[gmx-users] compile Gromacs using Cray compilers

Humayun Arafat hasagar at gmail.com
Tue May 21 16:44:30 CEST 2013 

I am working on some specific features of Cray compiler.
But it seems like other features are also necessary.

Thanks a lot for the patch.


On Mon, May 20, 2013 at 6:48 PM, Roland Schulz <roland at utk.edu> wrote:

> Hi,
>
> I agree with Mark that it is probably not worth it. Why are you
> interested in it? Are you working on the Cray compiler or planning to
> use some specific features?
>
> You need to apply the patch here: https://gerrit.gromacs.org/#/c/2343/
> to get it to compile. But of course then it will still be much slower
> than GCC (and untested - so make sure to run tests). It would need
> support for at least atomics and intrinsics to get comparable speed.
>
> Roland
>
> On Mon, May 20, 2013 at 7:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > 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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