/!\ '''This web page will no longer be updated.''' Please use this link for [[https://dv-zeuthen.desy.de/services/parallel_computing/|current information]].
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= Usage of the Linux Clusters at DESY Zeuthen =
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== Introduction ==
There are 3 dedicated parallel clusters (blade centers, Miriquid compute nodes) available for running parallel applications, but you can also run parallel MPI jobs in the SGE farm. The documentation in [[https://dv-zeuthen.desy.de/services/batch/|Batch System Usage]] applies there.
For discussions and information regarding the usage of the PAX cluster a mailing list has been introduced: <>. To get subscribed to that list, send an email to <> with the subject: '''subscribe zn-cluster'''
== Hardware ==
The PAX cluster consists of an interactive and a batch part. The interactive part is a blade center with 16 blade servers configured as workgroup servers. You can interactively log into the machines pax80 to pax8f to build and test your programs. Please don't use these machines to run long production code, use the batch system instead.
The batch part consists of three separate partitions that are not interconnected: pax11 and pax10 each consist of 32 compute nodes, connected via a FDR Infiniband network.The older system is pax9, 16 nodes connected by a QDR Infiniband network.
=== Nodes ===
All nodes have two CPUs (sockets).
||Name||CPU||Memory||
||pax9[0-f]||Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz||48G||
||pax10-[00-31]||Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz||64G||
||pax11-[00-31]||Intel(R) Xeon(R) CPU E5-2697A v4 @ 2.60GHz||128G||
== Building Applications ==
Use the 'module' command to first add a compiler implementation and then a version of MPI to your path e.g.:
{{{
module add gnu mvapich2
}}}
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.
||module name ||version ||depends on ||
||gnu ||5.4.0 || ||
||gnu7||7.2.0 || ||
||intel ||18.0.0 || ||
||openmpi ||1.10.6 ||gnu ||
||openmpi ||1.10.7 ||intel ||
||openmpi3||3.0.0||gnu7/intel||
||mvapich2 ||2.2 ||gnu/gnu7/intel ||
||opencoarrays ||1.8.5 || ||
==== Building applications ====
Build your application on any SL7 workgroup server, e.g. the pax8 machines pax80 to pax8f or the machine sl7.
==== Running your application interactively on pax8 ====
To run an MPI program outside the batch system, you must specify a machinefile listing all the machines and the number of cores your application should run on. A typical machine file looks like this:
{{{
pax8a slots=8
pax8b slots=8
pax8c slots=8
pax8d slots=8
}}}
The command line would look like this:
{{{
/opt/ohpc/pub/mpi/openmpi-gnu/1.10.6/bin/mpirun -np 32 -machinefile ./machinefile ./program
}}}
More information on openmpi is in the openmpi FAQ: http://www.open-mpi.org/faq/
==== Building and running programs interactively ====
To use mvapich2, add one of those versions to your path and compile your application with that mpi compiler. Applications built with mvapich2 can use only Infiniband network hardware, so they will work on the pax machines, but not on more than one farm machine or WGS.
The machine file format is different from the one for openmpi, you must list the host name for every core you want to use, e.g. if you want to run four processes, two processes on each of pax89 and pax88:
{{{
pax88
pax89
pax88
pax89
}}}
The preferred way to run a application with mvapich2 is mpiexec, e.g.:
{{{
/usr/lib64/mvapich2-intel/bin/mpiexec -n 4 -machinefile ./machinefile /usr/lib64/mvapich2-intel/bin/mpitests-IMB-MPI1
}}}
== Batch System Access ==
/!\ '''ATTENTION''': The PAX is now based on the SLURM scheduling system.
===== Local Disk Space =====
Each node has a local directory /scratch with 1TB of space. It is cleared automatically at the end of the job.
===== pax10 and pax11 I/O nodes =====
Most of the pax10 and pax11 machines have external 1GB/s Ethernet connections to the storage. To allow faster storage access, four machines each in the pax10 and pax11 partitions are equipped with 10GB/s Ethernet instead. To access them, you'll have to request the 10g feature in Slurm: {{{ --constraint=10g*1}}}. That way, the first process, the one executing the job scripts, will run on one of the machines with faster connectivity.
== SL7 changes ==
As the versions and paths of the MPI implementations have changed, programs are not compatible between SL6 and SL7. You should rebuild your application on SL7, but you could also try singularity.
The 'module' command was replaced by a different, more powerful implementation called lmod. It doesn't list all available module, instead it supports dependent modules, e.g. the MPI implementations build with 'gnu7' are shown after {{{module add gnu7}}}.
==== Running EL6 software using Singularity ====
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
}}}
== AFS Access ==
The application binary must be available to all nodes, that's why it should be placed in an AFS or Lustre directory.
== Monitoring ==
Ganglia provides a web monitoring interface. These pages are only available from the internal network.
[[http://ganglia.zeuthen.desy.de/ganglia/?c=Parallel%20Clusters&m=load_one&r=hour&s=descending&hc=4&mc=2|interactive machines]] [[http://ganglia.zeuthen.desy.de/ganglia/?c=Gridengine%20PAX%20Farm&m=load_one&r=hour&s=descending&hc=4&mc=2|parallel batch machines]]
== Further documentation ==
[[http://www-zeuthen.desy.de/technisches_seminar/texte/waschk_20100427.pdf|Paralleles Rechnen in Zeuthen - die neuen Cluster]] , 04/27/10, technical seminar
[[http://www-zeuthen.desy.de/technisches_seminar/texte/Technisches_Seminar_Waschk.pdf|HPC-Clusters at DESY Zeuthen]] , 11/22/06, technical seminar