[gmx-users] compile Gromacs using Cray compilers

[Humayun Arafat]

I am only interested in GPU code.
Is there anyway I can just run this using cray compilers?

thanks


On Mon, May 20, 2013 at 12:06 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> The thread-MPI library provides the thread affinity setting
> functionality to mdrun, hence certain parts of it will always be
> compiled in, even with GMX_MPI=ON. Apparently, the Cray compiler does
> not like some of the thread-MPI headers. Feel free to file a bug
> report on redmine.gromacs.org, but *don't* expect it to get high
> priority (reasons below).
>
> FYI, the Cray compiler does not support SIMD intrinsics and therefore
> you can't use any of the SIMD accelerated  code. hence, the overall
> performance will be at least 3x lower than with a compiler that has
> decent SIMD instrinsics support.
>
> --
> Szilárd
>
>
> On Mon, May 20, 2013 at 6:16 PM, Humayun Arafat <hasagar at gmail.com> wrote:
> > 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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