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habrok:job_management:scheduling_system [2022/12/22 12:41] – fokkehabrok:job_management:scheduling_system [2025/07/14 14:13] (current) – [Nodes and cores] pedro
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 ==== Nodes and cores ==== ==== Nodes and cores ====
  
-The requirements for nodes (full computers) and cores can be given using the parameters ''%%--%%nodes'', ''%%--%%ntasks'', ''--ntasks-per-node'', +The requirements for nodes (full computers) and cores can be given using the parameters ''%%--%%nodes'', ''%%--%%ntasks'', ''%%--%%ntasks-per-node'', 
 ''%%--%%ntasks-per-core'', ''%%--%%cpus-per-task'' and ''%%--%%ntasks-per-core''. Here is a basic description of what they mean: ''%%--%%ntasks-per-core'', ''%%--%%cpus-per-task'' and ''%%--%%ntasks-per-core''. Here is a basic description of what they mean:
  
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 Note that if you only use ''%%--%%ntasks'' to request N cores, these N cores may be distributed over 1 to N nodes. If your software cannot handle this or if you do not want this, you will have to use the ''%%--%%nodes'' parameter to limit the number of nodes. Note that if you only use ''%%--%%ntasks'' to request N cores, these N cores may be distributed over 1 to N nodes. If your software cannot handle this or if you do not want this, you will have to use the ''%%--%%nodes'' parameter to limit the number of nodes.
  
 +==== Multinode jobs requiring faster networking ====
 +
 +If your application is using MPI and may benefit from a high bandwidth (the amount of data transferred per second) and/or low latency (the amount of time it takes for the first bit to arrive) you can send the job to the ''omnipath'' partition. The nodes in this partition are equipped with an Omni-Path network adapter which has 100 Gbps bandwidth and a latency of a few microseconds. You can do this by specifying the partition in the jobscript using:
 +<code>
 +#SBATCH --partition=parallel
 +</code>
 +Since there are only limited resources available in this partition there are two important guidelines
 +  - When using just a few cores you might as well run your application on a single node
 +  - It would be wise to test the performance difference between a job running on the regular nodes and the omnipath nodes, since there may be more capacity available in the ''regular'' partition.
 ==== Memory ==== ==== Memory ====
  
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 The following table gives an overview and description of other useful parameters that can be used: The following table gives an overview and description of other useful parameters that can be used:
  
-^Parameter ^Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^ +^Parameter ^Description ^ 
-|%%--%%job-name |Specify a name for the job, which will be shown in the job overview                                                                                                                                                                                                                                                                                                                                                                                                                                                          | +|%%--%%job-name |Specify a name for the job, which will be shown in the job overview |                                                                                                                                                                                                                                                                                                                                                                                                                                                          
-|%%--%%mail-type|Comma-separated list of events for which an email notification should be sent. Valid event names are:\\ //ALL// - equivalent to: //BEGIN//, //END//, //FAIL// and //REQUEUE//\\ //BEGIN// - job started running\\ //END// - job completed\\ //FAIL// - job failed\\ //REQUEUE// - job is requeued\\ //TIME_LIMIT// - job exceeded time limit\\ //TIME_LIMIT_50// - job reached 50 percent of time limit\\ //TIME_LIMIT_80// - job reached 80 percent of time limit\\ //TIME_LIMIT_90// - job reached 90 percent of time limit| +| 
-|%%--%%mail-user|Email address to receive notifications of job state changes as requested with the —mail-type option\\ **WARNING: due to bans from Microsoft we put a limit on the number of mails that can be sent to Hotmail/Outlook/Live addresses. Therefore, please use your RUG email address here!**                                                                                                                                                                                                                                   | +|%%--%%output   |Name of the job output file (default: slurm-<jobid>.out). Use %j if you want to include a job id in the filename.                                                                                                                                                                                                                                                                                                                                                                                               |
-|%%--%%output   |Name of the job output file (default: slurm-<html><jobid></html>.out). Use %j if you want to include a job id in the filename.                                                                                                                                                                                                                                                                                                                                                                                               |+
 |%%--%%partition|Specify in which partition the job has to run                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | |%%--%%partition|Specify in which partition the job has to run                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
  
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 <code> <code>
 #SBATCH --job-name=my_first_slurm_job #SBATCH --job-name=my_first_slurm_job
-#SBATCH --mail-type=BEGIN,END 
-#SBATCH --mail-user=some@user.com 
 #SBATCH --output=job-%j.log #SBATCH --output=job-%j.log
 #SBATCH --partition=short #SBATCH --partition=short
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 module purge module purge
-module load GROMACS/4.6.7-ictce-7.2.4-mt+module load GROMACS/2021.5-foss-2021b
  
-srun mdrun+srun gmx_mpi <arguments>
 </code> </code>
-This script will ask for 2 nodes and 4 tasks per node. The maximum runtime is 2 days and 12 hours. The amount of memory available for the job is almost 4 GiB per node. Once the job is executed, it will first load the module for Gromacs 4.6. To start a parallel (MPI) run of mdrun, we use srun (instead of mpirun) to start all mdrun processes on the allocated nodes.+This script will ask for 2 nodes and 4 tasks per node. The maximum runtime is 2 days and 12 hours. The amount of memory available for the job is almost 4 GiB per node. Once the job is executed, it will first load the module for GROMACS 2021.5 To start a parallel (MPI) run, we use srun (instead of mpirun) to start all GROMACS processes on the allocated nodes.