Usage of the Linux Clusters at DESY Zeuthen

1. Introduction
2. Hardware
     2.1. Nodes
3. Building Applications
     3.1 Openmpi
     3.2 Mvapich2
4. Batch System Access
     4.1 pax10 I/O nodes
     4.2 Hybrid Openmp/MPI jobs
     4.3 Mvapich2
5. SL6 changes
6. AFS Access
7. Monitoring
8. Further documentation

1. Introduction

There are 8 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 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

2. 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 new batch system (pax10) consists of 32 compute nodes, connected via a FDR infiniband network.The old batch part consists of 6 blade centers (pax3 to pax7, pax9) with 16 nodes each, connected via a QDR infiniband network.

2.1. Nodes

All nodes have two CPUs (sockets).

Name

CPU

Memory

pax[30-7f]

Intel(R) Xeon(R) CPU X5560 @ 2.80GHz

24G

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

3. Building Applications

Use the 'module' command to add one of the MPI implementations to your path:

module name

version

compiler version

origin

openmpi-1.8-x86_64

1.8.1

gcc 4.4.7

Red Hat build

openmpi-1.10-x86_64

1.10.2

gcc 4.4.7

Red Hat build

openmpi-x86_64-intel

1.8.1

icc 15.0.1

self-maintained

openmpi-1.10-x86_64-intel

1.10.2

icc 17.0.3

self-maintained

mvapich2-x86_64

2.0rc1

gcc 4.4.7

Red Hat build

mvapich2-x86_64-intel

2.0rc1

icc 17.0.3

self-maintained

3.1 Openmpi

We ship with several versions that are not binary compatible. Be sure to use the right runtime. The paths are:

/usr/lib64/openmpi/bin
/usr/lib64/openmpi-1.10/bin
/usr/lib64/openmpi-1.10-intel/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


Building applications
Build your application on any SL6 workgroup server, e.g. the pax8 machines pax80 to pax8f 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.

3.2 Mvapich2

Two additional MPI implementations are installed on all pax machines, one GCC and one Intel compiler version.
The paths are:

/usr/lib64/mvapich2/bin
/usr/lib64/mvapich2-intel/bin


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


4. 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.csh


Switching 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/port6443
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 pax10 512


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


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 3 GB h_rss 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.


4.1 pax10 I/O nodes

Most of the pax10 machines have external 1GB/s Ethernet connections to the storage. To allow faster storage access, four machines are equipped with 10GB/s Ethernet instead. To access them, specify #$ -masterq pax10-master.q . That way, the first process, the one executing the job scripts, will run on one of the machines with faster connectivity.

4.2 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_rss=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

4.3 Mvapich2

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 -env MV2_USE_RDMA_CM 1 -n $NSLOTS yourapp


5. SL6 changes

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'.

6. AFS Access

The application binary must be available to all nodes, that's why it should be placed in an AFS or Lustre directory.

7. Monitoring

Ganglia provides a web monitoring interface. These pages are only available from the internal network.

 

8. Further documentation