Known Issues on JUSUF

This page collects known issues affecting JUSUF’s system and application software.

Note

The following list of known issue is intended to provide a quick reference for users experiencing problems on JUSUF. We strongly encourage all users to report the occurrence of problems, whether listed below or not, to the user support.

Open Issues

Fortran 2008 MPI bindings rewrite array bounds

Added: 2023-08-17

Affects: All systems at JSC

Description: Due to a bug in versions of the gfortran compiler installed in software stages earlier than 2024, the Fortran 2008 bindings (use mpi_f08) of MPICH-based MPI libraries (e.g. ParaStationMPI) erroneously modify the bounds of arrays passed into MPI routines as buffers.

Status: Open.

Workaround/Suggested Action: The issue can be avoided by using:

• gfortran version 12 or later (available in software stage 2024) or

• a Fortran compiler other than gfortran (e.g. the Intel Fortran compiler) or

• an MPI library that is not based on MPICH (e.g. OpenMPI).

Process affinity

Added: 2023-08-03

Affects: All systems at JSC

Description: After an update of Slurm to version 22.05 the process affinity has changed, which results in unexpected pinning in certain cases. This could have a major impact on code’s performance.

Status: Open.

Workaround/Suggested Action: Further information can be found in the warning section of Processor Affinity.

Flipping links

Added: 2022-09-28

Updated: 2023-05-25

Affects: JUWELS Booster and JURECA-DC

Description: A few months ago, we have identified an issue with the InfiniBand cabling of our Sequana XH2000 machines. Under certain circumstances not easily reproduceable at a small scale, an InfiniBand adapter will lose its link for a few seconds. Usually, this happens rarely and if the communication library just tries again, it will also not lead to a proper failure, but just a temporary delay. However this issue is more pronounced with the NCCL library, showing up more frequently at large scale, particularly with PyTorch.

Current situation: Since the problem has been identified, we have retrofitted all InfiniBand cables between compute nodes and switches with ferrite beads. This effectively reduced the frequency of these events, but did not fully solve the problem as it was initially expected. We are working together with Atos to find a final solution. In the meantime, if your job ends unexpectedly with this or a similar error, despite using the suggested workaround below, please contact sc@fz-juelich.de:

RuntimeError: NCCL communicator was aborted on rank X.  Original reason for failure was: NCCL error: unhandled system error, NCCL version 21.2.7
ncclSystemError: System call (socket, malloc, munmap, etc) failed.

Update 2023-05-25: All affected systems have received a second ferrite bead in the cables of the affected links. This has improved the situation significantly. However some jobs still trigger the problem ocassionally. The current strategy is to identify nodes where this happens and treat them as “weak” nodes which require a third ferrite bead or an InfiniBand card replacement. This is not considered a fix, but a workaround from the hardware side.

Status: Open.

Workaround/Suggested Action: While we wait for a definite fix, and besides the effort on the hardware side, we currently recommend the following environment variables to try to mitigate the link flip issue:

export NCCL_IB_TIMEOUT=50
export UCX_RC_TIMEOUT=4s
export NCCL_IB_RETRY_CNT=10

Slurm: wrong default task pinning with odd number of tasks/node

Added: 2022-06-20

Affects: All systems at JSC

Description: With default CPU bindings (’–cpu-bind=threads’) the task pinning is not the expected one when we have odd number of tasks per node and those tasks are using number of cores less or equal to half of the total cores on each node.

When we have even number of tasks/node then only real cores are being used by the tasks. When we have odd number of tasks/node then SMT is enabled and different tasks share the hardware threads of same cores (this shouldn’t happen). Following you can see a few examples on JUWELS-CLUSTER.

With 1 task/node and 48 cpus/task it uses SMT:

$ srun -N1 -n1 -c48 --cpu-bind=verbose exec
cpu_bind=THREADS - jwc00n001, task  0  0 [7321]: mask 0xffffff000000ffffff set

With 2 tasks/node and 24 cpus/task it uses only physical cores:

$ srun -N1 -n2 -c24 --cpu-bind=verbose exec
cpu_bind=THREADS - jwc00n001, task  0  0 [7340]: mask 0xffffff set
cpu_bind=THREADS - jwc00n001, task  1  1 [7341]: mask 0xffffff000000 set

With 3 tasks/node and 16 threads/task it uses SMT (task 0 and 1 are on physical cores but task 2 uses SMT):

$ srun -N1 -n3 -c16 --cpu-bind=verbose exec
cpu_bind=THREADS - jwc00n001, task  0  0 [7362]: mask 0xffff set
cpu_bind=THREADS - jwc00n001, task  1  1 [7363]: mask 0xffff000000 set
cpu_bind=THREADS - jwc00n001, task  2  2 [7364]: mask 0xff000000ff0000 set

With 4 tasks/node and 12 cpus/task uses only physical cores:

$ srun -N1 -n4 -c12 --cpu-bind=verbose exec
cpu_bind=THREADS - jwc00n001, task  0  0 [7387]: mask 0xfff set
cpu_bind=THREADS - jwc00n001, task  2  2 [7389]: mask 0xfff000 set
cpu_bind=THREADS - jwc00n001, task  1  1 [7388]: mask 0xfff000000 set
cpu_bind=THREADS - jwc00n001, task  3  3 [7390]: mask 0xfff000000000 set

Status: Open.

Workaround/Suggested Action: To workaround this behavior you have to disable SMT with srun option “–hint=nomultithread”. You can compare the cpu masks in the following examples:

$ srun -N1 -n3 -c16 --cpu-bind=verbose exec
cpu_bind=THREADS - jwc00n004, task  0  0 [17629]: mask 0x0000000000ffff set
cpu_bind=THREADS - jwc00n004, task  1  1 [17630]: mask 0x0000ffff000000 set
cpu_bind=THREADS - jwc00n004, task  2  2 [17631]: mask 0xff000000ff0000 set


$ srun -N1 -n3 -c16 --cpu-bind=verbose --hint=nomultithread exec
cpu_bind=THREADS - jwc00n004, task  0  0 [17652]: mask 0x00000000ffff set
cpu_bind=THREADS - jwc00n004, task  1  1 [17653]: mask 0x00ffff000000 set
cpu_bind=THREADS - jwc00n004, task  2  2 [17654]: mask 0xff0000ff0000 set

Slurm: srun options –exact and –exclusive change default pinning

Added: 2022-06-09

Affects: All systems at JSC

Description: In Slurm 21.08 the srun options “–exact” and “–exclusive” change the default pinning. For example on JURECA:

$ srun -N1 --ntasks-per-node=1 -c32 --cpu-bind=verbose exec
cpu_bind=THREADS - jrc0731, task  0  0 [3027]: mask 0xffff0000000000000000000000000000ffff000000000000 set
...
$ srun -N1 --ntasks-per-node=1 -c32 --cpu-bind=verbose --exact exec
cpu_bind=THREADS - jrc0731, task  0  0 [3068]: mask 0x3000300030003000300030003000300030003000300030003000300030003 set
...
$ srun -N1 --ntasks-per-node=1 -c32 --cpu-bind=verbose --exclusive exec
cpu_bind=THREADS - jrc0731, task  0  0 [3068]: mask 0x3000300030003000300030003000300030003000300030003000300030003 set
...

As you can see with the default pinning only physical cores are used but with “–exact” or “–exclusive” Slurm pins the tasks to SMT cores (Hardware Threads). Actually this means that the task distribution changes to “cyclic”.

Status: Open.

Workaround/Suggested Action: To workaround this behavior you have to request block distribution of the tasks using option “-m” like this:

$ srun -N1 --ntasks-per-node=1 -c32 --cpu-bind=verbose --exact -m *:block exec
cpu_bind=THREADS - jrc0731, task  0  0 [3027]: mask 0xffff0000000000000000000000000000ffff000000000000 set
...
$ srun -N1 --ntasks-per-node=1 -c32 --cpu-bind=verbose --exclusive -m *:block exec
cpu_bind=THREADS - jrc0731, task  0  0 [3027]: mask 0xffff0000000000000000000000000000ffff000000000000 set
...

ParaStationMPI: Cannot allocate memory

Added: 2021-10-06

Affects: All systems at JSC

Description: Using ParaStationMPI, the following error might occur:

ERROR mlx5dv_devx_obj_create(QP) failed, syndrome 0: Cannot allocate memory

Status: Open.

Workaround/Suggested Action: Use mpi-settings/[CUDA-low-latency-UD,CUDA-UD,UCX-UD] (Stage < 2022) or UCX-settings/[UD,UD-CUDA] (Stage >= 2022) to reduce the memory footprint. The particular module depends on the user requirements.

Cannot connect using old OpenSSH clients

Added: 2020-06-15

Affects: All systems at JSC

Description: In response to the recent security incident, the SSH server on JUSUF has been configured to only use modern cryptography algorithms. As a side effect, it is no longer possible to connect to JUSUF using older SSH clients. For OpenSSH, at least version 6.7 released in 2014 is required. Some operating systems with very long term support ship with older versions, e.g. RHEL 6 ships with OpenSSH 5.3.

Status: Open.

Workaround/Suggested Action: Use a more recent SSH client with support for the newer cryptography algorithms. If you cannot update the OpenSSH client (e.g. because you are not the administrator of the system you are trying to connect from) you can install your own version of OpenSSH from https://www.openssh.com. Logging in from a different system with a newer SSH client is another option. If you have to transfer data from a system with an old SSH client to JUSUF (e.g. using scp) you may have to transfer the data to a third system with a newer SSH client first (scp’s command line option -3 can be used to automate this).

Recently Resolved and Closed Issues

ParaStationMPI: GPFS backend for ROMIO (MPI I/O)

Added: 2023-04-03

Update: 2023-06-12

Affects: All systems at JSC

Description: GPFS backend for ROMIO (MPI I/O) in ParaStationMPI has been enabled in the 2023 stage after a bug has been fixed. However, occasional segmentation faults have been observed when ParaStationMPI is used with GPFS backend enabled, resulting in job failures. Disabling the GPFS backend, the issue not reproducible anymore, and the jobs complete successfully.

Status: Resolved.

Workaround/Suggested Action: Versions 5.7.1-1 and 5.8.1-1 include a patch to address this issue and have been installed. If you are affected by this issue please explicitly load these versions.

JUST: GPFS hanging waiters lead to stuck I/O

Added: 2023-04-12

Update: As of 2023-05-26 all systems have been updated to a GPFS version that fixed the issue

Affects: All systems at JSC

Description: We are aware, since the 15th of March, that some users have seen their jobs cause waiters on JUST, which leads to these jobs hanging seemingly indefinitely on I/O. This issue has been observed for a specific set of jobs and more frequently occurred on JURECA than other systems. IBM has identified a possible cause and are now in the process of developing a fix.

Status: Resolved.

Workaround/Suggested Action: There are no known workarounds. Once IBM releases the fix, we will shortly schedule a maintenance window and install the patch.

Job requeueing failures due to slurmctld prologue bug

Added: 2021-05-18

Affects: All systems at JSC

Description: There is a bug in slurmctld and currently the prologue mechanism and the job requeueing are broken. Normally before a job allocates any nodes the prologue runs and if it finds unhealthy nodes it drains them and requeues the job. Because of the bug now slurcmtld will cancel the jobs that were requeued at least once but finally landed on healthy nodes. We have reported this bug to SchedMD and they are working on it.

Status: Resolved.