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 <hasa...@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 <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? 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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? 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