[gmx-users] compile Gromacs using Cray compilers

Mark Abraham mark.j.abraham at gmail.com
Tue May 21 01:01:08 CEST 2013 

Hi,

Fixing or working around Cray's compilers (whether atomic support or vector
intrinsics) is really not worth any of our time if gcc+mpi is available.

Mark


On Tue, May 21, 2013 at 12:40 AM, Humayun Arafat <hasagar at gmail.com> wrote:

> Hi Roland,
>
> I can actually try to solve some issues with Cray compiler  if you can give
> me some idea what is needed.
> Currently I get error for the atomic.h inside thread_mpi. I think it needs
> intrinsics.
> Maybe there are some others as well.
>
> Please let me know the issues.
>
> thanks
>
>
>
> On Mon, May 20, 2013 at 5:09 PM, Roland Schulz <roland at utk.edu> wrote:
>
> > On Mon, May 20, 2013 at 1:23 PM, Humayun Arafat <hasagar at gmail.com>
> wrote:
> > > I am only interested in GPU code.
> > > Is there anyway I can just run this using cray compilers?
> > Why do you want to use the cray compilers? As Mark said those aren't
> > supported. We reported the problems with them to Cray but AFAIK they
> > haven't fixed them.
> > FYI Cray's also have other compilers usually installed. You usually
> > use them by something like: "module swap PrgEnv-cray PrgEnv-gnu"
> >
> > Roland
> >
> > >
> > > 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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