Hello Gilles, thank you very much for the prompt patch.
I can confirm that configure now prefers the external PMIx. I can confirm that the munge warnings and PMIx errors we observed are gone. An mpi hello world runs successfully with srun --mpi=pmix and --mpi=pmi2. I noticed that configure complained loudly about a missing external libevent (i.e. libevent-devel package), but did not complain at all that an external hwloc-devel was also missing. Best Regards Christof On Sat, May 20, 2023 at 06:54:54PM +0900, Gilles Gouaillardet wrote: > Christof, > > Open MPI switching to the internal PMIx is a bug I addressed in > https://github.com/open-mpi/ompi/pull/11704 > > Feel free to manually download and apply the patch, you will then need > recent autotools and run > ./autogen.pl --force > > An other option is to manually edit the configure file > > Look for the following snippet > > # Final check - if they didn't point us explicitly at an > external version > > # but we found one anyway, use the internal version if it is > higher > > if test "$opal_external_pmix_version" != "internal" && (test -z > "$with_pmix" || test "$with_pmix" = "yes") > > then : > > if test "$opal_external_pmix_version" != "3x" > > > and replace the last line with > > if test $opal_external_pmix_version_major -lt 3 > > > Cheers, > > Gilles > > On Sat, May 20, 2023 at 6:13 PM christof.koehler--- via users < > users@lists.open-mpi.org> wrote: > > > Hello Z. Matthias Krawutschke, > > > > On Fri, May 19, 2023 at 09:08:08PM +0200, Zhéxué M. Krawutschke wrote: > > > Hello Christoph, > > > what exactly is your problem with OpenMPI and Slurm? > > > Do you compile the products yourself? Which LINUX distribution and > > version are you using? > > > > > > If you compile the software yourself, could you please tell me what the > > "configure" command looks like and which MUNGE version is in use? From the > > distribution or compiled by yourself? > > > > > > I would be very happy to take on this topic and help you. You can also > > reach me at +49 176 67270992. > > > Best regards from Berlin > > > > please refer to (especially the end) of my first mail in this thread > > which is available here > > https://www.mail-archive.com/users@lists.open-mpi.org/msg35141.html > > > > I believe this contains the relevant information you are requesting. The > > second mail which you are replying to was just additional information. > > My apologies if this led to confusion. > > > > Please let me know if any relevant information is missing from my first > > email. At the bottom of this email I include the ompi_info output as > > further addendum. > > > > To summarize: I would like to understand where the munge warning > > and PMIx error described in the first email (and the github link > > included) come from. The explanation in the github issue > > does not appear to be correct as all munge libraries are > > available everywhere. To me, it appears at the moment that OpenMPIs > > configure decides erroneously to build and use the internal pmix > > instead of using the (presumably) newer externally available PMIx, > > leading to launcher problems with srun. > > > > > > Best Regards > > > > Christof > > > > Package: Open MPI root@admin.service Distribution > > Open MPI: 4.1.5 > > Open MPI repo revision: v4.1.5 > > Open MPI release date: Feb 23, 2023 > > Open RTE: 4.1.5 > > Open RTE repo revision: v4.1.5 > > Open RTE release date: Feb 23, 2023 > > OPAL: 4.1.5 > > OPAL repo revision: v4.1.5 > > OPAL release date: Feb 23, 2023 > > MPI API: 3.1.0 > > Ident string: 4.1.5 > > Prefix: /cluster/mpi/openmpi/4.1.5/gcc-11.3.1 > > Configured architecture: x86_64-pc-linux-gnu > > Configure host: admin.service > > Configured by: root > > Configured on: Wed May 17 18:45:42 UTC 2023 > > Configure host: admin.service > > Configure command line: '--enable-mpi1-compatibility' > > '--enable-orterun-prefix-by-default' > > '--with-ofi=/cluster/libraries/libfabric/1.18.0/' '--with-slurm' > > '--with-pmix' '--with-pmix-libdir=/usr/lib64' '--with-pmi' > > '--with-pmi-libdir=/usr/lib64' > > '--prefix=/cluster/mpi/openmpi/4.1.5/gcc-11.3.1' > > Built by: root > > Built on: Wed May 17 06:48:36 PM UTC 2023 > > Built host: admin.service > > C bindings: yes > > C++ bindings: no > > Fort mpif.h: yes (all) > > Fort use mpi: yes (full: ignore TKR) > > Fort use mpi size: deprecated-ompi-info-value > > Fort use mpi_f08: yes > > Fort mpi_f08 compliance: The mpi_f08 module is available, but due to > > limitations in the gfortran compiler and/or Open MPI, does not support > > the following: array subsections, direct passthru (where possible) to > > underlying Open MPI's C functionality > > Fort mpi_f08 subarrays: no > > Java bindings: no > > Wrapper compiler rpath: runpath > > C compiler: gcc > > C compiler absolute: /usr/bin/gcc > > C compiler family name: GNU > > C compiler version: 11.3.1 > > C++ compiler: g++ > > C++ compiler absolute: /usr/bin/g++ > > Fort compiler: gfortran > > Fort compiler abs: /usr/bin/gfortran > > Fort ignore TKR: yes (!GCC$ ATTRIBUTES NO_ARG_CHECK ::) > > Fort 08 assumed shape: yes > > Fort optional args: yes > > Fort INTERFACE: yes > > Fort ISO_FORTRAN_ENV: yes > > Fort STORAGE_SIZE: yes > > Fort BIND(C) (all): yes > > Fort ISO_C_BINDING: yes > > Fort SUBROUTINE BIND(C): yes > > Fort TYPE,BIND(C): yes > > Fort T,BIND(C,name="a"): yes > > Fort PRIVATE: yes > > Fort PROTECTED: yes > > Fort ABSTRACT: yes > > Fort ASYNCHRONOUS: yes > > Fort PROCEDURE: yes > > Fort USE...ONLY: yes > > Fort C_FUNLOC: yes > > Fort f08 using wrappers: yes > > Fort MPI_SIZEOF: yes > > C profiling: yes > > C++ profiling: no > > Fort mpif.h profiling: yes > > Fort use mpi profiling: yes > > Fort use mpi_f08 prof: yes > > C++ exceptions: no > > Thread support: posix (MPI_THREAD_MULTIPLE: yes, OPAL support: > > yes, OMPI progress: no, ORTE progress: yes, Event lib: yes) > > Sparse Groups: no > > Internal debug support: no > > MPI interface warnings: yes > > MPI parameter check: runtime > > Memory profiling support: no > > Memory debugging support: no > > dl support: yes > > Heterogeneous support: no > > mpirun default --prefix: yes > > MPI_WTIME support: native > > Symbol vis. support: yes > > Host topology support: yes > > IPv6 support: no > > MPI1 compatibility: yes > > MPI extensions: affinity, cuda, pcollreq > > FT Checkpoint support: no (checkpoint thread: no) > > C/R Enabled Debugging: no > > MPI_MAX_PROCESSOR_NAME: 256 > > MPI_MAX_ERROR_STRING: 256 > > MPI_MAX_OBJECT_NAME: 64 > > MPI_MAX_INFO_KEY: 36 > > MPI_MAX_INFO_VAL: 256 > > MPI_MAX_PORT_NAME: 1024 > > MPI_MAX_DATAREP_STRING: 128 > > MCA allocator: basic (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA allocator: bucket (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA backtrace: execinfo (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA btl: ofi (MCA v2.1.0, API v3.1.0, Component v4.1.5) > > MCA btl: self (MCA v2.1.0, API v3.1.0, Component > > v4.1.5) > > MCA btl: openib (MCA v2.1.0, API v3.1.0, Component > > v4.1.5) > > MCA btl: vader (MCA v2.1.0, API v3.1.0, Component > > v4.1.5) > > MCA btl: tcp (MCA v2.1.0, API v3.1.0, Component v4.1.5) > > MCA btl: usnic (MCA v2.1.0, API v3.1.0, Component > > v4.1.5) > > MCA compress: gzip (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA compress: bzip (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA crs: none (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA dl: dlopen (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA event: libevent2022 (MCA v2.1.0, API v2.0.0, > > Component v4.1.5) > > MCA hwloc: hwloc201 (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA if: linux_ipv6 (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA if: posix_ipv4 (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA installdirs: env (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA installdirs: config (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA memory: patcher (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA mpool: hugepage (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA patcher: overwrite (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA pmix: s2 (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA pmix: s1 (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA pstat: linux (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rcache: grdma (MCA v2.1.0, API v3.3.0, Component > > v4.1.5) > > MCA reachable: netlink (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA reachable: weighted (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA shmem: posix (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA shmem: mmap (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA shmem: sysv (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA timer: linux (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA errmgr: default_orted (MCA v2.1.0, API v3.0.0, > > Component v4.1.5) > > MCA errmgr: default_app (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA errmgr: default_tool (MCA v2.1.0, API v3.0.0, > > Component v4.1.5) > > MCA errmgr: default_hnp (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component v4.1.5) > > MCA ess: tool (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA ess: hnp (MCA v2.1.0, API v3.0.0, Component v4.1.5) > > MCA ess: env (MCA v2.1.0, API v3.0.0, Component v4.1.5) > > MCA filem: raw (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA grpcomm: direct (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA iof: orted (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA iof: hnp (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA iof: tool (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA odls: pspawn (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA odls: default (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA oob: tcp (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA plm: rsh (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA plm: isolated (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA regx: fwd (MCA v2.1.0, API v1.0.0, Component v4.1.5) > > MCA regx: reverse (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA regx: naive (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA rmaps: rank_file (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rmaps: ppr (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA rmaps: mindist (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rmaps: seq (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA rmaps: resilient (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rmaps: round_robin (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rml: oob (MCA v2.1.0, API v3.0.0, Component v4.1.5) > > MCA routed: radix (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA routed: binomial (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA routed: direct (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA rtc: hwloc (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA schizo: flux (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA schizo: orte (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA schizo: jsm (MCA v2.1.0, API v1.0.0, Component v4.1.5) > > MCA schizo: ompi (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA state: novm (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA state: tool (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA state: orted (MCA v2.1.0, API v1.0.0, Component > > v4.1.5) > > MCA state: hnp (MCA v2.1.0, API v1.0.0, Component v4.1.5) > > MCA state: app (MCA v2.1.0, API v1.0.0, Component v4.1.5) > > MCA bml: r2 (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA coll: tuned (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: libnbc (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: basic (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: monitoring (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: self (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: sync (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: sm (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA coll: adapt (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: inter (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA coll: han (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > MCA fbtl: posix (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA fcoll: individual (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA fcoll: dynamic_gen2 (MCA v2.1.0, API v2.0.0, > > Component v4.1.5) > > MCA fcoll: vulcan (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA fcoll: two_phase (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA fcoll: dynamic (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA fs: ufs (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA io: romio321 (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA io: ompio (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA mtl: ofi (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA mtl: psm2 (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA op: avx (MCA v2.1.0, API v1.0.0, Component v4.1.5) > > > > MCA osc: pt2pt (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA osc: monitoring (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA osc: rdma (MCA v2.1.0, API v3.0.0, Component > > v4.1.5) > > MCA osc: sm (MCA v2.1.0, API v3.0.0, Component v4.1.5) > > > > MCA pml: v (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA pml: ob1 (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA pml: cm (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA pml: monitoring (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA rte: orte (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA sharedfp: lockedfile (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA sharedfp: individual (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > MCA sharedfp: sm (MCA v2.1.0, API v2.0.0, Component v4.1.5) > > > > MCA topo: basic (MCA v2.1.0, API v2.2.0, Component > > v4.1.5) > > MCA topo: treematch (MCA v2.1.0, API v2.2.0, Component > > v4.1.5) > > MCA vprotocol: pessimist (MCA v2.1.0, API v2.0.0, Component > > v4.1.5) > > > > > > > > > > Z. Matthias Krawutschke > > > > > > > On Donnerstag, Mai 18, 2023 at 5:47 PM, christof.koehler--- via users < > > users@lists.open-mpi.org (mailto:users@lists.open-mpi.org)> wrote: > > > > Hello again, > > > > > > > > I should add that the openmpi configure decides to use the internal > > pmix > > > > > > > > configure: WARNING: discovered external PMIx version is less than > > internal version 3.x > > > > configure: WARNING: using internal PMIx > > > > ... > > > > ... > > > > checking if user requested PMI support... yes > > > > checking for pmi.h in /usr/include... not found > > > > checking for pmi.h in /usr/include/slurm... found > > > > checking pmi.h usability... yes > > > > checking pmi.h presence... yes > > > > checking for pmi.h... yes > > > > checking for libpmi in /usr/lib64... found > > > > checking for PMI_Init in -lpmi... yes > > > > checking for pmi2.h in /usr/include... not found > > > > checking for pmi2.h in /usr/include/slurm... found > > > > checking pmi2.h usability... yes > > > > checking pmi2.h presence... yes > > > > checking for pmi2.h... yes > > > > checking for libpmi2 in /usr/lib64... found > > > > checking for PMI2_Init in -lpmi2... yes > > > > checking for pmix.h in ... not found > > > > checking for pmix.h in /include... not found > > > > checking can PMI support be built... yes > > > > checking if user requested internal PMIx support(yes)... no > > > > checking for pmix.h in /usr... not found > > > > checking for pmix.h in /usr/include... found > > > > checking libpmix.* in /usr/lib64... found > > > > checking PMIx version... version file found > > > > checking version 4x... found > > > > checking PMIx version to be used... internal > > > > > > > > I am not sure how it decides that, the external one is already a quite > > > > new version. > > > > > > > > # srun --mpi=list > > > > MPI plugin types are... > > > > pmix > > > > cray_shasta > > > > none > > > > pmi2 > > > > specific pmix plugin versions available: pmix_v4 > > > > > > > > > > > > Best Regards > > > > > > > > Christof > > > > > > > > -- > > > > Dr. rer. nat. Christof Köhler email: c.koeh...@uni-bremen.de > > > > Universitaet Bremen/FB1/BCCMS phone: +49-(0)421-218-62334 > > > > Am Fallturm 1/ TAB/ Raum 3.06 fax: +49-(0)421-218-62770 > > > > 28359 Bremen > > > > > > > > -- > > Dr. rer. nat. Christof Köhler email: c.koeh...@uni-bremen.de > > Universitaet Bremen/FB1/BCCMS phone: +49-(0)421-218-62334 > > Am Fallturm 1/ TAB/ Raum 3.06 fax: +49-(0)421-218-62770 > > 28359 Bremen > > -- Dr. rer. nat. Christof Köhler email: c.koeh...@uni-bremen.de Universitaet Bremen/FB1/BCCMS phone: +49-(0)421-218-62334 Am Fallturm 1/ TAB/ Raum 3.06 fax: +49-(0)421-218-62770 28359 Bremen
