[gmx-users] Re: gmx 4.6 mpi installation through openmpi?

[Mark Abraham]

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.castillo at 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:
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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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