To make it short: Fat Tree, right, blocking, yes.Hi,
a few questions/points form my side:
- Claix 18 is using Intel OPA. What network topology is used? I guess it is a Fat tree. Is it blocking or non-blocking? Is it 1:2 blocking as on Claix 16?
Since we are still in the acceptance phase, this is not the case. But will be in the future.
- Have you configured topology-aware resource allocation within the SLURM scheduler, in other words does the scheduler knows the topology and tries to minimize the hop-count?
I'm not sure, if TurboBoost is activated, normally we try to fix the frequency to the maximum. Perhaps Sascha and/or Paul can answer this part.- I assume TurboBoost is enabled by default? Is it possible (or will it be possible in the future) to include an option to switch TurboBoost off? E.g. on JURECA it is possible to disable TurboBoost with `#SBATCH --disable-turbomode` for measurements.
Otherwise it is possible to set frequencies with likwid?
The nrm nodes are the first batch of the new Tier3 system. Seems, something is still odd with them. I took them out of the partition again.- I tried to run jobs with 256 nodes. I am getting an MPI error (cf. job 92414):
nrm008.hpc.itc.rwth-aachen.de.233340PSM2 no hfi units are active (err=23)
[245] MPI startup(): tmi fabric is not available and fallback fabric is not enabledAny ideas where this is coming from? Should I manually adjust I_MPI_FABRICS? I don't want to set the fallback fabric, since this would be TCP and would significantly impact performance. Affected jobs are not canceled but are running into the time limit.
Theses errors are only occurring on the nrm nodes, not on the ncm nodes. Could there be a problem with the nrm nodes? Currently I am using the partition c18m, which contains both nodes types. How can I only select ncm nodes?
not sure about that one, I always thought, you could get details of jobs shown with squeue. This means, completed jobs will not be shown. I could find nothing about that in the man page though.
- Historic jobs can not be viewed with scontrol or sstat. sacct on the other hand works. For example:
$ scontrol show job 90949
slurm_load_jobs error: Invalid job id specified
excerpt from the manpage:$ sstat --format=AveCPU,AvePages,AveRSS,AveVMSize,JobID -j 90945
AveCPU AvePages AveRSS AveVMSize JobID
---------- ---------- ---------- ---------- ------------
sstat: error: couldn't get steps for job 90945
[2019-01-24T12:16:54.089] _slurm_rpc_submit_batch_job: JobId=92365 InitPrio=103522 usec=8187
- Some of my jobs don't appear in the queue and are not scheduled, even if sbatch returns `Submitted batch job 92365`
Hi Paul, I think, this is your part.- You are using a hand-build module system. One issue with this approach is that dependencies are not dissolved properly. For example loading the module python does something unexpected. A short example:
$ module load intel; ldd main.x | grep mkl
intel/19.0 already loaded, doing nothing [ WARNING ]
libmkl_intel_lp64.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_intel_lp64.so (0x00002ac58b9ee000)
libmkl_core.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_core.so (0x00002ac58c53c000)
libmkl_intel_thread.so => /opt/intel/Compiler/19.0/1.144/rwthlnk/mkl/lib/intel64_lin/libmkl_intel_thread.so (0x00002ac5906c8000)$ module load python; ldd main.x | grep mkl
Loading python 2.7.12 [ OK ]
The SciPy Stack available: http://www.scipy.org/stackspec.html
Build with GCC compilers.
libmkl_intel_lp64.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_intel_lp64.so (0x00002abea70ad000)
libmkl_core.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_core.so (0x00002abea7bcb000)
libmkl_intel_thread.so => /usr/local_rwth/sw/python/2.7.12/x86_64/extra/lib/libmkl_intel_thread.so (0x00002abea96ba000)Using mkl_get_version_string() shows that the python mkl is version 2017.0.0 instead of the expected 2019.0.1 version that should be loaded.
A different approach to a hand-build module system would be using easybuild to create the module system. This would avoid such issues.
The blue print paper can be found here:
http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7830454
JSC has published there easybuild configuration on github:
https://github.com/easybuilders/JSC
The config files from HPC-UGent are also publicly available.
Best,
Sebastian
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