Slurm Installation for Pax Cluster

Slurm is currently being tested as scheduler for the pax11 machines, named pax11-[00-31].

The client software is currently available on the machine sl7.

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:

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:

Time format

The runtime of a job is given as minutes, hours, minutes and seconds (HH:MM:SS) 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.

EL7 changes

The new system is based on EL7, binaries built for EL6 will not run, they must be recompiled and linked to the new MPI libraries. We install the MPI software built by the OpenHPC project, this includes both mvapich2 and openmpi for the Intel and GNU compilers. If you need additional software provided by the OpenHPC project that wasn't installed yet, please request it.

Running EL6 software

It is possible to run software built on EL6 in a Singularity container. This works with mvapich2 binaries by calling singularity in the batch script like this:

mpiexec singularity exec /project/singularity/images/SL6.img yourbinary

However, Mvapich2 2.2 isn't optimized yet for Singularity, so this is slower than running native programs.

For Openmpi, singularity is supported in Openmpi >= 2.1, that's why you'll have to rebuild your program with openmpi3 as installed in the SL6 singularity container:

singularity exec /project/singularity/images/SL6.img /usr/lib64/openmpi-3.0/bin/mpicc yourprog.c -o yourprog.sl6

and in the job script:

module add gnu7 openmpi3 prun
prun singularity exec -B /scratch /project/singularity/images/SL6.img yourprog.sl6

Available Software

OpenHPC provides the module command from the lmod project. It supports more features then the old environment-modules, including dependent modules, that are shown only after loading the prequisites, e.g. for openmpi you'll have to load the intel module first.

Local Disk Space

Each node has a local directory /scratch with 1TB of space. It is cleared automatically at the end of the job.

Known Issues

1. Openmpi3 has a bug that makes the program hang in certain situations: https://github.com/open-mpi/ompi/issues/3251