[gmx-users] compile Gromacs using Cray compilers

[Humayun Arafat]

Hi,

I enabled mpich2 and used that to compile gromacs using this command
cmake   -DGMX_MPI=ON ..

But I am still getting the error.

[ 10%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/gmx_thread_affinity.c.o
CC-20 craycc: ERROR File =
/home/users/mmm/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;


It seems like even though it is disabling threadmpi, it is still making
some tests
I added some part of the cmake output.

-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Checking for CRAY XT Catamount compile
-- Checking for CRAY XT Catamount target - no
CMake Warning at cmake/ThreadMPI.cmake:52 (message):
  Atomic operations not found for this CPU+compiler combination.  Thread
  support will be unbearably slow: disable threads.  Atomic operations
should
  work on all but the most obscure CPU+compiler combinations; if your system
  is not obscure -- like, for example, x86 with gcc -- please contact the
  developers.
Call Stack (most recent call first):
  cmake/ThreadMPI.cmake:100 (test_tmpi_atomics)
  CMakeLists.txt:558 (include)


thanks a lot for your help.



On Mon, May 20, 2013 at 10:34 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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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