[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Szilárd Páll]

On Thu, Oct 22, 2015 at 6:06 PM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> so is it ok to try this?
>

Trying rarely hurts. :)


> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>


The CMKAE_SKIP_RPATH=ON part is only needed if you need/want to build
static binaries for the compute nodes.  As the Cray wrappers do some magic
behind the scenes in order to link statically, this ends up confusig cmake
which assumes that the resulting binaries will be dynamically linked.
Hence, the last step of setting the RPATH would fail (except if you tell
the Cray wrappers to stop the trickery and link dynamically: export
CRAYPE_LINK_TYPE=dynamic').

To build dynamically linked binaries for login nodes omitting RPATH is not
be necessary - and in fact it makes your/the users' life harder because
LD_LIBRARY_PATH will need to be set whenever running tools.



>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Your blas and lapack were compiled with gfortran, but in a way that they
> > require that one links further dependencies to use them later on. So
> > compile them better, or use dynamic linking.
> >
> > But 99.9% of GROMACS users do not need to get involved with this, so just
> > leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
> > internal versions.
> >
> > Mark
> >
> >
> --
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