[gmx-users] Running gromacs 4.6.5 on BGQ

[Mark Abraham]

Compiling a functional BG/Q installation of GROMACS requires using two
different compilers. Your first installation has MPI, which is not useful
for the tools (see
http://www.gromacs.org/Documentation/Installation_Instructions#5.3.2._BlueGene.2fQ),
and (apparently, from your symptoms) the XL compiler for the back end, not
gcc for the front end. See your-build-dir/src/buildinfo.h to confirm. You
will need to consult your local documentation for how to set up your
environment to use the recommended front-end compiler, so that a new run of
cmake will detect it.

Mark


On Fri, Dec 13, 2013 at 6:24 AM, didymos <tomek.wlodarski at gmail.com> wrote:

> Hi,
>
> I installed the newest version of gromacs on BGQ:
> I used these options for whole installation
> cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/
> -DGMX_DOUBLE=ON -DCMAKE_PREFIX_PATH=$HOME/fftw/  ..
>
>
> and this option for mdrun installation:
> cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX -DGMX_DOUBLE=ON
> -DCMAKE_PREFIX_PATH=$HOME/fftw/ ..
>
>
> And it installed without errors.
> But, whenever I try to run any gromacs tool both on access node or in the
> queue I always end up with this error:
>
>
> /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h:102:
>
> /bgsys/source/srcV1R2M0.3103/comm/sys/buildtools/pami/common/bgq/BgqPersonality.h<102>
> Abort
>
> I tried to install with and without static links but it does not help
> much...
> I use gcc 4.4.6 and XL 12.1.0
> Any ideas?
> Thank you.
> Best,
>
> tomek
>
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