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