Hi, Okay, after some communication with the administrators, it appeared that this arose from some misloaded (mpi) libraries both at compiletime and at runtime. My mistake, obviously. Let's see if I get it right this time.
Cheers, Tsjerk On Tue, Mar 17, 2009 at 10:53 AM, Ran Friedman <[email protected]> wrote: > 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 > -- 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 [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
