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 <rol...@utk.edu> wrote: > On Mon, May 20, 2013 at 1:23 PM, Humayun Arafat <hasa...@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.p...@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 <hasa...@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.abra...@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 <hasa...@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.abra...@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 < > hasa...@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 > >> >> > > > -- > >> >> > > > gmx-users mailing list gmx-users@gromacs.org > >> >> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> > > > * Please search the archive at > >> >> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > >> posting! > >> >> > > > * Please don't post (un)subscribe requests to the list. Use the > >> >> > > > www interface or send it to gmx-users-requ...@gromacs.org. > >> >> > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > >> >> > > > > >> >> > > -- > >> >> > > gmx-users mailing list gmx-users@gromacs.org > >> >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> > > * Please search the archive at > >> >> > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> >> > > * Please don't post (un)subscribe requests to the list. Use the > >> >> > > www interface or send it to gmx-users-requ...@gromacs.org. > >> >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > > > >> >> > -- > >> >> > gmx-users mailing list gmx-users@gromacs.org > >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> > * Please search the archive at > >> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> >> > * Please don't post (un)subscribe requests to the list. Use the > >> >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > > >> >> -- > >> >> gmx-users mailing list gmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> * Please search the archive at > >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> >> * Please don't post (un)subscribe requests to the list. Use the > >> >> www interface or send it to gmx-users-requ...@gromacs.org. > >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > * Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists