[gmx-users] Compilation issues with GROMACS 5 beta 2

[Roland Schulz]

Hi

we have fixed quite a few installation issues since beta2. Could you try to
download the latest version from git?
git clone git://git.gromacs.org/gromacs.git

Let us know if you still see the issue.

If you don't have git you can download it from:
https://github.com/gromacs/gromacs/archive/master.zip

Roland


On Mon, Mar 17, 2014 at 8:10 AM, jk <broodkiller at gmail.com> wrote:

> Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently
> downloaded and tried to compile the second beta of GROMACS 5, and run into
> some issues along the way, so I decided to ask around and see if I can find
> some help. Basically, what I wanted to do was to compile a few different
> variants of GROMACS 5 to see how they perform against each other. I was
> interested in comparing single and double precision builds, CUDA vs no CUDA
> and MPI vs no MPI, in various combinations. Eventually though, I have only
> managed to succesfully compile a single-precision, CUDA-extended and
> MPI-paralellized build, and none other.
>
>
> Now to the details:
> (1) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=OFF
> terminates early with a fatal error of lacking MPI headers:
>
> [  3%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o
> In file included from
>
> /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/commrec.h:40:0,
>                  from
>
> /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/coulomb.h:43,
>                  from
>
> /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/gmxpreprocess/calc_verletbuf.c:49:
>
> /media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/../../utility/gmxmpi.h:62:17:
> fatal error: mpi.h: No such file or directory
> compilation terminated.
> make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o]
> Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> (2) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=ON
> terminates exactly the same, but after some CUDA stuff is compiled.
>
> (3) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=ON and -DGMX_GPU=OFF
> terminates at link with a fatal error of lacking CUDA-specific objects:
>
> [ 92%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
> `nbnxn_cuda_init_const'
> (...some more undefined refs)
> ../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
> `pick_compatible_gpus'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> (4) Compiling with -DGMX_DOUBLE=OFF, -DGMX_GPU=ON and -DGMX_MPI=ON works
> fine, as mentioned before.
>
> (5) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=OFF and -DGMX_GPU=OFF
> terminates identically as (1)
>
> (6) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=ON and -DGMX_GPU=OFF
> terminates identically as (3)
>
>
> Each recompilation attempt was made in a fresh direction, with all the
> files
> from a previous build removed, so as to avoid any conflicts. I can post
> links to complete compilation logs to PasteBin, if necessary. On the
> technical side of things, I am running a 64-bit Ubuntu 12.04 system on a
> quad-core i7-860 CPU, with 16GB of RAM and a brand new GTX 780Ti gfx card
> on
> hand-compiled CUDA 5.5 (driver+toolkit).
> Of the relevant libs, I have the latest FFTW-3.3.3 compiled nicely in
> single
> ('--enable-float --enable-shared --enable-sse2') and double precision
> ('--enable-shared --enable-sse2') variants stored in separate folders,
> which
> I pass to Cmake through the -DFFTW(F)_LIBRARY parameter. I have OpenMPI
> 1.4.3.2, MPICH2 and libboost 1.46.1, all from the offical Ubuntu repo.
>
> My guess is that the build system somehow disregards the flags sent to it
> and wants MPI/CUDA files even when directly told to skip them. Any ideas on
> how to fix/work around this?
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Compilation-issues-with-GROMACS-5-beta-2-tp5015221.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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