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 ? -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php