +
 +JOBS PER QOS:
 +--------------
 +             regular:  3
 +                long:  1
 +
 +JOBS PER STATE:
 +--------------
 +             RUNNING:  3
 +             PENDING:  1
 +==========================================
 +Total JOBS in cluster:  4
 </code> </code>
 Common job states: Common job states: