Differences between revisions 49 and 160 (spanning 111 versions)

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

Usage of the Linux Clusters at DESY Zeuthen

Contents

Usage of the Linux Clusters at DESY Zeuthen

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

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

-  ⇤ ← Revision 49 as of 2010-11-12 14:20:00 → 
  Size: 5207
  Editor: GötzWaschk
  Comment: ini
+   ← 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:
+/!\ '''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 2:
+Line 5:
-There are 8 dedicated parallel clusters (blade centers) in testing mode, but you can also run parallel MPI jobs in the SGE farm. The documentation in [[Batch_System_Usage]] applies there.
+<<TableOfContents>>

== 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 [[https://dv-zeuthen.desy.de/services/batch/|Batch System Usage]] applies there.
-Line 6:
+Line 12:
+== 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
}}}
-Line 7:
+Line 27:
-=== Openmpi ===
Since SL5, all batch worker nodes have the openmpi implementation of the MPI standard installed. Recently the machines were upgraded to the default SL5.5 packages of openmpi. For 64 bit applications use the installation in /usr/lib64/openmpi/1.4-gcc/bin, for 32 bit use  the binaries from /usr/lib/openmpi/1.4-gcc/bin .
+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 10:
+Line 51:
-Additional openmpi versions are installed to support the Intel and PGI compilers:
+=== 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 12:
+Line 54:
-{{{
/usr/lib64/openmpi/1.4-icc/bin
/usr/lib64/openmpi-1.3.2-pgi/bin
}}}
If you don't want to specify the full path to your preferred MPI implementation, configure a default by using the ini command or running mpi-selector-menu on a build machine.

==== Building applications ====
64 bit MPI Applications can be compiled on any 64 bit SL5 machine, e.g. sl5-64.ifh.de.

==== Running your application ====
+==== OpenMPI ====
-Line 25:
+Line 58:
-pax0c slots=8
pax0d slots=8
pax0e slots=8
pax0f slots=8
+pax8a slots=8
pax8b slots=8
pax8c slots=8
pax8d slots=8
-Line 33:
+Line 66:
-/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np 32 -machinefile ./machinefile  ./program
+/opt/ohpc/pub/mpi/openmpi-gnu/1.10.7/bin/mpirun -np 32 -machinefile ./machinefile  ./program
-Line 37:
+Line 70:
-=== Mvapich / Mvapich2 ===
Three additional mpi implementations are installed on all pax machines:
+==== 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:
-Line 41:
+Line 76:
-/usr/lib64/mvapich/1.2.0-gcc/bin
/usr/lib64/mvapich2/1.4-gcc/bin
/usr/lib64/mvapich2/1.4-intel/bin
+pax88
pax89
pax88
pax89
-Line 45:
+Line 81:
-To use mvapich, add one of those versions to your path, compile your application with that mpi compiler and run it as specified here: http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.4.html#x1-160005.2

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 pax19 and pax18:
+The preferred way to run a application with mvapich2 is mpiexec, e.g.:
-Line 50:
+Line 83:
-pax18
pax19
pax18
pax19
}}}
You must also first create the file ~/.mpd.conf that contains of one line like this:

{{{
MPD_SECRETWORD=password
}}}
== 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
+/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
-Line 83:
+Line 86:
-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 on a single node:
+==== 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 85:
+Line 93:
+== Batch System Access ==
/!\ '''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 ||

=== 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 [[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:
-Line 86:
+Line 149:
-#$ -pe multicore-mpi 8
+mpiexec apptainer exec /project/singularity/images/SL6.img yourbinary
-Line 88:
+Line 151:
-For more MPI processes that have no big communication overhead, use -pe mpi.
+However, Mvapich2 2.2 isn't optimized yet for Apptainer, so this is slower than running native programs.
-Line 90:
+Line 153:
-Be sure to call the right mpirun version for your architecture. If you application was compiled for 64 bit, use
-Line 92:
+Line 154:
+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:
-Line 93:
+Line 156:
-/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np $NSLOTS yourapp
+singularity exec /project/singularity/images/SL6.img /usr/lib64/openmpi-3.0/bin/mpicc yourprog.c -o yourprog.sl6
-Line 95:
+Line 158:
-The MPI runtime will automatically select the right network type.

For more demanding MPI jobs you can select one of the pax blade centers like this in your job script. You can request up to 128 slots, as a blade center contains 128 CPU cores:
+and in the job script:
-Line 100:
+Line 160:
-#$ -pe pax? 128

/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np $NSLOTS yourapp
+module add gnu7 openmpi3 prun
prun singularity exec -B /scratch /project/singularity/images/SL6.img yourprog.sl6
-Line 104:
+Line 163:
-Currently, only openmpi is supported in the batch system, mvapich2 does not work /!\

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 3GB h_vmem in your job scripts. Otherwise your job won't start!
+== 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 111:
+Line 167:
-The application binary must be available to all nodes, that's why it should be placed in an AFS directory.
+The application binary must be available to all nodes, that's why it should be placed in an AFS or Lustre directory.
-Line 113:
+Line 169:
-== BLAS library ==
Both ATLAS and GotoBLAS are available.
+== Monitoring ==
Ganglia provides a web monitoring interface. These page is only available from the internal network.
-Line 116:
+Line 172:
- * ATLAS is in /opt/products/atlas
+[[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 118:
+Line 174:
- * libgoto is in /usr/lib or /usr/lib64 respectively.
+== 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`

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