Hi Tsjerk, I've encountered problem #2 with GMX 4.0.2 before. I'm not exactly sure what went wrong, but it may have been due to mpi. With lammpi things work.
Hope that helps, Ran. Tsjerk Wassenaar wrote: > Hi, > > I'm running in trouble trying to compile gromacs 4.0.x on our national > Intel Xeon Linux cluster (Lisa/Sara). The same problem pops up with > different compilers (GNU GCC 3.4, 4.1 (default on the cluster :p), > Intel). I'm using fftw-3.2.1 and mpich/gnu c.q. mpich/intel. mdrun > compiles, but when I try to run it, it 1. starts running in the > gromacs installation directory and 2. starts the same job for every > processor rather than one job on all of them. Trying to run mdrun in > an interactive PBS job shows that it's really a problem with mdrun > itself. I must be overlooking something. Anyone have an idea? > > Neither ./configure nor make report any problems. The former I include > below for completeness. Of course I'd be happy to supply more > information on request or do some additional tests. > > I'll also contact the support team of the facility and report back if > they come up with a solution. > > Cheers, > > Tsjerk > > tsj...@login-ng1:~/gromacs-4.0.4$ ./configure > --prefix=/home/tsjerk/GMX404/ --enable-mpi --program-suffix="_mpi" > --disable-nice > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... /bin/mkdir -p > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking how to create a ustar tar archive... gnutar > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc-3.4 accepts -g... yes > checking for gcc-3.4 option to accept ISO C89... none needed > checking for style of include used by make... GNU > checking dependency style of gcc-3.4... gcc3 > checking dependency style of gcc-3.4... gcc3 > checking for mpxlc... no > checking for mpicc... mpicc > checking whether the MPI cc command works... yes > checking for catamount... no > checking how to run the C preprocessor... mpicc -E > checking whether mpicc accepts -O3... yes > checking whether mpicc accepts -funroll-all-loops... yes > checking whether mpicc accepts -O3 -fomit-frame-pointer > -finline-functions -Wall -Wno-unused -funroll-all-loops... yes > checking for grep that handles long lines and -e... /bin/grep > checking for egrep... /bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking whether byte ordering is bigendian... no > checking for int... yes > checking size of int... 4 > checking for long int... yes > checking size of long int... 4 > checking for long long int... yes > checking size of long long int... 8 > checking for off_t... yes > checking size of off_t... 4 > checking that size_t can hold pointers... yes > checking floating-point format... IEEE754 (little-endian byte and word order) > checking for a BSD-compatible install... /usr/bin/install -c > checking whether ln -s works... yes > checking whether make sets $(MAKE)... (cached) yes > checking for a sed that does not truncate output... /bin/sed > checking for ld used by mpicc... /usr/bin/ld > checking if the linker (/usr/bin/ld) is GNU ld... yes > checking for /usr/bin/ld option to reload object files... -r > checking for BSD-compatible nm... /usr/bin/nm -B > checking how to recognise dependent libraries... pass_all > checking dlfcn.h usability... yes > checking dlfcn.h presence... yes > checking for dlfcn.h... yes > checking for g++... g++ > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > checking dependency style of g++... gcc3 > checking the maximum length of command line arguments... 32768 > checking command to parse /usr/bin/nm -B output from mpicc object... ok > checking for objdir... .libs > checking for ar... ar > checking for ranlib... ranlib > checking for strip... strip > checking if mpicc supports -fno-rtti -fno-exceptions... no > checking for mpicc option to produce PIC... -fPIC > checking if mpicc PIC flag -fPIC works... yes > checking if mpicc static flag -static works... yes > checking if mpicc supports -c -o file.o... yes > checking whether the mpicc linker (/usr/bin/ld) supports shared libraries... > yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... no > checking whether to build static libraries... yes > configure: creating libtool > appending configuration tag "CXX" to libtool > appending configuration tag "F77" to libtool > checking for special C compiler options needed for large files... no > checking for _FILE_OFFSET_BITS value needed for large files... 64 > checking for _LARGEFILE_SOURCE value needed for large files... 1 > checking for sqrt in -lm... yes > checking for fftw3.h... yes > checking for main in -lfftw3f... yes > checking rpc/rpc.h usability... yes > checking rpc/rpc.h presence... yes > checking for rpc/rpc.h... yes > checking for rpc/xdr.h... yes > checking for xdr_float in -lnsl... yes > checking for working memcmp... yes > checking return type of signal handlers... void > checking for off_t... (cached) yes > checking for vprintf... yes > checking for _doprnt... no > checking if malloc debugging is wanted... no > checking for strcasecmp... yes > checking for strdup... yes > checking for bool... no > checking for X... libraries , headers > checking for gethostbyname... yes > checking for connect... yes > checking for remove... yes > checking for shmat... yes > checking for IceConnectionNumber in -lICE... yes > checking libxml/parser.h usability... yes > checking libxml/parser.h presence... yes > checking for libxml/parser.h... yes > checking for main in -lxml2... yes > checking limits.h usability... yes > checking limits.h presence... yes > checking for limits.h... yes > checking for strings.h... (cached) yes > checking for unistd.h... (cached) yes > checking for unistd.h... (cached) yes > checking for an ANSI C-conforming const... yes > checking for size_t... yes > checking whether struct tm is in sys/time.h or time.h... time.h > checking for uid_t in sys/types.h... yes > checking for inline... inline > checking whether your compiler can handle assembly files (*.s)... yes > checking whether as fully supports ia32 SSE... yes > checking whether as fully supports ia32 3DNow! instructions... yes > checking whether byte ordering is bigendian... (cached) no > checking if the compiler supports gcc inline assembly... yes > checking if the compiler supports MSVC inline assembly... no > configure: creating ./config.status > config.status: creating Makefile > config.status: creating src/Makefile > config.status: creating src/gmxlib/Makefile > config.status: creating src/gmxlib/gmx_blas/Makefile > config.status: creating src/gmxlib/gmx_lapack/Makefile > config.status: creating src/gmxlib/nonbonded/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile > config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile > config.status: creating include/Makefile > config.status: creating include/types/Makefile > config.status: creating src/mdlib/Makefile > config.status: creating src/kernel/Makefile > config.status: creating src/tools/Makefile > config.status: creating src/ngmx/Makefile > config.status: creating src/contrib/Makefile > config.status: creating scripts/Makefile > config.status: creating admin/Makefile > config.status: creating share/Makefile > config.status: creating share/tutor/Makefile > config.status: creating share/tutor/gmxdemo/Makefile > config.status: creating share/tutor/nmr1/Makefile > config.status: creating share/tutor/nmr2/Makefile > config.status: creating share/tutor/water/Makefile > config.status: creating share/tutor/mixed/Makefile > config.status: creating share/tutor/methanol/Makefile > config.status: creating share/tutor/speptide/Makefile > config.status: creating share/template/Makefile > config.status: creating share/top/Makefile > config.status: creating share/html/Makefile > config.status: creating share/html/images/Makefile > config.status: creating share/html/online/Makefile > config.status: creating man/Makefile > config.status: creating man/man1/Makefile > config.status: creating src/config.h > config.status: executing depfiles commands > > * On most platforms you can save 10X space with dynamic libraries, although > the binaries might be less portable. Why not try --enable-shared ? > > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [email protected] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
