[gmx-users] compile Gromacs using Cray compilers
Humayun Arafat
hasagar at gmail.com
Tue May 21 00:40:21 CEST 2013
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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>
>
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