Yes, it looks like you are mixing multiple versions of Open MPI. It looks like you have installed Open MPI v1.10.0 via RPM in the system defaults location (perhaps in /usr/bin and /usr/lib and the like?), and then installed Open MPI v2.1.1 via building from source under your home directory (/home/user/EMAN2/bin and /home/user/EMAN2/lib and the like).
Your statement about your program working fine with MCA 2.0 is a little suspicious -- your should first clear up your PATH issues, recompile your application, and try running again. If that fails, please provide all the information listed in https://www.open-mpi.org/community/help/. > On Oct 13, 2017, at 11:41 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote: > > Hi, > > I'm bit confused now. > When I supply ompi_info, it gives: > [user@localhost openmpi-x86_64]$ ompi_info > [localhost.localdomain:11068] Error: Unable to get the current working > directory > Package: Open MPI root@3fecdf07461e Distribution > Open MPI: 2.1.1 > Open MPI repo revision: v2.1.0-100-ga2fdb5b > Open MPI release date: May 10, 2017 > Open RTE: 2.1.1 > Open RTE repo revision: v2.1.0-100-ga2fdb5b > Open RTE release date: May 10, 2017 > OPAL: 2.1.1 > OPAL repo revision: v2.1.0-100-ga2fdb5b > OPAL release date: May 10, 2017 > MPI API: 3.1.0 > Ident string: 2.1.1 > Prefix: /home/user/EMAN2 > Configured architecture: x86_64-unknown-linux-gnu > > Form the Bold line, I assume it is sourcing this version and loading 2.1.1 by > default. > > But when I provide: rpm -qf /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap.so > It gives me: openmpi-1.10.0-10.el7.x86_64 > > So, I think I'm having some sort of path issue. Is that right ? The program I > wish to run will go fine with MCA 2.0. > > On Fri, Oct 13, 2017 at 3:06 PM, Jeff Squyres (jsquyres) <jsquy...@cisco.com> > wrote: > From the output you supplied, it looks like you are running Open MPI v2.1.x. > > Did you install Open MPI v2.1.x from source, and install it into the same > directory that you had previously installed Open MPI v2.0.x? > > If so, the warnings you are seeing (not errors) are likely the fact that > there are some Open MPI v2.0.x plugins left over in the Open MPI v2.1.x > installation tree (installing version B of Open MPI over a previous > installation of Open MPI version A does *not* remove all of version A's > files). > > You should probably get a clean install of Open MPI v2.1.x, and the warnings > will disappear. > > See https://www.open-mpi.org/faq/?category=building#install-overwrite for > more details. > > > > > On Oct 13, 2017, at 10:02 AM, Gilles Gouaillardet > > <gilles.gouaillar...@gmail.com> wrote: > > > > one more thing, > > can you run > > rpm -qf /usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap.so > > and make sure this comes from the openmpi rpm ? > > > > if not, you can remove the openmpi rpm, rm -rf > > /usr/lib64/openmpi/lib/openmpi and then re-install the rpm > > > > Cheers, > > > > Gilles > > > > On Fri, Oct 13, 2017 at 10:49 PM, Gilles Gouaillardet > > <gilles.gouaillar...@gmail.com> wrote: > >> can you run ldd on your binary ? > >> i suspect it might not use the right Open MPI library > >> > >> Cheers, > >> > >> Gilles > >> > >> On Fri, Oct 13, 2017 at 10:41 PM, abhisek Mondal <abhisek.m...@gmail.com> > >> wrote: > >>> Hello, > >>> > >>> I'm getting this following error: > >>> [localhost.localdomain:00307] mca_base_component_repository_open: shmem > >>> "/usr/lib64/openmpi/lib/openmpi/mca_shmem_mmap" uses an MCA interface that > >>> is not recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- > >>> ignored > >>> [localhost.localdomain:00307] mca_base_component_repository_open: unable > >>> to > >>> open mca_shmem_posix: /usr/lib64/openmpi/lib/openmpi/mca_shmem_posix.so: > >>> undefined symbol: opal_shmem_base_output (ignored) > >>> [localhost.localdomain:00307] mca_base_component_repository_open: shmem > >>> "/usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv" uses an MCA interface that > >>> is not recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- > >>> ignored > >>> > >>> I had installed it using yum command: yum install openmpi-1.10.0-10.el7 > >>> > >>> My current MCA version is showing 2.1.0. > >>> > >>> On Fri, Oct 13, 2017 at 1:24 PM, Gilles Gouaillardet > >>> <gilles.gouaillar...@gmail.com> wrote: > >>>> > >>>> Hi, > >>>> > >>>> let's take one or two steps back. > >>>> > >>>> which version of Open MPI did you use in order to build your program ? > >>>> > >>>> what does "not working under MCA2.1" mean ? > >>>> link error ? unresolved symbols ? runtime crash ? > >>>> > >>>> please detail your environment and post all relevant error messages > >>>> > >>>> Cheers, > >>>> > >>>> Gilles > >>>> > >>>> On Fri, Oct 13, 2017 at 10:17 PM, abhisek Mondal <abhisek.m...@gmail.com> > >>>> wrote: > >>>>> > >>>>> Hi, > >>>>> > >>>>> I have installed an openmpi using following command: > >>>>> yum install openmpi-1.10.0-10.el7 > >>>>> > >>>>> When I put ompi_info command it shows me that it is using MCAv.2.1. Is > >>>>> there > >>>>> any way I can use MCA2.0 ? > >>>>> > >>>>> My program is not working under MCA2.1. > >>>>> Please help me out here. > >>>>> > >>>>> Thank you. > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Abhisek Mondal > >>>>> Senior Research Fellow > >>>>> Structural Biology and Bioinformatics Division > >>>>> CSIR-Indian Institute of Chemical Biology > >>>>> Kolkata 700032 > >>>>> INDIA > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>> > >>> > >>> > >>> > >>> -- > >>> Abhisek Mondal > >>> Senior Research Fellow > >>> Structural Biology and Bioinformatics Division > >>> CSIR-Indian Institute of Chemical Biology > >>> Kolkata 700032 > >>> INDIA > >>> > >>> _______________________________________________ > >>> 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 > > > -- > Jeff Squyres > jsquy...@cisco.com > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users > > > > -- > Abhisek Mondal > Senior Research Fellow > Structural Biology and Bioinformatics Division > CSIR-Indian Institute of Chemical Biology > Kolkata 700032 > INDIA > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users -- Jeff Squyres jsquy...@cisco.com _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
