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 <rol...@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.abra...@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 <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/Searchbefore > >> > >> 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 > >> > > -- > > 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
