Hi Roland,
That's fantastic, thanks for linking those files.
It works as expected with only MPI processes. I am careful in compiling and running with the same (and only) OpenMPI installation on the cluster, so this should be OK.
Finding a Slurm to SGE conversion table, there is no SGE equivalent to ncpus-per-task from Slurm, rather it is the allocation type of the given parallel environment that does this. I.e. the backend.
https://srcc.stanford.edu/sge-slurm-conversion
Further, in the submit script of ranger, the crucial line
#$ -pe @(@PPN_USED@/@NUM_THREADS@)@way @PROCS_REQUESTED@
shows that you request @PROCS_REQUESTED@ slots (as I currently have) and the first argument shows that the name of the parallel environment is dependent upon @NUM_THREADS@. From what I take from this, I need to set up a parallel environment that has hardcoded the number of threads I want per MPI process and then use that parallel environment. I'll see how I go there, but it isn't initially obvious how to do this!
Cheers,
Chris
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Dr Chris Stevens
Lecturer in Applied Mathematics
Rm 602, Jack Erskine building
School of Mathematics and Statistics
T: +64 3 369 0396 (Internal 90396)
University of Canterbury | Te Whare Wānanga o Waitaha
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________________________________ From: Roland Haas Sent: Thursday, October 07, 2021 06:22 To: Chris Stevens Cc: users@einsteintoolkit.org Subject: Re: [Users] Einstein toolkit with Sun Grid Engine
Hello Chris,
We used SGE a long time ago on some of the TACC machines.
You can find an old setup for TACC's Ranger cluster in an old commit like so:
git checkout fed9f8d6fae4c52ed2d0a688fcc99e51b94e608e
and then look at the "ranger" files in OUTDATED subdirectories of machines, runscripts, submitscripts.
Having all MPI ranks on a single node might also be caused by using different MPI stacks when compiling and when running so you must make sure that the "mpirun" (or equivalent command) you use is the one that belongs to the MPI library that you used when linking your code.
Finally you may also have to check if this is an issue with threads and MPI ranks. Ie I would check if things are still wrong if you use only MPI processes and no OpenMP threads at all (in that case you would have to check what SGE counts: threads (cores) or MPI ranks (processes)).
Yours, Roland
Hi everyone,
I have set up the Einstein toolkit on a local cluster of 20 nodes with the SGE scheduler. I have not seen any examples of this scheduler being used with the Einstein toolkit.
I have managed to get it working; however it seems if I ask for a certain number of slots that requires more than one node, it correctly allocates these, however all processes and threads are run on the one node and is oversubscribed.
My question is whether anybody has used SGE with the Einstein toolkit and if this is a good thing or not? If it is possible, I can send more details if there are people willing to help solve this inter-node communication problem.
Thanks in advance,
Chris
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Dr Chris Stevens
Lecturer in Applied Mathematics
Rm 602, Jack Erskine building
School of Mathematics and Statistics
T: +64 3 369 0396 (Internal 90396)
University of Canterbury | Te Whare Wānanga o Waitaha
Private Bag 4800, Christchurch 8140, New Zealand
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