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Usage of the Linux Clusters at DESY Zeuthen
- Usage of the Linux Clusters at DESY Zeuthen
There are 9 dedicated parallel clusters (blade centers) available for running parallel applications, but you can also run parallel MPI jobs in the SGE farm. The documentation in Batch_System_Usage applies there.
For discussions and information regarding the usage of the PAX cluster a mailing list has been introduced: <zn-cluster AT desy DOT de>. To get subscribed to that list, send an email to <sympa AT desy DOT de> with the subject: subscribe zn-cluster
The PAX cluster consists of an interactive and a batch part. The interactive part is a blade center with 14 blade servers configured as workgroup servers. You can interactively log into the machines pax80 to pax8d 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 8 blade centers with 16 nodes each, connected via a QDR infiniband network.
All cluster machines have been migrated to SL6. On SL6, use the 'module' command to add one of the MPI implementations to your path.
SL6.6 ships with openmpi 1.8.1. The paths to the runtime have changed from SL5. Also, you must rebuild your application for the new ABI. The paths to the openmpi versions are:
/usr/lib/openmpi/bin /usr/lib64/openmpi/bin /usr/lib64/openmpi-intel/bin
Instead of 'ini', please use the 'module' command to add a MPI compiler to your path, e.g. module add openmpi-x86_64-intel .
Build your application on any SL6 workgroup server, e.g. the pax8 machines pax80 to pax8e or the machine sl6.
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:
/usr/lib64/openmpi/bin/mpirun -np 32 -machinefile ./machinefile ./program
More information on openmpi is in the openmpi FAQ: http://www.open-mpi.org/faq/
Two additional mpi implementations are installed on all pax machines, one GCC and one Intel compiler version.
The paths have changed from SL5 to
Building and running programs interactively
To use mvapich2, add one of those versions to your path and compile your application with that mpi compiler. To run it outside the batch system, follow these instructions: http://mvapich.cse.ohio-state.edu/overview/mvapich2/
Applications built with mvapich2 will only run on machines with Infiniband hardware, so they will work on the pax machines but not on desktops, workgroup servers or the farm.
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.
Batch System Access
ATTENTION: The PAX cluster was split off the normal Zeuthen batch. To access the PAX batch system you will need to call ini pax.
Alternatively source a script:
- zsh users:
[oreade38] ~ % . /usr/gridengine/pax/common/settings.sh
- tcsh users:
[oreade38] ~ $ source /usr/gridengine/pax/common/settings.cshSwitching back to use the standard farm works similarly:
- zsh users:
[oreade38] ~ % . /usr/gridengine/default/common/settings.sh
- tcsh users:
[oreade38] ~ $ source /usr/gridengine/default/common/settings.csh
Please make sure that your Gridengine certificates are in place:
[oreade38] ~ % ls -l $HOME/.sge/port537 lrwxr-xr-x. 1 ahaupt sysprog 11 Aug 20 09:52 /afs/ -> sge_qmaster [oreade38] ~ % ls -l $HOME/.sge/cert.pem -rw-------. 1 ahaupt sysprog 1464 Aug 20 09:52 /afs/ [oreade38] ~ % ls -l $HOME/.sge/key.pem -rw-------. 1 ahaupt sysprog 887 Aug 20 09:52 /afs/
A job script designated for a parallel job needs to specify the parallel environment and the number of required CPUs. The parameter looks like this for up to 8 slots for 8 MPI processes:
#$ -pe pax 8
Be aware, that the allocation rule for the pax parallel environment may distribute a the processes on up to 8 nodes. To force a node-based allocation, use one of the numbered PEs, e.g. like this:
#$ -pe pax5 64
or for 16 processes per node on the latest hardware:
#$ -pe pax9 256
Bugs in the batch system implementation made using wild card selection of PEs impossible, be aware that -pe pax? is rewritten as -pe pax automatically.
Be sure to call the right mpirun version for your architecture. If you application was compiled for 64 bit on SL6, use
/usr/lib64/openmpi/bin/mpirun -np $NSLOTS yourapp
The MPI runtime will automatically select the right network type.
You can request up to 1024 slots, as a blade center contains 128 CPU cores and the batch system contains 8 blade centers:
#$ -pe pax 128 /usr/lib64/openmpi/bin/mpirun -np $NSLOTS yourapp
Finally, here's a list of common pitfalls when using the pax batch system:
Please be aware that all requested resources (via the -l qsub switch) are meant per job slot. As the pax nodes only provide 24GB (8 core systems -> 3GB per job slot), you cannot request more than 3500 MB h_vmem in your job scripts. Otherwise your job won't start! Please make sure your MPI processes don't use more than 3GB per slot, the memory overcommittment should be used for mpirun overhead for large jobs (>=512 slots) only.
If your MPI application relies on LD_LIBRARY_PATH to load its shared libraries or modules, this will fail on remote notes, as the batch system will remove this variable from the environment. In that case you'll have to wrap yourapp in a shell script that sets up the environment and calls your binary application.
Hybrid Openmp/MPI jobs
Jobs that use both Openmp threads and MPI for communication must not run more threads than the number of physical cores. To run 4 threads and 2 MPI processes on two nodes, use this command line:
#$ -pe pax 4 #$ -l h_vmem=12G export OMP_NUM_THREADS=4 /usr/lib64/openmpi/bin/mpirun -np 8 -machinefile pax8e-f -map-by socket:PE=2 mpi-program
If your Openmp program was built with the Intel compiler, you must run a wrapper script instead of the MPI binary which sets the LD_LIBRARY_PATH variable to the Intel compiler home, you cannot do that in the job script: export LD_LIBRARY_PATH=/opt/intel/2015/lib/intel64:$LD_LIBRARY_PATH
With mvapich2 1.7, there is working integration into the SGE batch system. Just use a command like this:
#$ -pe pax 128 /usr/lib64/mvapich2/bin/mpiexec -n $NSLOTS yourapp
As the versions and paths of the MPI implementations have changed, programs are not compatible between SL5 and SL6. You must rebuild your application on SL6. You'll also have to rebuild your application on SL6.6, as it contains another incompatible version of mvapich2.
The 'ini' command is no longer in use for selecting MPI versions, it was replaced by the very similar 'module'. The command 'module avail' lists the installed modules. To load Open-MPI for the Intel compiler, use the command 'module add openmpi-x86_64-intel'.
The application binary must be available to all nodes, that's why it should be placed in an AFS directory.
Both ATLAS and GotoBLAS are available.
- ATLAS is in /opt/products/atlas
- libgoto is in /usr/lib or /usr/lib64 respectively.
Ganglia provides a web monitoring interface. These pages are only available from the internal network.
Paralleles Rechnen in Zeuthen - die neuen Cluster , 04/27/10, technical seminar
HPC-Clusters at DESY Zeuthen , 11/22/06, technical seminar