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--- doku:slurm [2023/03/14 12:29] – [Node allocation policy] goldenberg
+++ doku:slurm [2024/02/07 10:55] (current) – [The job submission script] katrin
@@ Line 41: / Line 41: @@
 ==== Node allocation policy ====
-On VSC-4 there are a set of nodes which accept jobs that do not require entire nodes (anythong from 1 core to less than a full node). These nodes are set up to accomodate different jobs from different users until they are full. They are automatically used for such types of jobs. All other nodes are assigned completely to a job.
+On VSC-4 & VSC-5 there is a set of nodes that accept jobs that do not require entire exclusive nodes (anything from 1 core to less than a full node). These nodes are set up to accommodate different jobs from different users until they are full. They are automatically used for such types of jobs. All other nodes are assigned completely (and exclusively) to a job whenever the '-N' argument is used.
-On VSC-5 that feature is not yet active, so only complete nodes are assigned to jobs.
@@ Line 55: / Line 55: @@
 ==== The job submission script====
-It is recommended to write the job script using a [[doku:win2vsc&#the_job_filetext_editors_on_the_cluster|text editor]] on the VSC //Linux// cluster.
+It is recommended to write the job script using a [[doku:win2vsc&#the_job_filetext_editors_on_the_cluster|text editor]] on the VSC //Linux// cluster or on any Linux/Mac system.
-Editors in //Windows// may add additional invisible characters to the job file which render it unreadable and, thus, it is not executed.
+Editors in //Windows// may add additional invisible characters to the job file which render it unreadable and, thus, it cannot be not executed.
 Assume a submission script ''check.slrm''
@@ Line 64: / Line 64: @@
 #SBATCH -J chk
 #SBATCH -N 2
-#SBATCH --ntasks-per-node=16
+#SBATCH --ntasks-per-node=48
 #SBATCH --ntasks-per-core=1
 #SBATCH --mail-type=BEGIN    # first have to state the type of event to occur
@@ Line 71: / Line 71: @@
 # when srun is used, you need to set:
-<srun -l -N2 -n32 a.out >
+<srun -l -N2 -n96 a.out >
 # or
-<mpirun -np 32 a.out>
+<mpirun -np 96 a.out>
 </code>
   * **-J**     job name,\\
-  * **-N**     number of nodes requested (16 cores per node available)\\
+  * **-N**     number of nodes requested\\
   * **-n, --ntasks=<number>** specifies the number of tasks to run,
   * **--ntasks-per-node**     number of processes run in parallel on a single node \\
@@ Line 85: / Line 85: @@
   * **--mail-user** sends an email to this address
-In order to send the job to specific queues, see [[doku:vsc3_queue|Queue/Partition setup on VSC-3]].
+In order to send the job to specific queues, see [[doku:vsc4_queue|Queue | Partition setup on VSC-4]] or [[doku:vsc5_queue|Queue | Partition setup on VSC-5]].
 ====Job submission====
 <code>
-[username@l31 ~]$ sbatch check.slrm    # to submit the job
+[username@l42 ~]$ sbatch check.slrm    # to submit the job
-[username@l31 ~]$ squeue -u `whoami`   # to check the status  of own jobs
+[username@l42 ~]$ squeue -u `whoami`   # to check the status  of own jobs
-[username@l31 ~]$ scancel  JOBID       # for premature removal, where JOBID
+[username@l42 ~]$ scancel  JOBID       # for premature removal, where JOBID
                                        # is obtained from the previous command
 </code>
@@ Line 98: / Line 98: @@
-====A word on srun and mpirun:====
-Currently (27th March 2015), **srun** only works when the application uses **intel mpi** and is compiled with the **intel compiler**. We will provide compatible versions of MVAPICH2 and OpenMPI in the near future.
-At the moment, it is recommended to use **mpirun** in case of MVAPICH2 and OpenMPI.
@@ Line 157: / Line 153: @@
 #SBATCH -J chk
 #SBATCH -N 4
-#SBATCH --ntasks-per-node=16
+#SBATCH --ntasks-per-node=48
 #SBATCH --ntasks-per-core=1
@@ Line 163: / Line 159: @@
 scontrol show hostnames $SLURM_NODELIST  > ./nodelist
-srun -l -N2 -r0 -n32 job1.scrpt &
+srun -l -N2 -r0 -n96 job1.scrpt &
-srun -l -N2 -r2 -n32 job2.scrpt &
+srun -l -N2 -r2 -n96 job2.scrpt &
 wait
-srun -l -N2 -r2 -n32 job3.scrpt &
+srun -l -N2 -r2 -n96 job3.scrpt &
-srun -l -N2 -r0 -n32 job4.scrpt &
+srun -l -N2 -r0 -n96 job4.scrpt &
 wait
@@ Line 276: / Line 272: @@
 #SBATCH -J par                      # job name
 #SBATCH -N 2                        # number of nodes=2
-#SBATCH --ntasks-per-node=16        # uses all cpus of one node
+#SBATCH --ntasks-per-node=48        # uses all cpus of one node
 #SBATCH --ntasks-per-core=1
 #SBATCH --threads-per-core=1
@@ Line 286: / Line 282: @@
 rm machines_tmp
-tasks_per_node=16         # change number accordingly
+tasks_per_node=48         # change number accordingly
 nodes=2                   # change number accordingly
 for ((line=1; line<=nodes; line++))
@@ Line 338: / Line 334: @@
   - continue at 2. for further dependent jobs
-===== Licenses =====
-Software, that uses a license server, has to be specified upon job submission. A list of all available licensed software for your user can be shown by using the command:
-<code>
-slic
-</code>
-Within the job script add the flags as shown with 'slic', e.g. for using both Matlab and Mathematica:
-<code>
-#SBATCH -L matlab@vsc,mathematica@vsc
-</code>
 ===== Prolog Error Codes =====