[OMPI users] undefined reference to `MPI::Comm::Comm()
Hi, I am trying to locally compile software which uses openmpi (1.6.3), but I got this error: restraint_camshift2.o:(.toc+0x98): undefined reference to `ompi_mpi_cxx_op_intercept' restraint_camshift2.o: In function `Intracomm': /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' restraint_camshift2.o: In function `Intracomm': /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm_inln.h:23: undefined reference to `MPI::Comm::Comm()' restraint_camshift2.o: In function `Intracomm': /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25: undefined reference to `MPI::Comm::Comm()' restraint_camshift2.o:/home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25: more undefined references to `MPI::Comm::Comm()' follow restraint_camshift2.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48): undefined reference to `MPI::Win::Free()' restraint_camshift2.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78): undefined reference to `MPI::Datatype::Free()' collect2: error: ld returned 1 exit status make[3]: *** [mdrun] Error 1 make[3]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 I am using gcc 4.7.3 Any ideas or suggestions? Thanks! Best, tomek
Re: [OMPI users] undefined reference to `MPI::Comm::Comm()
So I am running OpenMPi1.6.3 (config.log attached) And I would like to install gromacs patched with plumed (scientific computing). Both uses openmpi. Gromacs alone compiles without errors (openMPI works). But when patched I got one mentioned before. I am sending config file for patched gromacs. If you need any other file I would be happy to provide. Thanks a lot! Best, tomek config_gromacs.log.bz2 Description: BZip2 compressed data config_openmpi.log.bz2 Description: BZip2 compressed data
Re: [OMPI users] undefined reference to `MPI::Comm::Comm()
I used mpicc but when I switched in Makefile to mpic++ it compiled without errors. Thanks a lot! Best, tomek On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres) wrote: > I don't see all the info requested from that web page, but it looks like OMPI > built the C++ bindings ok. > > Did you use mpic++ to build Gromacs? > > > On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski wrote: > >> So I am running OpenMPi1.6.3 (config.log attached) >> And I would like to install gromacs patched with plumed (scientific >> computing). Both uses openmpi. >> Gromacs alone compiles without errors (openMPI works). But when >> patched I got one mentioned before. >> I am sending config file for patched gromacs. >> If you need any other file I would be happy to provide. >> Thanks a lot! >> Best, >> >> tomek >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] undefined reference to `MPI::Comm::Comm()
Oh you are right. Thanks. Best tomek On Tue, Jul 9, 2013 at 2:44 PM, Jeff Squyres (jsquyres) wrote: > If you care, the issue is that it looks like Gromacs is using the MPI C++ > bindings. You therefore need to use the MPI C++ wrapper compiler, mpic++ > (vs. mpicc, which is the MPI C wrapper compiler). > > > On Jul 9, 2013, at 9:41 AM, Tomek Wlodarski wrote: > >> I used mpicc but when I switched in Makefile to mpic++ it compiled >> without errors. >> Thanks a lot! >> Best, >> >> tomek >> >> On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres) >> wrote: >>> I don't see all the info requested from that web page, but it looks like >>> OMPI built the C++ bindings ok. >>> >>> Did you use mpic++ to build Gromacs? >>> >>> >>> On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski >>> wrote: >>> >>>> So I am running OpenMPi1.6.3 (config.log attached) >>>> And I would like to install gromacs patched with plumed (scientific >>>> computing). Both uses openmpi. >>>> Gromacs alone compiles without errors (openMPI works). But when >>>> patched I got one mentioned before. >>>> I am sending config file for patched gromacs. >>>> If you need any other file I would be happy to provide. >>>> Thanks a lot! >>>> Best, >>>> >>>> tomek >>>> ___ >>>> users mailing list >>>> us...@open-mpi.org >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> -- >>> Jeff Squyres >>> jsquy...@cisco.com >>> For corporate legal information go to: >>> http://www.cisco.com/web/about/doing_business/legal/cri/ >>> >>> >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
