Dear Users: I am attempting to use the new BGQ kernels with the version of gromacs at https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:
git init git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 && git checkout FETCH_HEAD I then attempted to compile like this: module purge module load vacpp/12.1 xlf/14.1 mpich2/xl module load cmake/2.8.8 module load fftw/3.3.2 export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2 cmake ../source/ \ -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \ -DCMAKE_INSTALL_PREFIX=$(pwd) \ -DGMX_X11=OFF \ -DGMX_MPI=OFF \ -DGMX_PREFER_STATIC_LIBS=ON make -j 4 make install ####################### That gave me the following error during make: Scanning dependencies of target gromacs_include_links [ 0%] Generating gromacs [ 0%] Built target gromacs_include_links Scanning dependencies of target gmx [ 0%] [ 0%] [ 0%] [ 0%] [ 0%] [ 0%] [ 0%] [ 0%] [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md_logging.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o [ 1%] [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cpuid.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o [ 1%] [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_thread_affinity.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o [ 1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_omp.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o "/home/p/pomes/cneale/exec/gromacs-4.6.3_bgq/source/src/gmxlib/network.c", line 264.10: 1506-296 (S) #include file <spi/include/kernel/location.h> not found. make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 ####################### After some looking around, I added the following line before cmake: export CFLAGS=-I/bgsys/drivers/ppcfloor That solved the initial problem, but now I have the following error: ... [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o [ 2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o [ 3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o "/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 34.10: 1506-296 (S) #include file "kernel_impl.h" not found. "/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 36.10: 1506-296 (S) #include file "kernel_impl.h" not found. "/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 194.10: 1506-296 (S) #include file "process_impl.h" not found. "/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 173.10: 1506-296 (S) #include file "location_impl.h" not found. make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 ####################### And it's harder to know what to do now since there are multiple instances of kernel_impl.h , etc.: bgqdev-fen1-$ find /bgsys/drivers/ppcfloor/spi/include/kernel/|grep kernel_impl.h /bgsys/drivers/ppcfloor/spi/include/kernel/cnk/kernel_impl.h /bgsys/drivers/ppcfloor/spi/include/kernel/firmware/kernel_impl.h /bgsys/drivers/ppcfloor/spi/include/kernel/klinux/kernel_impl.h Does this indicate that the computer that I am using really has such a non-standard BG/Q setup? or is it possible that compiling on the BG/Q with the new verlet kernel requires an entirely different approach? I understand that the Jenkins Buildbot has successfully compiled this code. Is it possible to get a copy of that compilation script (I've never used Jenkins, perhaps it is not that simple)? Thank you, Chris. -- 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
