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| Slurm was configured to always schedule complete nodes to each job. The pax11 machines have hyperthreading enabled, each hardware thread is seen as a CPU core by Slurm, so by default, on a 32 core machine with hyperthreading, 64 MPI processes are assigned. To prevent that, use the option {{{-c 2}}} for sbatch, salloc or slurm. | Slurm was configured to always schedule complete nodes to each job. The pax11 machines have hyperthreading enabled, each hardware thread is seen as a CPU core by Slurm, so by default, on a 32 core machine with hyperthreading, 64 MPI processes are assigned. To prevent that, use the option {{{-c 2}}} for sbatch, salloc or srun. |
Slurm Installation for Pax Cluster
Slurm is currently being tested as scheduler for the pax11 machines, named pax11-[00-31].
Kerberos Integration
You need to acquire an addressless Kerberos ticket for Slurm to work. This is the default on supported DESY machines. On self-maintained machines like notebooks, simply set noaddresses=true in the file /etc/krb5.conf. To check if your ticket is addressless, call klist -v (Heimdal klist only).
Slurm Commands
The most important commands:
Information about the cluster |
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Show current job list |
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Parallel command execution |
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Submit a batch job |
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Reserve ressources for interactive commands |
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Abort a job |
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Show accounting information |
Allocation
Slurm was configured to always schedule complete nodes to each job. The pax11 machines have hyperthreading enabled, each hardware thread is seen as a CPU core by Slurm, so by default, on a 32 core machine with hyperthreading, 64 MPI processes are assigned. To prevent that, use the option -c 2 for sbatch, salloc or srun.
Parallel Execution
Slurm has integrated execution support for parallel programs, replacing mpirun. However, it depends on the used MPI library if you can use slurm's srun command or mpirun. To start a program based on mvapich2, run it with a command like srun --mpi=pmi2 -n 4 -N 2 program for 4 processes on two nodes. For openmpi, use mpirun instead.
MPI Support
Before running MPI programs, the LD_LIBRARY_PATH variable must first be set, this is done by loading the right environment module, e.g. module add intel openmpi.
Job scripts
Parameters to slurm can be set on the sbatch command line or starting with a #SBATCH in the script. The most important parameters are:
-J |
job name |
--get-user-env |
copy environment variables |
-n |
number of cores |
-N |
number of nodes |
-t |
run time of the job, default is 30 minutes |
-A |
account, default the same as UNIX group |
-p |
partition of the cluster |
--mail-type |
configure email notifications, e.g. use --mail-type=ALL |
Time format
The runtime of a job is given as minutes, hours and minutes (HH:MM) or days and hours (DD-HH). The maximum run time was set to 48 hours.
Examples
An example job script is in slurm-mpi.job
Accounting
The jobs and their resources usage is stored in a database that is used for the fair share part of the scheduler. You can view your account's jobs with the command sacct. With no parameters,only today's jobs are shown, to view all jobs since May 1st, use the command sacct -S 2014-05-01 . To view jobs from other accounts as well, use the --allusers option.