* Package: sci-chemistry/gromacs-4.5.1  * Repository: gentoo  * Maintainer: sci-chemistry@gentoo.org  * USE: X bash-completion blas doc elibc_glibc fftw gsl kernel_linux lapack mpi single-precision threads userland_GNU x86 xml >>> Unpacking source... >>> Unpacking gromacs-4.5.1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work >>> Unpacking gromacs-4.5.pdf to /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work unpack gromacs-4.5.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1 ... * mdrun uses only threads OR mpi, and gromacs favours the * use of mpi over threads, so a mpi-version of mdrun will * be compiled. If you want to run mdrun on shared memory * machines only, you can safely disable mpi * Running eautoreconf in '/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1' ... * Running aclocal -I config ...  [ ok ] * Running true --copy --force --install --automake ...  [ ok ] * Running aclocal -I config ...  [ ok ] * Running autoconf ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy --foreign ...  [ ok ] * Running elibtoolize in: gromacs-4.5.1/config/ * Applying install-sh-1.5.4.patch ... * Applying portage-1.5.10.patch ... * Applying sed-1.5.6.patch ... * Applying as-needed-1.5.26.patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1 ... * You have enabled mpi, only mdrun will make use of mpi, that is why * we configure/compile gromacs twice (with and without mpi) and only * install mdrun with mpi support. In addtion you will get libgmx and * libmd with and without mpi support. * Configuring for single precision * econf: updating gromacs-4.5.1/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating gromacs-4.5.1/config/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datadir=/usr/share --bindir=/usr/bin --libdir=/usr/lib --docdir=/usr/share/doc/gromacs-4.5.1 --without-dmalloc --with-fft=fftw3 --with-gsl --with-x --with-xml --enable-threads --disable-bluegene --disable-fortran --with-external-blas --with-external-lapack --disable-all-static --enable-shared --disable-static --enable-float --program-suffix='' --disable-mpi CC=i686-pc-linux-gnu-gcc F77= configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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 i686-pc-linux-gnu-cc... i686-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether i686-pc-linux-gnu-gcc accepts -O3... yes checking whether i686-pc-linux-gnu-gcc accepts -msse2... yes checking whether i686-pc-linux-gnu-gcc accepts -funroll-all-loops... yes checking whether i686-pc-linux-gnu-gcc accepts -std=gnu99... yes checking whether i686-pc-linux-gnu-gcc accepts -fexcess-precision=fast... no ****************************************** * Using CFLAGS from environment variable * ****************************************** 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 for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... i686-pc-linux-gnu-gcc checking if atomic operations are supported... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) 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 i686-pc-linux-gnu-gcc ... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking for /usr/i686-pc-linux-gnu/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 i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking how to run the C++ preprocessor... i686-pc-linux-gnu-g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok checking for objdir... .libs checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC checking if i686-pc-linux-gnu-gcc PIC flag -fPIC works... yes checking if i686-pc-linux-gnu-gcc static flag -static works... yes checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no 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... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC checking if i686-pc-linux-gnu-g++ PIC flag -fPIC works... yes checking if i686-pc-linux-gnu-g++ static flag -static works... yes checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) 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... 64 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 limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for sys/time.h... (cached) yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working memcmp... yes checking return type of signal handlers... void checking for off_t... 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 gettimeofday... yes checking for cbrt... yes checking for isnan... yes checking for _isnan... no checking for isfinite... no checking for _isfinite... no checking for fsync... yes checking for fileno... yes checking for bool... no checking for library containing posix_memalign... none required checking for library containing memalign... none required checking for _aligned_malloc... no checking size of int... 4 checking size of long int... 4 checking size of long long int... 8 checking size of off_t... 8 checking size of void*... 4 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 gsl/gsl_version.h usability... yes checking gsl/gsl_version.h presence... yes checking for gsl/gsl_version.h... yes checking for main in -lgslcblas... yes checking for main in -lgsl... 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 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 inline... inline checking for C/C++ restrict keyword... __restrict checking for uid_t... yes checking for gid_t... yes checking for sig_atomic_t... yes checking whether your compiler can handle assembly files (*.s)... yes checking whether as fully supports ia32 SSE... 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 checking if dlopen supported... 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/libgmx.pc config.status: creating src/gmxlib/gmx_blas/Makefile config.status: creating src/gmxlib/gmx_lapack/Makefile config.status: creating src/gmxlib/selection/Makefile config.status: creating src/gmxlib/statistics/Makefile config.status: creating src/gmxlib/trajana/Makefile config.status: creating src/gmxlib/thread_mpi/Makefile config.status: creating src/gmxlib/nonbonded/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_c/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 src/gmxlib/nonbonded/nb_kernel_power6/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile config.status: creating include/Makefile config.status: creating include/types/Makefile config.status: creating include/thread_mpi/Makefile config.status: creating include/thread_mpi/atomic/Makefile config.status: creating src/mdlib/Makefile config.status: creating src/mdlib/libmd.pc config.status: creating src/kernel/Makefile config.status: creating src/kernel/libgmxpreprocess.pc config.status: creating src/tools/Makefile config.status: creating src/tools/libgmxana.pc 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/top/gmx.ff/Makefile config.status: creating share/top/gmx2.ff/Makefile config.status: creating share/top/encadv.ff/Makefile config.status: creating share/top/encads.ff/Makefile config.status: creating share/top/oplsaa.ff/Makefile config.status: creating share/top/gromos43a1.ff/Makefile config.status: creating share/top/gromos43a2.ff/Makefile config.status: creating share/top/gromos45a3.ff/Makefile config.status: creating share/top/gromos53a5.ff/Makefile config.status: creating share/top/gromos53a6.ff/Makefile config.status: creating share/top/charmm27.ff/Makefile config.status: creating share/top/amber94.ff/Makefile config.status: creating share/top/amber96.ff/Makefile config.status: creating share/top/amberGS.ff/Makefile config.status: creating share/top/amber99.ff/Makefile config.status: creating share/top/amber99sb.ff/Makefile config.status: creating share/top/amber99sb-ildn.ff/Makefile config.status: creating share/top/amber03.ff/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 man/man7/Makefile config.status: creating Doxyfile config.status: creating src/config.h config.status: executing depfiles commands * econf: updating gromacs-4.5.1/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating gromacs-4.5.1/config/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datadir=/usr/share --bindir=/usr/bin --libdir=/usr/lib --docdir=/usr/share/doc/gromacs-4.5.1 --without-dmalloc --with-fft=fftw3 --with-gsl --with-x --with-xml --enable-threads --disable-bluegene --disable-fortran --with-external-blas --with-external-lapack --disable-all-static --enable-shared --disable-static --enable-float --program-suffix='' --enable-mpi CC=i686-pc-linux-gnu-gcc F77= configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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 i686-pc-linux-gnu-cc... i686-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no ****************************************** * Using CFLAGS from environment variable * ****************************************** checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) 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/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking for /usr/i686-pc-linux-gnu/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 whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-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... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no 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... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by mpicc... /usr/i686-pc-linux-gnu/bin/ld checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes checking whether the mpicc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC 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/i686-pc-linux-gnu/bin/ld) 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... 64 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 limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking unistd.h usability... yes checking unistd.h presence... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/types.h usability... yes checking sys/types.h presence... yes checking for sys/types.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working memcmp... yes checking return type of signal handlers... void checking for off_t... 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 gettimeofday... yes checking for cbrt... yes checking for isnan... yes checking for _isnan... no checking for isfinite... no checking for _isfinite... no checking for fsync... yes checking for fileno... yes checking for bool... no checking for library containing posix_memalign... none required checking for library containing memalign... none required checking for _aligned_malloc... no checking size of int... 4 checking size of long int... 4 checking size of long long int... 8 checking size of off_t... 8 checking size of void*... 4 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 gsl/gsl_version.h usability... yes checking gsl/gsl_version.h presence... yes checking for gsl/gsl_version.h... yes checking for main in -lgslcblas... yes checking for main in -lgsl... 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 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 inline... inline checking for C/C++ restrict keyword... __restrict checking for uid_t... yes checking for gid_t... yes checking for sig_atomic_t... yes checking whether your compiler can handle assembly files (*.s)... yes checking whether as fully supports ia32 SSE... 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 checking if dlopen supported... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/gmxlib/Makefile config.status: creating src/gmxlib/libgmx_mpi.pc config.status: creating src/gmxlib/gmx_blas/Makefile config.status: creating src/gmxlib/gmx_lapack/Makefile config.status: creating src/gmxlib/selection/Makefile config.status: creating src/gmxlib/statistics/Makefile config.status: creating src/gmxlib/trajana/Makefile config.status: creating src/gmxlib/thread_mpi/Makefile config.status: creating src/gmxlib/nonbonded/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_c/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 src/gmxlib/nonbonded/nb_kernel_power6/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile config.status: creating include/Makefile config.status: creating include/types/Makefile config.status: creating include/thread_mpi/Makefile config.status: creating include/thread_mpi/atomic/Makefile config.status: creating src/mdlib/Makefile config.status: creating src/mdlib/libmd_mpi.pc config.status: creating src/kernel/Makefile config.status: creating src/kernel/libgmxpreprocess_mpi.pc config.status: creating src/tools/Makefile config.status: creating src/tools/libgmxana_mpi.pc 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/top/gmx.ff/Makefile config.status: creating share/top/gmx2.ff/Makefile config.status: creating share/top/encadv.ff/Makefile config.status: creating share/top/encads.ff/Makefile config.status: creating share/top/oplsaa.ff/Makefile config.status: creating share/top/gromos43a1.ff/Makefile config.status: creating share/top/gromos43a2.ff/Makefile config.status: creating share/top/gromos45a3.ff/Makefile config.status: creating share/top/gromos53a5.ff/Makefile config.status: creating share/top/gromos53a6.ff/Makefile config.status: creating share/top/charmm27.ff/Makefile config.status: creating share/top/amber94.ff/Makefile config.status: creating share/top/amber96.ff/Makefile config.status: creating share/top/amberGS.ff/Makefile config.status: creating share/top/amber99.ff/Makefile config.status: creating share/top/amber99sb.ff/Makefile config.status: creating share/top/amber99sb-ildn.ff/Makefile config.status: creating share/top/amber03.ff/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 man/man7/Makefile config.status: creating Doxyfile config.status: creating src/config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1 ... * Compiling for single precision make -j1 Making all in include make[1]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include' Making all in . make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include' Making all in types make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/types' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/types' Making all in thread_mpi make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi' Making all in atomic make[3]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi/atomic' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi/atomic' make[3]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi' make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include/thread_mpi' make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/include' Making all in src make[1]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src' (CDPATH="${ZSH_VERSION+.}:" && cd /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1 && /bin/sh /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/config/missing --run autoheader) configure.ac:454: warning: AC_CACHE_VAL(ac_o3, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_faltivec, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_maltivec, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_mabialtivec, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_fno_schedule_insns, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_m_tune_970, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_m_cpu_powerpc, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_msse2, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_funroll_all_loops, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_stdgnu99, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_fexcess_precision_fast, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_guessed_cflags, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:255: ACX_CHECK_CC_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:454: warning: AC_CACHE_VAL(ac_guessed_fflags, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:281: ACX_CHECK_F77_FLAGS is expanded from... acinclude.m4:407: ACX_COMPILER_MAXOPT is expanded from... configure.ac:454: the top level configure.ac:496: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2591: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2607: AC_COMPILE_IFELSE is expanded from... configure.ac:496: the top level configure.ac:566: warning: AC_CACHE_VAL(acx_float_format, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:164: ACX_FLOAT_FORMAT is expanded from... configure.ac:566: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1690: AC_LIBTOOL_COMPILER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:3726: _LT_AC_LANG_C_CONFIG is expanded from... acinclude.m4:3725: AC_LIBTOOL_LANG_C_CONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_static_works, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1735: AC_LIBTOOL_LINKER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:3726: _LT_AC_LANG_C_CONFIG is expanded from... acinclude.m4:3725: AC_LIBTOOL_LANG_C_CONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2662: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2679: AC_LINK_IFELSE is expanded from... acinclude.m4:1364: _LT_AC_SYS_LIBPATH_AIX is expanded from... acinclude.m4:6417: AC_LIBTOOL_PROG_LD_SHLIBS is expanded from... acinclude.m4:3726: _LT_AC_LANG_C_CONFIG is expanded from... acinclude.m4:3725: AC_LIBTOOL_LANG_C_CONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2662: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2679: AC_LINK_IFELSE is expanded from... acinclude.m4:1364: _LT_AC_SYS_LIBPATH_AIX is expanded from... acinclude.m4:3807: _LT_AC_LANG_CXX_CONFIG is expanded from... acinclude.m4:3806: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1690: AC_LIBTOOL_COMPILER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:3807: _LT_AC_LANG_CXX_CONFIG is expanded from... acinclude.m4:3806: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_CXX, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1735: AC_LIBTOOL_LINKER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:3807: _LT_AC_LANG_CXX_CONFIG is expanded from... acinclude.m4:3806: AC_LIBTOOL_LANG_CXX_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1690: AC_LIBTOOL_COMPILER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:4974: _LT_AC_LANG_F77_CONFIG is expanded from... acinclude.m4:4973: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_F77, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1735: AC_LIBTOOL_LINKER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:4974: _LT_AC_LANG_F77_CONFIG is expanded from... acinclude.m4:4973: AC_LIBTOOL_LANG_F77_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_pic_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1690: AC_LIBTOOL_COMPILER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:5076: _LT_AC_LANG_GCJ_CONFIG is expanded from... acinclude.m4:5075: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_CACHE_VAL(lt_prog_compiler_static_works_GCJ, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:2032: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2053: AC_CACHE_CHECK is expanded from... acinclude.m4:1735: AC_LIBTOOL_LINKER_OPTION is expanded from... acinclude.m4:5890: AC_LIBTOOL_PROG_COMPILER_PIC is expanded from... acinclude.m4:5076: _LT_AC_LANG_GCJ_CONFIG is expanded from... acinclude.m4:5075: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level configure.ac:573: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:194: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2662: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2679: AC_LINK_IFELSE is expanded from... acinclude.m4:1364: _LT_AC_SYS_LIBPATH_AIX is expanded from... acinclude.m4:6417: AC_LIBTOOL_PROG_LD_SHLIBS is expanded from... acinclude.m4:5076: _LT_AC_LANG_GCJ_CONFIG is expanded from... acinclude.m4:5075: AC_LIBTOOL_LANG_GCJ_CONFIG is expanded from... acinclude.m4:2862: _LT_AC_TAGCONFIG is expanded from... acinclude.m4:1155: AC_LIBTOOL_SETUP is expanded from... acinclude.m4:1135: _AC_PROG_LIBTOOL is expanded from... acinclude.m4:1100: AC_PROG_LIBTOOL is expanded from... configure.ac:573: the top level rm -f stamp-h1 touch /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/config.h.in cd .. && /bin/sh ./config.status src/config.h config.status: creating src/config.h config.status: src/config.h is unchanged make all-recursive make[2]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src' Making all in gmxlib make[3]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib' Making all in nonbonded make[4]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib/nonbonded' Making all in nb_kernel_ia32_sse make[5]: Entering directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib/nonbonded/nb_kernel_ia32_sse' /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel010_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel010_ia32_sse.s mkdir .libs i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel010_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel010_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel030_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel030_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel030_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel030_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel100_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel100_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel100_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel100_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel101_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel101_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel101_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel101_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel102_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel102_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel102_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel102_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel103_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel103_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel103_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel103_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel104_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel104_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel104_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel104_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel110_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel110_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel110_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel110_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel111_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel111_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel111_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel111_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel112_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel112_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel112_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel112_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel113_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel113_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel113_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel113_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel114_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel114_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel114_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel114_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel130_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel130_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel130_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel130_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel131_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel131_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel131_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel131_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel132_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel132_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel132_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel132_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel133_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel133_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel133_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel133_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel134_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel134_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel134_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel134_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel200_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel200_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel200_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel200_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel201_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel201_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel201_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel201_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel202_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel202_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel202_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel202_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel203_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel203_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel203_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel203_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel204_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel204_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp 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i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel331_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel331_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel332_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel332_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel332_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel332_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel333_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel333_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel333_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel333_ia32_sse.o /bin/sh ../../../../libtool --mode=compile i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c -o nb_kernel334_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel334_ia32_sse.s i686-pc-linux-gnu-gcc -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel334_ia32_sse.s -fPIC -DPIC -o .libs/nb_kernel334_ia32_sse.o /bin/sh ../../../../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse -I../../../../src -I/usr/include/libxml2 -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -DGMXLIBDIR=\"/usr/share/top\" -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -MT nb_kernel400_ia32_sse.lo -MD -MP -MF .deps/nb_kernel400_ia32_sse.Tpo -c -o nb_kernel400_ia32_sse.lo /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse -I../../../../src -I/usr/include/libxml2 -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -DGMXLIBDIR=\"/usr/share/top\" -O2 -march=athlon-xp -fomit-frame-pointer -pthread -I/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include -MT nb_kernel400_ia32_sse.lo -MD -MP -MF .deps/nb_kernel400_ia32_sse.Tpo -c /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c -fPIC -DPIC -o .libs/nb_kernel400_ia32_sse.o In file included from /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:22: /usr/lib/gcc/i686-pc-linux-gnu/4.4.4/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled" In file included from /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:24: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:128: error: expected declaration specifiers or ‘...’ before ‘__m128i’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘printxmmi’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:132: error: ‘__m128i’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:132: error: (Each undeclared identifier is reported only once /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:132: error: for each function it appears in.) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:132: error: expected expression before ‘)’ token /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_log_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:192: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:193: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘expbase_m1’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:193: error: ‘expbase_m1’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:211: error: ‘__m128i’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:211: error: expected ‘;’ before ‘iexp’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:219: error: ‘iexp’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_exp_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:306: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘expbase’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:306: error: ‘expbase’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:316: error: ‘__m128i’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:316: error: expected ‘;’ before ‘iexppart’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:323: error: ‘iexppart’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_sincos_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:368: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘_sincosf_izero’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:368: error: ‘_sincosf_izero’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:369: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘_sincosf_ione’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:369: error: ‘_sincosf_ione’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:370: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘_sincosf_itwo’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:370: error: ‘_sincosf_itwo’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:371: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘_sincosf_ithree’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:371: error: ‘_sincosf_ithree’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:382: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:383: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:397: error: ‘__m128i’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:397: error: expected ‘;’ before ‘_sincosf_q’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:398: error: expected ‘;’ before ‘_sincosf_offsetSin’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:399: error: expected ‘;’ before ‘_sincosf_offsetCos’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:413: error: ‘_sincosf_q’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:416: error: ‘_sincosf_offsetSin’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:417: error: ‘_sincosf_offsetCos’ undeclared (first use in this function) In file included from /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:24: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_asin_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:483: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_acos_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:551: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h: In function ‘gmx_mm_atan_ps’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/include/gmx_sse2_single.h:588: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c: In function ‘nb_kernel400_ia32_sse’: /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:93: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:94: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:95: error: can't convert between vector values of different size /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:97: error: ‘__m128i’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:97: error: expected ‘;’ before ‘n0’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:98: error: expected ‘;’ before ‘n0B’ /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:217: error: ‘n0’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:218: error: ‘n0B’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:221: error: ‘nnn’ undeclared (first use in this function) /var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1/src/gmxlib/nonbonded/nb_kernel_ia32_sse/nb_kernel400_ia32_sse.c:222: error: ‘nnnB’ undeclared (first use in this function) make[5]: *** [nb_kernel400_ia32_sse.lo] Error 1 make[5]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib/nonbonded/nb_kernel_ia32_sse' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1-single/src' make: *** [all-recursive] Error 1 emake failed * ERROR: sci-chemistry/gromacs-4.5.1 failed: * emake for single precision failed * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 3155: Called die * The specific snippet of code: * emake || die "emake for ${x} precision failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.5.1', * the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.5.1'. * The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.1/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/gromacs-4.5.1/work/gromacs-4.5.1'