[gmx-users] gromacs 4 mpi weirdness

[Ran Friedman]

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
------------------------------------------------------