[gmx-users] gromacs 4 mpi weirdness

Tue Mar 17 13:57:10 CET 2009

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 <r.friedman at bioc.uzh.ch> 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
>>
>> tsjerk at 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: r.friedman at bioc.unizh.ch
> Skype: ran.friedman
> ------------------------------------------------------
>
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-- 
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