[gmx-users] compilation fails on MAC OSX - Leopard

Thu Nov 15 13:05:45 CET 2007

Hi Hadas,

I think the problem is that the make command for some reason thinks it
should build the Itanium inner loops:

> ld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in

though on your machine the x86_64 kernels should be build. Probably one
can set the correct architecture with a flag to the configure command
like --build=... or --host=...

But I'm not an expert here.

Carsten

Hadas Leonov wrote:
> Hi all,
> 
> I am trying to install Gromacs 3.3.2 on the new Leopard Mac OSX. the OSX
> was installed anew, and not from an upgrade. Developer tools were
> installed too.
> 
> I have already compiled and installed lam-7.0.6 and fftw-3.0.1 (single
> and double precision) without a problem.
> The configure parameters were:
>   
> for lam: ./configure --with-fc=/usr/local/bin/gfortran
> for fftw (single): ./configure --enable-float --enable-threads --enable-sse
> for fftw (double): ./configure --enable-threads --enable-sse2
> 
> 
> For gromacs, the configuration is:  ./configure --enable-mpi
> when I type make, compilation begins and end with the following lines: 
> 
> mpicc -I/sw/include -framework Accelerate -o grompp topio.o toppush.o
> topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o
> vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o
> compute_io.o  -L/usr/local/lib ../mdlib/.libs/libmd_mpi.a -L/usr/X11/lib
> -L/sw/lib ../gmxlib/.libs/libgmx_mpi.a /usr/local/lib/libfftw3f.a -lm
> /usr/X11/lib/libSM.6.0.0.dylib /usr/X11/lib/libICE.6.3.0.dylib
> /usr/X11/lib/libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib
> /usr/X11/lib/libXdmcp.6.0.0.dylib
> ld: in ../gmxlib/.libs/libgmx_mpi.a(nb_kernel204_ia32_sse.o), in section
> __TEXT,__text reloc 1: bad pc-rel vanilla relocation length
> 
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> 
> attached below is configure output for Gromacs. 
> 
> Has anyone else encountered this problem or has any idea how to deal
> with it ?
> 
> Thanks in advance,
> 
> Hadas Leonov. 
> hleonov at cc.huji.ac.il <mailto:hleonov at cc.huji.ac.il>
> Department of Biological Chemistry
> Alexander Silberman institute of Life Sciences
> The Hebrew University, 
> Jerusalem, Israel
> 
> 
> ------------------------------------------------------------------------
> 
> checking build system type... i386-apple-darwin9.0.0
> checking host system type... i386-apple-darwin9.0.0
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... config/install-sh -c -d
> checking for gawk... no
> checking for mawk... no
> checking for nawk... no
> checking for awk... awk
> 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... yes
> checking whether mpicc accepts -funroll-all-loops... yes
> ******************************************
> * Using CFLAGS from environment variable *
> ******************************************
> 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... 4
> 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/libexec/gcc/i686-apple-darwin9/4.0.1/ld
> checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU ld... no
> checking for /usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -p
> 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... 196608
> checking command to parse /usr/bin/nm -p 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... -fno-common
> checking if mpicc PIC flag -fno-common works... yes
> checking if mpicc static flag -static works... no
> checking if mpicc supports -c -o file.o... yes
> checking whether the mpicc linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries... yes
> checking dynamic linker characteristics... darwin9.0.0 dyld
> 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/libexec/gcc/i686-apple-darwin9/4.0.1/ld
> checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) is GNU ld... no
> checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries... yes
> checking for g++ option to produce PIC... -fno-common
> checking if g++ PIC flag -fno-common works... yes
> checking if g++ static flag -static works... no
> checking if g++ supports -c -o file.o... yes
> checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries... yes
> checking dynamic linker characteristics... darwin9.0.0 dyld
> checking how to hardcode library paths into programs... immediate
> appending configuration tag "F77" to libtool
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... no
> checking whether to build static libraries... yes
> checking for /usr/local/bin/gfortran option to produce PIC... -fno-common
> checking if /usr/local/bin/gfortran PIC flag -fno-common works... yes
> checking if /usr/local/bin/gfortran static flag -static works... no
> checking if /usr/local/bin/gfortran supports -c -o file.o... yes
> checking whether the /usr/local/bin/gfortran linker (/usr/libexec/gcc/i686-apple-darwin9/4.0.1/ld) supports shared libraries... yes
> checking dynamic linker characteristics... darwin9.0.0 dyld
> checking how to hardcode library paths into programs... immediate
> 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... no
> 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/X11/lib, headers /usr/X11/include
> checking whether -R must be followed by a space... no
> 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 (none), 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 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 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.
> 
> 
> 
> ------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php