Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Jeff Hammond
You must be using an older version of Gromacs, because the version I'm looking at (git master) has nary a reference to the C++ bindings. Since you say that Gromacs alone compiles fine, I suspect the problem is that Plumed uses the C++ bindings. The Plumed download site hosted by Google Docs (yuck

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Tomek Wlodarski
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 c

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Jeff Squyres (jsquyres)
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 Makefi

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Tomek Wlodarski
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 us

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Jeff Squyres (jsquyres)
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 w

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Tomek Wlodarski
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

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

2013-07-09 Thread Jeff Squyres (jsquyres)
Please send all the information listed here: http://www.open-mpi.org/community/help/ On Jul 9, 2013, at 8:36 AM, Tomek Wlodarski wrote: > 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 r