That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you can see in that file what the FFTW build thinks about its compiler.
Mark On Mon, Jun 3, 2013 at 4:00 PM, escajarro <juan-manuel.casti...@mv.uni-kl.de > wrote: > Hello all, > > I have a very similar problem, but compiling both Gromacs 4.6 and 4.6.1 > with > cmake and MPI support (no problems with non-MPI installation). I have cmake > version 2.8.7, openmpi version 1.4.1, and I am using gcc version 4.6.3 in a > linux Ubuntu 4.6.3. I use the cmake options: > > cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi > > A summary of the output given by this command is: > > CUDA_TOOLKIT_ROOT_DIR not found or specified > -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR > CUDA_NVCC_EXECUTABLE > CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "3.2") > -- The GROMACS-managed build of FFTW 3 will configure with the following > optimizations: --enable-sse2 > -- Configuring done > -- Generating done > -- Build files have been written to: /home/smith/gromacs-4.6 > > I believe that not having CUDA installed is not a problem, as I do not plan > to run in GPU, and nowhere in the installation manual says that it is > obligatory. After running make, the simulation stops with the following > message: > > Linking C shared library libgmx_mpi.so > [ 53%] Built target gmx > Scanning dependencies of target gromacs_include_links > [ 53%] Generating gromacs > [ 53%] Built target gromacs_include_links > Scanning dependencies of target template > [ 53%] Building C object > share/template/CMakeFiles/template.dir/template.c.o > Linking C executable template > ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__mth_i_dfloatuk' > ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to > `__builtin_va_gparg1' > ../../src/gmxlib/libgmx_mpi.so.6: undefined reference to `__pgdbg_stub' > collect2: ld returned 1 exit status > make[2]: *** [share/template/template] Error 1 > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 > make: *** [all] Error 2 > > It looks like I lack one library somehow, but I do not know which one. I > tried to install fftw before installing gromacs, and tried with both shared > and dynamic libraries with the same result. > > Can anybody help? > > Thanks > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/gmx-4-6-mpi-installation-through-openmpi-tp5006975p5008730.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists