[gmx-users] compile Gromacs using Cray compilers

[Mark Abraham]

Specify an MPI compiler and use cmake -DGMX_MPI=on by itself. That is
mutually exclusive with thread mpi.

Mark


On Mon, May 20, 2013 at 5:01 PM, Humayun Arafat <hasagar at gmail.com> wrote:

> Hi,
>
> I tried different options.
>
> cmake -DGMX_MPI=ON/OFF ..
> cmake -DGMX_THREAD_MPI=OFF/ON ..
>
> I tried both of these two flags together. But none of them worked.
> The compilation fail in either gmx_omp.c or gmx_thread_affinity.c
>
> Can you please suggest me another way to turn off the thread mpi?
>
> Thanks
> Humayun
>
> On Fri, May 17, 2013 at 6:54 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > Cray's compiler is largely/wholly untested. I'd suggest you use the
> version
> > of gcc that you know works.
> >
> > For use on a big cluster, you probably don't want Thread MPI anyway. Does
> > cmake -DGMX_MPI work?
> >
> > Mark
> >
> >
> > On Sat, May 18, 2013 at 12:01 AM, Humayun Arafat <hasagar at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > >
> > > I need some help for the compilation of gromacs using Cray
> > compilers(CCE).
> > >
> > > I can compile gromacs using GNU compilers but not using CCE.
> > >
> > > I am using gromacs 4.6 and cmake 2.8.4 on Cray XE6
> > >
> > >
> > >
> > > After doing cmake, when I try to do make, I am getting this error.
> > >
> > >
> > >
> > > CC-20 craycc: ERROR File =
> > > /home/users/me/gromacs/include/thread_mpi/atomic.h, Line = 202
> > >
> > > The identifier "tMPI_Thread_mutex_t" is undefined.
> > >
> > > static tMPI_Thread_mutex_t tMPI_Atomic_mutex =
> > > TMPI_THREAD_MUTEX_INITIALIZER;
> > >
> > > ^
> > >
> > >
> > >
> > > Then I checked that the cmake  configuration had errors for this
> atomic.h
> > > header file.
> > >
> > > It does not find any atomic operations for cray compilers.
> > >
> > > Inside this header file, I see that there is nothing for Cray
> compilers.
> > >
> > > It has GNU,Intel, xlc….
> > >
> > > My guess is that probably it is not adding any atomic header file for
> > CCE.
> > >
> > >
> > >
> > >
> > > Please suggest me some ways to fix this.
> > >
> > > Thank you for your help.
> > >
> > >
> > > Thanks
> > >
> > > Humayun
> > > --
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