[OMPI users] error while using open mpi to compile parallel-netcdf-1.8.1
Hi I compiled openmpi-3.1.2 using pgi 18.10 on our IBM power9 machine. After that, I used openmpi-3.1.2 to compile parallel-netcdf-1.8.1. However, I got the following error. ./nc_test -c-d . [c699login01:12104] mca_base_component_repository_open: unable to open mca_plm_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored) [c699login01:12104] mca_base_component_repository_open: unable to open mca_ras_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored) -- WARNING: There are more than one active ports on host 'c699login01', but the default subnet GID prefix was detected on more than one of these ports. If these ports are connected to different physical IB networks, this configuration will fail in Open MPI. This version of Open MPI requires that every physically separate IB subnet that is used between connected MPI processes must have different subnet ID values. Please see this FAQ entry for more details: http://www.open-mpi.org/faq/?category=openfabrics#ofa-default-subnet-gid NOTE: You can turn off this warning by setting the MCA parameter btl_openib_warn_default_gid_prefix to 0. -- [c699login01:12103] *** Process received signal *** [c699login01:12103] Signal: Segmentation fault (11) [c699login01:12103] Signal code: (3) [c699login01:12103] Failing at address: 0x615f6c61706f0064 [c699login01:12103] [ 0] [0x200504d8] [c699login01:12103] [ 1] [0x34333164] [c699login01:12103] [ 2] /lib64/libc.so.6(__sbrk+0x98)[0x20729b28] [c699login01:12103] [ 3] /lib64/libc.so.6(__default_morecore+0x18)[0x206aece8] [c699login01:12103] [ 4] /lib64/libc.so.6(+0x9511c)[0x206a511c] [c699login01:12103] [ 5] /lib64/libc.so.6(+0x96ff4)[0x206a6ff4] [c699login01:12103] [ 6] /lib64/libc.so.6(__libc_malloc+0x8c)[0x206a938c] [c699login01:12103] [ 7] /home/vy57456/application/pgi/18.10/openmpi-3.1.2/lib/libopen-pal.so.40(opal_show_help_yylex+0x98)[0x2099a8e0] [c699login01:12103] [ 8] /home/vy57456/application/pgi/18.10/openmpi-3.1.2/lib/libopen-pal.so.40(opal_show_help_vstring+0x25c)[0x2099a2f4] [c699login01:12103] [ 9] /home/vy57456/application/pgi/18.10/openmpi-3.1.2/lib/libopen-rte.so.40(orte_show_help+0x70)[0x20838f48] [c699login01:12103] [10] /home/vy57456/application/pgi/18.10/openmpi-3.1.2/lib/openmpi/mca_btl_openib.so(+0x160d4)[0x236060d4] For detail about error, please see the attached file. Best, Zhifeng make -C test testing make[1]: Entering directory `/autofs/home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/test' make -w -C common testing make[2]: Entering directory `/autofs/home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/test/common' make[2]: Nothing to be done for `testing'. make[2]: Leaving directory `/autofs/home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/test/common' make -w -C nc_test testing make[2]: Entering directory `/autofs/home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/test/nc_test' /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o nc_test nc_test.o error.o util.o test_get.o test_put.o test_iget.o test_iput.o test_read.o test_write.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o t_nc t_nc.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o tst_misc tst_misc.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o tst_norm tst_norm.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o tst_small tst_small.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o tst_names tst_names.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib /home/vy57456/application/pgi/source_code/parallel-netcdf-1.8.1/src/lib/libpnetcdf.a -ltestutils -lm /home/vy57456/application/pgi/18.10/openmpi-3.1.2/bin/mpicc -g -o tst_atts3 tst_atts3.o -L../common -L/home/vy57456/application/pgi/18.10/netcdf-4.6.1/lib
Re: [OMPI users] IRC/Discord?
Oh, you would get overwhelmed, almost certainly. On Wed, Mar 6, 2019 at 10:47 AM Ralph H Castain wrote: > > We currently reserve the Slack channel for developers. We might be willing to > open a channel for users, but we’d have to discuss it - there is a concern > that we not get overwhelmed :-) > > > > On Mar 6, 2019, at 3:06 AM, George Marselis > > wrote: > > > > Cool! May I please get an invitation? > > > > > > Best Regards, > > > > > > George Marselis > > > > > > From: users on behalf of Ralph H Castain > > > > Sent: Tuesday, March 5, 2019 5:12 PM > > To: Open MPI Users > > Subject: Re: [OMPI users] IRC/Discord? > > > > Not IRC or discord, but we do make significant use of Slack: > > open-mpi.slack.com > > > > > >> On Mar 5, 2019, at 8:04 AM, George Marselis > >> wrote: > >> > >> Hey guys, > >> > >> Sorry to bother you. I was wondering if there is an IRC or discord channel > >> for this mailing list. > >> > >> (there is an IRC channel on Freenode under #openmpi but it's like 2 people > >> in it) > >> > >> Thank you for your time > >> > >> Best Regards, > >> > >> > >> George Marselis > >> ___ > >> users mailing list > >> users@lists.open-mpi.org > >> https://lists.open-mpi.org/mailman/listinfo/users > > > > ___ > > users mailing list > > users@lists.open-mpi.org > > https://lists.open-mpi.org/mailman/listinfo/users > > ___ > > users mailing list > > users@lists.open-mpi.org > > https://lists.open-mpi.org/mailman/listinfo/users > > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] IRC/Discord?
We currently reserve the Slack channel for developers. We might be willing to open a channel for users, but we’d have to discuss it - there is a concern that we not get overwhelmed :-) > On Mar 6, 2019, at 3:06 AM, George Marselis > wrote: > > Cool! May I please get an invitation? > > > Best Regards, > > > George Marselis > > > From: users on behalf of Ralph H Castain > > Sent: Tuesday, March 5, 2019 5:12 PM > To: Open MPI Users > Subject: Re: [OMPI users] IRC/Discord? > > Not IRC or discord, but we do make significant use of Slack: > open-mpi.slack.com > > >> On Mar 5, 2019, at 8:04 AM, George Marselis >> wrote: >> >> Hey guys, >> >> Sorry to bother you. I was wondering if there is an IRC or discord channel >> for this mailing list. >> >> (there is an IRC channel on Freenode under #openmpi but it's like 2 people >> in it) >> >> Thank you for your time >> >> Best Regards, >> >> >> George Marselis >> ___ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users > > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] IRC/Discord?
Cool! May I please get an invitation? Best Regards, George Marselis From: users on behalf of Ralph H Castain Sent: Tuesday, March 5, 2019 5:12 PM To: Open MPI Users Subject: Re: [OMPI users] IRC/Discord? Not IRC or discord, but we do make significant use of Slack: open-mpi.slack.com > On Mar 5, 2019, at 8:04 AM, George Marselis > wrote: > > Hey guys, > > Sorry to bother you. I was wondering if there is an IRC or discord channel > for this mailing list. > > (there is an IRC channel on Freenode under #openmpi but it's like 2 people in > it) > > Thank you for your time > > Best Regards, > > > George Marselis > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
