| 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. 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.
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