Differences between revisions 89 and 160 (spanning 71 versions)
⇤ ← Revision 89 as of 2016-09-01 13:00:44 →
Size: 9269
Editor: GötzWaschk
Comment: compilers and MPI runtimes
← Revision 160 as of 2023-04-28 09:56:09 → ⇥
Size: 11571
Editor: GötzWaschk
Comment: readd documentation for pax11
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
/!\ '''This web page will no longer be updated.''' Please use this link for [[https://dv-zeuthen.desy.de/services/parallel_computing/|current information]].
----
<<BR>>
Line 5: Line 8:
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. There are two dedicated parallel clusters available for running parallel applications, but you can also run parallel MPI jobs in the HTCondor farm. The documentation in [[https://dv-zeuthen.desy.de/services/batch/|Batch System Usage]] applies there.
Line 10: Line 13:
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 system consists of two partition: pax12 (rome) has 16 nodes and HDR Infiniband. pax11 (broadwell) consists of 30 compute nodes, connected via a FDR Infiniband network.
=== Nodes ===
The AMD machines (pax12) have one socket, the Intel machines (pax11) have two.
||Name||CPU||Code Name||Cores||Memory||
||pax12-[00-15]||AMD EPYC 7702P 64-Core Processor @ 2GHz||Rome||64||256G||
||pax11-[00-31]||Intel(R) Xeon(R) CPU E5-2697A v4 @ 2.60GHz||Broadwell||16||128G||
Line 12: Line 20:
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. == Software Environment ==
The pax machines have a software environment that is slightly different from the normal installation, it includes the OpenHPC software stack and a different version of the {{{module}}} command. To build on any machine in the right environment, run the {{{/project/apptainer/images/pax.img}}} image. You can submit your jobs if you run the apptainer container on a EL7 WGS like this:
{{{
apptainer run -B /etc/passwd /project/apptainer/images/pax.img
}}}
Line 15: Line 27:
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 16.0.3||self-maintained||
||mvapich2-x86_64||2.0rc1||gcc 4.4.7||Red Hat build||
||mvapich2-x86_64-intel||2.0rc1||icc 16.0.3||self-maintained||		 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||7.3.0 || ||
||gnu8||8.3.0 || ||
||gnu9||9.3.0 || ||
||gnu12||12.2.0|| ||
||intel ||2021.4|| ||
||hdf5||1.10.1||gnu||
||openmpi ||1.10.7 ||gnu/intel ||
||openmpi3||3.1.0||gnu7||
||openmpi3||3.1.4||gnu8/intel||
||openmpi4||4.0.5||gnu8/gnu9/gnu12/intel||
||mvapich2 ||2.2 ||gnu/gnu7 ||
||mvapich2 || 2.3.2||gnu8/intel||
||impi||2021.4||gnu/gnu8/intel||
||opencoarrays ||1.8.11 || ||
||opencoarrays||2.3.1||gnu7 openmpi3||
||opencoarrays||2.8.0||gnu8 openmpi3||
Line 24: Line 51:
=== Interactive tests ===
You can run interactive jobs in Slurm after allocating nodes with salloc, e.g.: {{{salloc -p rome -N 2 -c 2}}}. To get an interactive shell on the allocated machines, use the command {{{srun --pty bash}}}.
Line 25: Line 54:
=== 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 ====		 ==== OpenMPI ====
Line 51: Line 66:
/usr/lib64/openmpi/bin/mpirun -np 32 -machinefile ./machinefile ./program /opt/ohpc/pub/mpi/openmpi-gnu/1.10.7/bin/mpirun -np 32 -machinefile ./machinefile ./program
Line 54: Line 69:
=== Mvapich2 ===
Two additional MPI implementations are installed on all pax machines, one GCC and one Intel compiler version.
Line 57: Line 70:
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. 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.		 ==== Mvapich2 ====
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.
Line 76: Line 81:
The preferred way to run a application with mvapich2 is mpiexec. The preferred way to run a application with mvapich2 is mpiexec, e.g.:
{{{
/opt/ohpc/pub/mpi/mvapich2-intel/2.2/bin/mpiexec -n 4 -machinefile ./machinefile /opt/ohpc/pub/libs/intel/mvapich2/imb/2018.1/bin/IMB-MPI1
}}}

==== Intel MPI ====
To use Intel MPI, add a compiler module followed by impi. Use the compiler wrappers like 'mpicc' and 'mpif90' for GNU or 'mpiicc' and 'mpiifort' for the Intel compiler. To run the resulting application, set the environment variable like this:
{{{
export FI_PROVIDER=verbs
}}}
In a Slurm job, please use the prun wrapper to start your application.
Line 79: Line 94:
/!\ '''ATTENTION''': The PAX cluster was split off the normal Zeuthen batch. To access the PAX batch system you will need to call `ini pax`. /!\ '''ATTENTION''': The PAX is now based on the SLURM scheduling system.
=== Slurm Commands ===
The most important commands:
||[[http://slurm.schedmd.com/sinfo.html|sinfo]] ||Information about the cluster ||
||[[http://slurm.schedmd.com/squeue.html|squeue]] ||Show current job list ||
||[[http://slurm.schedmd.com/srun.html|srun]] ||Parallel command execution ||
||[[http://slurm.schedmd.com/sbatch.html|sbatch]] ||Submit a batch job ||
||[[http://slurm.schedmd.com/salloc.html|salloc]] ||Reserve ressources for interactive commands ||
||[[http://slurm.schedmd.com/scancel.html|scancel]] ||Abort a job ||
||[[https://slurm.schedmd.com/sview.html|sview]]||Graphical user interface to view and modify Slurm state||
||[[http://slurm.schedmd.com/sacct.html|sacct]] ||Show accounting information ||
Line 81: Line 106:
Alternatively source a script: === Allocation ===
Slurm was configured to always schedule complete nodes to each job. The pax 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. To work around slight differences in needed options, use prun instead of srun for starting MPI application. You'll have to load the prun module first.
Line 83: Line 111:
 * zsh users:
 {{{
[oreade38] ~ % . /usr/gridengine/pax/common/settings.sh		 === 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 ||

Be careful with {{{--get-user-env}}}, it will also copy loaded modules to the job.

==== 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 [[attachment: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.


=== Local Disk Space ===
Each node has a local directory /scratch with up to 770GB of space. It is cleared automatically at the end of the job.

=== I/O nodes ===
Most of the pax11 machines have external 1GB/s Ethernet connections to the storage. To allow faster storage access, four machines in the pax11 partition 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. All pax12 machines have 10GB/s Ethernet as well.

=== Partitions and backfilling ===
The cluster consists of two partitions: rome has the faster machines and is the default, broadwell has the older nodes. Jobs can run on only one type of node. The special partition backfill is used for filling up otherwise empty nodes. Jobs running there are automatically terminated by slurm if another job on the main partition needs the nodes.

==== Running EL6 software using Singularity ====
It is possible to run software built on EL6 in a [[Apptainer]] container. This works with mvapich2 binaries by calling Apptainer in the batch script like this:
{{{
mpiexec apptainer exec /project/singularity/images/SL6.img yourbinary
Line 87: Line 151:
 * tcsh users:
 {{{
[oreade38] ~ $ source /usr/gridengine/pax/common/settings.csh		 However, Mvapich2 2.2 isn't optimized yet for Apptainer, 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
Line 91: Line 158:
 Switching back to use the standard farm works similarly:
 * zsh users:
 {{{
[oreade38] ~ % . /usr/gridengine/default/common/settings.sh		 and in the job script:
{{{
module add gnu7 openmpi3 prun
prun singularity exec -B /scratch /project/singularity/images/SL6.img yourprog.sl6
Line 96: Line 163:
 * 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
}}}
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 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.

==== 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}}}
=== 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
}}}
== 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'.		 == Additional Software ==
The software installation is based on the [[http://openhpc.community|OpenHPC project]]. We provide only a subset of the available software. If you need any of the other [[https://github.com/openhpc/ohpc/wiki/Component-List-v1.3.9|available components]], send a request to zn-cluster@desy.de
Line 173: Line 167:
The application binary must be available to all nodes, that's why it should be placed in an AFS directory.

== BLAS library ==
Both ATLAS and GotoBLAS are available.

 * ATLAS is in /opt/products/atlas

 * libgoto is in /usr/lib or /usr/lib64 respectively.		 The application binary must be available to all nodes, that's why it should be placed in an AFS or Lustre directory.
Line 183: Line 170:
Ganglia provides a web monitoring interface. These pages are only available from the internal network. Ganglia provides a web monitoring interface. These page is only available from the internal network.
Line 185: Line 172:
[[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]] [[http://ganglia.zeuthen.desy.de/ganglia/?c=Slurm%20PAX%20farm&m=load_one&r=hour&s=descending&hc=4&mc=2|Parallel Batch Machines]]
Line 187: Line 174:
== Known Issues ==
 1. Openmpi3 has a bug that makes the program hang in certain situations: https://www.mail-archive.com/users@lists.open-mpi.org//msg31839.html Use openmpi instead.
 1. 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).
 1. The command {{{sbcast}}} cannot be used to copy a file to /scratch, as that is a bind mounted directory. Use /batch/job.${SLURM_JOB_ID}.0/scratch as target.
 1. The {{{module}}} command might be unavailable for tcsh login shell users. As workaround, they can run {{{bash -l}}} and use the {{{--get-user-env}}} option in the job.
 1. There are some compatibility problems between third-party module files (e.g. Intel 2021) and the module command.
 1. In the pax apptainer image, `squeue` shows all users as ''nobody''. To work around, run `apptainer run -B /etc/passwd /project/apptainer/images/pax.img`

/!\ This web page will no longer be updated. Please use this link for current information.


Usage of the Linux Clusters at DESY Zeuthen

Contents

  1. Usage of the Linux Clusters at DESY Zeuthen
    1. Introduction
    2. Hardware
      1. Nodes
    3. Software Environment
    4. Building Applications
      1. Interactive tests
        1. OpenMPI
        2. Mvapich2
        3. Intel MPI
    5. Batch System Access
      1. Slurm Commands
      2. Allocation
      3. Parallel Execution
      4. MPI Support
      5. Job scripts
        1. Time format
        2. Examples
      6. Accounting
      7. Local Disk Space
      8. I/O nodes
      9. Partitions and backfilling
        1. Running EL6 software using Singularity
    6. Additional Software
    7. AFS Access
    8. Monitoring
    9. Known Issues
    10. Further documentation

Introduction

There are two dedicated parallel clusters available for running parallel applications, but you can also run parallel MPI jobs in the HTCondor 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

Hardware

The batch system consists of two partition: pax12 (rome) has 16 nodes and HDR Infiniband. pax11 (broadwell) consists of 30 compute nodes, connected via a FDR Infiniband network.

Nodes

The AMD machines (pax12) have one socket, the Intel machines (pax11) have two.

Name

CPU

Code Name

Cores

Memory

pax12-[00-15]

AMD EPYC 7702P 64-Core Processor @ 2GHz

Rome

64

256G

pax11-[00-31]

Intel(R) Xeon(R) CPU E5-2697A v4 @ 2.60GHz

Broadwell

16

128G

Software Environment

The pax machines have a software environment that is slightly different from the normal installation, it includes the OpenHPC software stack and a different version of the module command. To build on any machine in the right environment, run the /project/apptainer/images/pax.img image. You can submit your jobs if you run the apptainer container on a EL7 WGS like this: 

apptainer run -B /etc/passwd /project/apptainer/images/pax.img

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

7.3.0

gnu8

8.3.0

gnu9

9.3.0

gnu12

12.2.0

intel

2021.4

hdf5

1.10.1

gnu

openmpi

1.10.7

gnu/intel

openmpi3

3.1.0

gnu7

openmpi3

3.1.4

gnu8/intel

openmpi4

4.0.5

gnu8/gnu9/gnu12/intel

mvapich2

2.2

gnu/gnu7

mvapich2

2.3.2

gnu8/intel

impi

2021.4

gnu/gnu8/intel

opencoarrays

1.8.11

opencoarrays

2.3.1

gnu7 openmpi3

opencoarrays

2.8.0

gnu8 openmpi3

Interactive tests

You can run interactive jobs in Slurm after allocating nodes with salloc, e.g.: salloc -p rome -N 2 -c 2. To get an interactive shell on the allocated machines, use the command srun --pty bash.

OpenMPI

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/1.10.7/bin/mpirun -np 32 -machinefile ./machinefile  ./program

More information on openmpi is in the openmpi FAQ: http://www.open-mpi.org/faq/

Mvapich2

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.: 

/opt/ohpc/pub/mpi/mvapich2-intel/2.2/bin/mpiexec -n 4 -machinefile ./machinefile /opt/ohpc/pub/libs/intel/mvapich2/imb/2018.1/bin/IMB-MPI1

Intel MPI

To use Intel MPI, add a compiler module followed by impi. Use the compiler wrappers like 'mpicc' and 'mpif90' for GNU or 'mpiicc' and 'mpiifort' for the Intel compiler. To run the resulting application, set the environment variable like this: 

export FI_PROVIDER=verbs

In a Slurm job, please use the prun wrapper to start your application.

Batch System Access

/!\ ATTENTION: The PAX is now based on the SLURM scheduling system.

Slurm Commands

The most important commands:

sinfo

Information about the cluster

squeue

Show current job list

srun

Parallel command execution

sbatch

Submit a batch job

salloc

Reserve ressources for interactive commands

scancel

Abort a job

sview

Graphical user interface to view and modify Slurm state

sacct

Show accounting information

Allocation

Slurm was configured to always schedule complete nodes to each job. The pax 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. To work around slight differences in needed options, use prun instead of srun for starting MPI application. You'll have to load the prun module first.

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

Be careful with --get-user-env, it will also copy loaded modules to the job.

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.

Local Disk Space

Each node has a local directory /scratch with up to 770GB of space. It is cleared automatically at the end of the job.

I/O nodes

Most of the pax11 machines have external 1GB/s Ethernet connections to the storage. To allow faster storage access, four machines in the pax11 partition 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. All pax12 machines have 10GB/s Ethernet as well.

Partitions and backfilling

The cluster consists of two partitions: rome has the faster machines and is the default, broadwell has the older nodes. Jobs can run on only one type of node. The special partition backfill is used for filling up otherwise empty nodes. Jobs running there are automatically terminated by slurm if another job on the main partition needs the nodes.

Running EL6 software using Singularity

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

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

However, Mvapich2 2.2 isn't optimized yet for Apptainer, 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

Additional Software

The software installation is based on the OpenHPC project. We provide only a subset of the available software. If you need any of the other available components, send a request to zn-cluster@desy.de

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 page is only available from the internal network.

Parallel Batch Machines

Known Issues

  1. Openmpi3 has a bug that makes the program hang in certain situations: https://www.mail-archive.com/users@lists.open-mpi.org//msg31839.html Use openmpi instead.

  2. 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).

  3. The command sbcast cannot be used to copy a file to /scratch, as that is a bind mounted directory. Use /batch/job.${SLURM_JOB_ID}.0/scratch as target.

  4. The module command might be unavailable for tcsh login shell users. As workaround, they can run bash -l and use the --get-user-env option in the job.

  5. There are some compatibility problems between third-party module files (e.g. Intel 2021) and the module command.

  6. In the pax apptainer image, squeue shows all users as nobody. To work around, run apptainer run -B /etc/passwd /project/apptainer/images/pax.img

Further documentation

Paralleles Rechnen in Zeuthen - die neuen Cluster , 04/27/10, technical seminar

HPC-Clusters at DESY Zeuthen , 11/22/06, technical seminar

Cluster (last edited 2023-04-28 09:56:09 by GötzWaschk)