[slurm-users] slurm-wlm package OpenMPI PMIx implementation

Thu Dec 10 18:48:13 UTC 2020

Hey Chris,

No code to test -- mpi works just not with slurm to call it.

Thanks for your help, I think I'm going to be recompiling from source.
~Avery Grieve
They/Them/Theirs please!
University of Michigan

On Thu, Dec 10, 2020 at 12:58 PM Christopher J Cawley <ccawley2 at gmu.edu>
wrote:

> Hi Avery -
>
> No worries,
>
> I took all of the defaults for software, etc.
> Jetson's are locked into ubuntu 18.04.5,
> slurm 19.05.7, etc.
>
> Do you have code to test?  I'm more of a python person.
>
> Thanks
> Chris
>
>
> *Christopher J. Cawley*
>
> *Systems Engineer/Linux Engineer, Information Technology Services*
>
> *223 Aquia Building, Ffx,** MSN**: 1B5*
>
> *George Mason University*
>
> *Phone:** (703) 993-6397*
>
> *Email:* *ccawley2 at gmu.edu*
> 
>
> ------------------------------
> *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of
> Avery Grieve <agrieve at umich.edu>
> *Sent:* Thursday, December 10, 2020 11:38 AM
> *To:* Slurm User Community List <slurm-users at lists.schedmd.com>
> *Subject:* Re: [slurm-users] slurm-wlm package OpenMPI PMIx implementation
>
> Oop, sorry I meant to also include the following:
>
> # srun --mpi=list
> srun: MPI types are...
> srun: none
> srun: pmi2
> srun: openmpi
>
> running srun with --mpi=openmpi gives the same errors as with
> MpiDefault=none.
>
> ~Avery Grieve
> They/Them/Theirs please!
> University of Michigan
>
>
> On Thu, Dec 10, 2020 at 11:34 AM Avery Grieve <agrieve at umich.edu> wrote:
>
> Hi Chris,
>
> Thank you for the offer. Here's some quick information on my system:
>
> All nodes on Debian 10 (armbian buster converted to DietPi v6.33.3).
> sinfo --version: slurm-wlm 18.08.5-2
>
> With MpiDefault=pmix I get the following srun errors:
> srun: error: Couldn't find the specified plugin name for mpi/pmix looking
> at all files
> srun: error: cannot find mpi plugin for mpi/pmix
> srun: error: cannot create mpi context for mpi/pmix
> srun: error: invalid MPI type 'pmix', --mpi=list for acceptable types
>
> With MpiDefault=none
> I get OpenMPI yelling at me and giving me two options, only one relevant
> to the version of Slurm I'm running:
> version 16.05 or later: you can use SLURM's PMIx support. This
>   requires that you configure and build SLURM --with-pmix.
>
> However, as I stated, I'm using the slurm-wlm package which seems to not
> include the pmix functionality by default.
>
> The other option provided:
> Versions earlier than 16.05: you must use either SLURM's PMI-1 or
>   PMI-2 support. SLURM builds PMI-1 by default, or you can manually
>   install PMI-2. You must then build Open MPI using --with-pmi pointing
>   to the SLURM PMI library location.
>
> Similar issue, not building slurm from source doesn't include the PMI
> library. I've installed some develop level packages, including the
> libpmi2-0 package
> <https://secure-web.cisco.com/10RRF9yf9i-7-zx463otbTEYwHQ8PfAu0MWZDt-sp7LOW0FINJnwC3j6h5vCPjyEOcW_d4xkUjeu3yTU6e1aZhW7bYufUDkpZVQ_-IyrDmd5Zl9_4fUvMFvlohRkxN3_18FcN6caXv3CyLnSbizh35atzHBeuC4aREJBiZNIfqjJfrO5LI5pK6coWiyFVqweLpTWOQUWbdjzpnAG7whBZiDXOyp20-eAgY5v3ChNlgtjLNr_9d-OV97ux4pQyrfVyOZ2yTcVNF-THuyFtghkAO6wbbfRVQ9bRhzVsADarrzAyye3nTdVUQeehuf2hANuF7JLIXPuBmV-cAwMpZfuoC6PYr_FI0PoBsPUDaBCrFbagrJzfPr3ufkZsVxor3fyBaY8Vcphc-CfnpwfraZSpFHI8BC4Xq0l475bH5OSBCoQAFV8aE_hF-rycPo-gDRkmSqqHnKTUMuyHb5G46NQ7NQ/https%3A%2F%2Fpackages.debian.org%2Fbuster%2Flibpmi2-0>
> which didn't seem to actually install anything useful as far as I can tell
> using the "find" command.
>
> It's sort of looking like I should be looking at building slurm from
> source again, I guess.
>
> Thanks,
>
> ~Avery Grieve
> They/Them/Theirs please!
> University of Michigan
>
>
> On Thu, Dec 10, 2020 at 11:16 AM Christopher J Cawley <ccawley2 at gmu.edu>
> wrote:
>
> I have a 7 node jetson nano cluster running at home.
>
> Send me what you want me to take a look at .  If it's not
> a big deal, then I can let you know.
>
> Ubuntu 18 / slurm <some version from rpm>
>
> Thanks
> Chris
>
>
> *Christopher J. Cawley*
>
> *Systems Engineer/Linux Engineer, Information Technology Services*
>
> *223 Aquia Building, Ffx,** MSN**: 1B5*
>
> *George Mason University*
>
> *Phone:** (703) 993-6397*
>
> *Email:* *ccawley2 at gmu.edu*
> 
>
> ------------------------------
> *From:* slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of
> Avery Grieve <agrieve at umich.edu>
> *Sent:* Thursday, December 10, 2020 10:51 AM
> *To:* slurm-users at lists.schedmd.com <slurm-users at lists.schedmd.com>
> *Subject:* [slurm-users] slurm-wlm package OpenMPI PMIx implementation
>
> Hi Forum,
>
> I've been putting together an ARM cluster for fun/learning and I've been a
> bit lost about how to get OpenMPI and slurm to behave together.
>
> I have installed the slurm-wlm package
> <https://secure-web.cisco.com/14EwNb3UZYABzVqRN7IxszUw4L04o_2Bv7wm3a5vivtuqZhDuY3UrhulGE47J31qdoC16rhtMefWeyLXhK10TMim7oOCehTuBJR_47pTBDKcO_xYDX3yqOG1yzamsO31hXo3HS9tSUpOssM40vTLwy4Mxfggu2Qu_yXjJqtLE43mV2CrECvinY7hMt_cRMzi4b8xrKZXqngR31DMmyA9DzimeyLsN7nwxh6kJRMhcg2MjHlCOhu356VVZrErEM9ZafOD66sDUMluigARg1icclZaJOLhXE-7PlFRtAdk2dhXLEvRqSL3SUKrVeBy01MCmSi7sH8bkIijrujncTBU-DfWxY_JOwqhhsJAyXl0XJgjoOiGWHKcLPRRvrCbn_SGHGSw2Ogq3aC4sJLY1tBLwpgvXcOxFoURgb6y6WfJJg04H9ewyQ-Azr7kA_en7DIk_4KOux310uOWzo7XrHTxnLg/https%3A%2F%2Fpackages.debian.org%2Fbuster%2Fslurm-wlm>from
> the Debian apt search and compiled OpenMPI from source on my compute nodes.
> OpenMPI has been compiled with the option --with-slurm and the configure
> time log indicates openmpi has pmix v3 built in. I thought that would be
> enough for slurm and calling a job with "srun -n 4 -N1 executable" (with
> slurm.conf having MpiDefault=pmix_v3) would be enough.
>
> Not the case, unfortunately as slurm doesn't have any idea what pmix_v3
> means without being compiled against it I guess. I have also attempted to
> compile openmpi from source with the --with-pmi option but the slurm-wlm
> package doesn't install any of the libraries/headers (pmi.h pmi2.h pmix.h
> etc). Neither does any of the slurm-llnl develop packages, so I'm at a loss
> of what to do here.
>
> A few notes: OpenMPI is working across my compute nodes. I'm able to ssh
> to my compute node and start a job manually with mpirun that executes
> successfully across the nodes. My slurmctld and slurmd daemons work for
> single thread resource allocation (and presumably OpenMP multithreading,
> though I haven't tested this).
>
> Beyond compiling slurm from source (assuming this installs the pmi headers
> that I can use to build openmpi), which I have tried with no luck on my
> devices, is there a way to get slurm and openmpi to behave together using
> the precompiled package slurm-wlm?
>
> Thank you,
>
> ~Avery Grieve
> They/Them/Theirs please!
> University of Michigan
>
>
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