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Both sides previous revision Previous revision Next revision | Previous revision Next revisionBoth sides next revision | ||
doku:slurm [2023/03/14 12:34] – [The job submission script] goldenberg | doku:slurm [2024/02/07 10:55] – [The job submission script] katrin | ||
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==== Node allocation policy ==== | ==== Node allocation policy ==== | ||
- | On VSC-4 there are a set of nodes which accept jobs that do not require entire nodes (anythong | + | On VSC-4 & VSC-5 there is a set of nodes that accept jobs that do not require entire |
- | On VSC-5 that feature | + | |
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It is recommended to write the job script using a [[doku: | It is recommended to write the job script using a [[doku: | ||
- | 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 '' | Assume a submission script '' | ||
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</ | </ | ||
* **-J** | * **-J** | ||
- | * **-N** | + | * **-N** |
* **-n, --ntasks=< | * **-n, --ntasks=< | ||
* **--ntasks-per-node** | * **--ntasks-per-node** | ||
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< | < | ||
- | [username@l31 ~]$ sbatch check.slrm | + | [username@l42 ~]$ sbatch check.slrm |
- | [username@l31 ~]$ squeue -u `whoami` | + | [username@l42 ~]$ squeue -u `whoami` |
- | [username@l31 ~]$ scancel | + | [username@l42 ~]$ scancel |
# is obtained from the previous command | # is obtained from the previous command | ||
</ | </ | ||
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- | |||
- | ====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. | ||
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#SBATCH -J chk | #SBATCH -J chk | ||
#SBATCH -N 4 | #SBATCH -N 4 | ||
- | #SBATCH --ntasks-per-node=16 | + | #SBATCH --ntasks-per-node=48 |
#SBATCH --ntasks-per-core=1 | #SBATCH --ntasks-per-core=1 | ||
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scontrol show hostnames $SLURM_NODELIST | scontrol show hostnames $SLURM_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 | 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 | wait | ||
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#SBATCH -J par # job name | #SBATCH -J par # job name | ||
#SBATCH -N 2 # number of nodes=2 | #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 --ntasks-per-core=1 | ||
#SBATCH --threads-per-core=1 | #SBATCH --threads-per-core=1 | ||
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rm machines_tmp | rm machines_tmp | ||
- | tasks_per_node=16 # change number accordingly | + | tasks_per_node=48 # change number accordingly |
nodes=2 | nodes=2 | ||
for ((line=1; line< | for ((line=1; line< | ||
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- continue at 2. for further dependent jobs | - 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: | ||
- | |||
- | < | ||
- | slic | ||
- | </ | ||
- | |||
- | Within the job script add the flags as shown with ' | ||
- | |||
- | < | ||
- | #SBATCH -L matlab@vsc, | ||
- | </ | ||
===== Prolog Error Codes ===== | ===== Prolog Error Codes ===== |