Thank you for your assistance! I tried to compile it with either the --enabled-shared or --enable-static flag and they both seemed to have the same error as before (lnuma and ludev) unfortunately. A dropbox link to full output for each install is below:
https://www.dropbox.com/s/axnbze56iokyyqe/ompi-output_static_v_shared.tar.bz2?dl=0 I appreciate your help. I will run this by the admins of our HPC as well. Best, JD *Jeffrey D. (JD) Tamucci * University of Connecticut Molecular & Cell Biology RA in Lab of Eric R. May PhD / MPH Candidate he/him On Wed, Oct 5, 2022 at 1:53 PM Jeff Squyres (jsquyres) <jsquy...@cisco.com> wrote: > *Message sent from a system outside of UConn.* > > Actually, I think the problem might be a little more subtle. > > I see that you configured with both --enable-static and --enable-shared. > > My gut reaction is that there might be some kind of issue with enabling > both of those options (by default, shared is enabled and static is > disabled). If you configure+build with just one of those two options, does > it work? > > -- > Jeff Squyres > jsquy...@cisco.com > ------------------------------ > *From:* users <users-boun...@lists.open-mpi.org> on behalf of Pritchard > Jr., Howard via users <users@lists.open-mpi.org> > *Sent:* Wednesday, October 5, 2022 11:47 AM > *To:* Jeffrey D. (JD) Tamucci <jeffrey.tamu...@uconn.edu> > *Cc:* Pritchard Jr., Howard <howa...@lanl.gov>; Open MPI Users < > users@lists.open-mpi.org> > *Subject:* Re: [OMPI users] [EXTERNAL] Beginner Troubleshooting OpenMPI > Installation - pmi.h Error > > > Hi Jeff, > > > > I think you are now in the “send the system admin an email to install > RPMs, in particular ask that the numa and udev devel rpms be installed”. > They will need to install these rpms on the compute node image(s) as well. > > > > Howard > > > > > > *From: *"Jeffrey D. (JD) Tamucci" <jeffrey.tamu...@uconn.edu> > *Date: *Wednesday, October 5, 2022 at 9:20 AM > *To: *"Pritchard Jr., Howard" <howa...@lanl.gov> > *Cc: *"bbarr...@amazon.com" <bbarr...@amazon.com>, Open MPI Users < > users@lists.open-mpi.org> > *Subject: *Re: [EXTERNAL] [OMPI users] Beginner Troubleshooting OpenMPI > Installation - pmi.h Error > > > > Gladly, I tried it that way and it worked in that it was able to find > pmi.h. Unfortunately there's a new error about finding lnuma and ludev. > > > > make[2]: Entering directory '/shared/maylab/src/openmpi-4.1.4/opal' > CCLD libopen-pal.la > <https://urldefense.com/v3/__http:/libopen-pal.la__;!!Bt8fGhp8LhKGRg!BWR7snajnpicZF4YgkUocF-Zm3n1tT0PSpwsOGfvHrB1qcFmYIq9xU56yhcjTEBv6oq1Z5meQDixEwQJWs4fc6wp3HEFfA$> > /usr/bin/ld: cannot find -lnuma > /usr/bin/ld: cannot find -ludev > collect2: error: ld returned 1 exit status > make[2]: *** [Makefile:2249: libopen-pal.la > <https://urldefense.com/v3/__http:/libopen-pal.la__;!!Bt8fGhp8LhKGRg!BWR7snajnpicZF4YgkUocF-Zm3n1tT0PSpwsOGfvHrB1qcFmYIq9xU56yhcjTEBv6oq1Z5meQDixEwQJWs4fc6wp3HEFfA$>] > Error 1 > make[2]: Leaving directory '/shared/maylab/src/openmpi-4.1.4/opal' > make[1]: *** [Makefile:2394: install-recursive] Error 1 > make[1]: Leaving directory '/shared/maylab/src/openmpi-4.1.4/opal' > make: *** [Makefile:1912: install-recursive] Error 1 > > > > Here is a dropbox link to the full output: > https://www.dropbox.com/s/4rv8n2yp320ix08/ompi-output_Oct4_2022.tar.bz2?dl=0 > <https://urldefense.com/v3/__https:/www.dropbox.com/s/4rv8n2yp320ix08/ompi-output_Oct4_2022.tar.bz2?dl=0__;!!Bt8fGhp8LhKGRg!BWR7snajnpicZF4YgkUocF-Zm3n1tT0PSpwsOGfvHrB1qcFmYIq9xU56yhcjTEBv6oq1Z5meQDixEwQJWs4fc6y8gBZt9g$> > > > > Thank you for your help! > > > > JD > > > > > > *Jeffrey D. (JD) Tamucci * > > University of Connecticut > > Molecular & Cell Biology > > RA in Lab of Eric R. May > > PhD / MPH Candidate > > he/him > > > > > > On Tue, Oct 4, 2022 at 1:51 PM Pritchard Jr., Howard <howa...@lanl.gov> > wrote: > > *Message sent from a system outside of UConn.* > > > > Could you change the –with-pmi to be > > --with-pmi=/cm/shared/apps/slurm21.08.8 > > > > ? > > > > > > *From: *"Jeffrey D. (JD) Tamucci" <jeffrey.tamu...@uconn.edu> > *Date: *Tuesday, October 4, 2022 at 10:40 AM > *To: *"Pritchard Jr., Howard" <howa...@lanl.gov>, "bbarr...@amazon.com" < > bbarr...@amazon.com> > *Cc: *Open MPI Users <users@lists.open-mpi.org> > *Subject: *Re: [EXTERNAL] [OMPI users] Beginner Troubleshooting OpenMPI > Installation - pmi.h Error > > > > Hi Howard and Brian, > > > > Of course. Here's a dropbox link to the full folder: > https://www.dropbox.com/s/raqlcnpgk9wz78b/ompi-output_Sep30_2022.tar.bz2?dl=0 > <https://urldefense.com/v3/__https:/www.dropbox.com/s/raqlcnpgk9wz78b/ompi-output_Sep30_2022.tar.bz2?dl=0__;!!Bt8fGhp8LhKGRg!Gbf2ik51d_yyLNSd0MxiRpzUUleMIUbnc_K_GZiX3bNyn_5hxYeebIpaGygYEZebCOMxxbVZugqOTreswGqTKVLD8RFMow$> > > > > This was the configure and make commands: > > ./configure \ > --prefix=/shared/maylab/mayapps/mpi/openmpi/4.1.4 \ > --with-slurm \ > --with-lsf=no \ > --with-pmi=/cm/shared/apps/slurm/21.08.8/include/slurm \ > --with-pmi-libdir=/cm/shared/apps/slurm/21.08.8/lib64 \ > --with-hwloc=/cm/shared/apps/hwloc/1.11.11 \ > --with-cuda=/gpfs/sharedfs1/admin/hpc2.0/apps/cuda/11.6 \ > --enable-shared \ > --enable-static && > make -j 32 && > make -j 32 check > make install > > The output of the make command is in the install_open-mpi_4.1.4_hpc2.log > file. > > > > > > *Jeffrey D. (JD) Tamucci * > > University of Connecticut > > Molecular & Cell Biology > > RA in Lab of Eric R. May > > PhD / MPH Candidate > > he/him > > > > > > On Tue, Oct 4, 2022 at 12:33 PM Pritchard Jr., Howard <howa...@lanl.gov> > wrote: > > *Message sent from a system outside of UConn.* > > > > HI JD, > > > > Could you post the configure options your script uses to build Open MPI? > > > > Howard > > > > *From: *users <users-boun...@lists.open-mpi.org> on behalf of "Jeffrey D. > (JD) Tamucci via users" <users@lists.open-mpi.org> > *Reply-To: *Open MPI Users <users@lists.open-mpi.org> > *Date: *Tuesday, October 4, 2022 at 10:07 AM > *To: *"users@lists.open-mpi.org" <users@lists.open-mpi.org> > *Cc: *"Jeffrey D. (JD) Tamucci" <jeffrey.tamu...@uconn.edu> > *Subject: *[EXTERNAL] [OMPI users] Beginner Troubleshooting OpenMPI > Installation - pmi.h Error > > > > Hi, > > > > I have been trying to install OpenMPI v4.1.4 on a university HPC cluster. > We use the Bright cluster manager and have SLURM v21.08.8 and RHEL 8.6. I > used a script to install OpenMPI that a former co-worker had used to > successfully install OpenMPI v3.0.0 previously. I updated it to include new > versions of the dependencies and new paths to those installs. > > > > Each time, it fails in the *make install *step. There is a fatal error > about finding pmi.h. It specifically says: > > > > make[2]: Entering directory > '/shared/maylab/src/openmpi-4.1.4/opal/mca/pmix/s1' > CC libmca_pmix_s1_la-pmix_s1_component.lo > CC libmca_pmix_s1_la-pmix_s1.lo > pmix_s1.c:29:10: fatal error: pmi.h: No such file or directory > 29 | #include <pmi.h> > > > > I've looked through the archives and seen others face similar errors in > years past but I couldn't understand the solutions. One person suggested > that SLURM may be missing PMI libraries. I think I've verified that SLURM > has PMI. I include paths to those files and it seems to find them earlier > in the process. > > > > I'm not sure what the next step is in troubleshooting this. I have > included a bz2 file containing my install script, a log file containing the > script output (from build, make, make install), the config.log, and the > opal_config.h file. If anyone could provide any guidance, I'd sincerely > appreciate it. > > > > Best, > > JD > >
