[gmx-users] Gromacs installation: cannot find LibXmu.la

[Diego Enry]

I think I saw this before... check if openmotif contains this library
and install it or just try.

./configure --without-x --enable-mpi

Cheers,
Diego Enry.

On Jan 18, 2008 6:45 AM, Andreas Kukol <a.kukol at herts.ac.uk> wrote:
> On SuseLinux 10.3 the command ./configure --enable-mpi works fine but make
> terminates at this point. Using the option --disable-shared did not change anything.
>
> I would be grateful for any help.
>
> Many thanks
> Andreas
>
> Output of make:
> ----
> mv -f .deps/nb_free_energy.Tpo .deps/nb_free_energy.Plo
> /bin/sh ../../../libtool --tag=CC   --mode=link mpicc  -O3 -fomit-frame-pointe
>    r -finline-functions -Wall -Wno-unused -funroll-all-loops   -o
> libnonbonded.la      nonbonded.lo nb_free_energy.lo
> nb_kernel_x86_64_sse/libnb_    kernel_x86_64_sse.la
> nb_kernel/libnb_kernel.la                -L/usr/lib64 -lnsl -lfftw3f -lm
> -L/usr/lib64 -lXm -lXt  -lSM -lICE -lX11
> mkdir .libs
> libtool: link: cannot find the library `/usr/lib/libXmu.la' or unhandled argum
>    ent `/usr/lib/libXmu.la'
> make[5]: *** [libnonbonded.la] Error 1
> make[5]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib/nonbonded'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/usr/local/gromacs-3.3.2/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/usr/local/gromacs-3.3.2/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/usr/local/gromacs-3.3.2/src'
> make: *** [all-recursive] Error 1
> ------
>
> This is the output of configure:
>
> -----
> hecking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-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 cc... cc
> 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 cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... no
> checking for mpicc... mpicc
> checking whether the MPI cc command works... yes
> checking how to run the C preprocessor... mpicc -E
> checking whether mpicc accepts -O3... yes
> checking whether mpicc accepts -malign-double... no
> 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... /usr/bin/grep
> checking for egrep... /usr/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... 8
> checking for long long int... yes
> checking size of long long int... 8
> 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... /usr/bin/sed
> checking for ld used by mpicc... /usr/x86_64-suse-linux/bin/ld
> checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
> checking for /usr/x86_64-suse-linux/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 how to run the C++ preprocessor... g++ -E
> 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/x86_64-suse-linux/bin/ld -m elf_x86_64)
> 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
> checking for ld used by g++... /usr/x86_64-suse-linux/bin/ld -m elf_x86_64
> checking if the linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) is GNU
> ld... yes
> checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking for g++ option to produce PIC... -fPIC
> checking if g++ PIC flag -fPIC works... yes
> checking if g++ static flag -static works... yes
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64)
> supports shared libraries... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> 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... no
> checking for _LARGEFILE_SOURCE value needed for large files... no
> 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 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 /usr/lib64, headers
> checking whether -R must be followed by a space... neither works
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for Motif... libraries /usr/lib64, headers in default path
> checking for libXext and libXp... no
> checking for only libXext... no
> 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 X86_64 SSE instructions... yes
> checking whether byte ordering is bigendian... (cached) 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 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
>
> * Seems you are compiling with MPI support. You can install the MPI-
>    enabled programs with suffixed names to have both MPI and non-MPI
>    versions. This is useful e.g. on supercomputers where you usually
>    cannot run MPI-linked programs on the login node.
>    Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
>    You only need MPI for mdrun, so if you already have non-MPI stuff
>    installed you can issue make mdrun; make install-mdrun.
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.