* Package:    sci-chemistry/gromacs-4.5.5-r1
 * Repository: gentoo
 * Maintainer: sci-chemistry@gentoo.org
 * USE:        X amd64 blas consolekit double-precision elibc_glibc fftw kernel_linux lapack multilib policykit sse2 threads userland_GNU xml
 * FEATURES:   preserve-libs sandbox
>>> Unpacking source...
>>> Unpacking gromacs-4.5.5.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work
>>> Unpacking 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work
>>> Unpacking 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz to /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ...
 * Applying 0001-Make-stack-non-executable-for-GAS-assembly.patch ...
 [ ok ]
 * Applying 0002-Make-stack-non-executable-for-ATT-assembly.patch ...
 [ ok ]
 * Applying gromacs-4.5.5-cmake-cpp-asm.patch ...
 [ ok ]
 * Applying gromacs-4.5.5-enable-see.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ...
 * 
 * For most simulations single precision is accurate enough. In some
 * cases double precision is required to get reasonable results:
 * 
 * -normal mode analysis, for the conjugate gradient or l-bfgs minimization
 *  and the calculation and diagonalization of the Hessian 
 * -calculation of the constraint force between two large groups of	atoms
 * -energy conservation: this can only be done without temperature coupling and
 *  without cutoffs
 * 
 * Configuring for double precision
удалён «/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/cmake/FindBLAS.cmake»
удалён «/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/cmake/FindLAPACK.cmake»
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/gentoo_common_config.cmake -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_X11=ON -DGMX_EXTERNAL_BLAS=ON -DGMX_GSL=OFF -DGMX_EXTERNAL_LAPACK=ON -DGMX_THREADS=ON -DGMX_XML=ON -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION=sse -DGMXLIB=lib64 -DGMX_DOUBLE=ON -DGMX_MPI=OFF -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/gentoo_rules.cmake  /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/gentoo_common_config.cmake
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Using manually set binary suffix: ""
-- Using manually set library suffix: ""
-- Looking for include files HAVE_STRING_H
-- Looking for include files HAVE_STRING_H - found
-- Looking for include files HAVE_MATH_H
-- Looking for include files HAVE_MATH_H - found
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-- Looking for include files HAVE_LIMITS_H - found
-- Looking for include files HAVE_MEMORY_H
-- Looking for include files HAVE_MEMORY_H - found
-- Looking for include files HAVE_UNISTD_H
-- Looking for include files HAVE_UNISTD_H - found
-- Looking for include files HAVE_DIRECT_H
-- Looking for include files HAVE_DIRECT_H - not found.
-- Looking for include files HAVE_PWD_H
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-- Looking for include files HAVE_STDINT_H
-- Looking for include files HAVE_STDINT_H - found
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-- Looking for include files HAVE_PTHREAD_H
-- Looking for include files HAVE_PTHREAD_H - found
-- Looking for include files HAVE_DIRENT_H
-- Looking for include files HAVE_DIRENT_H - found
-- Looking for include files HAVE_INTTYPES_H
-- Looking for include files HAVE_INTTYPES_H - found
-- Looking for include files HAVE_REGEX_H
-- Looking for include files HAVE_REGEX_H - found
-- Looking for include files HAVE_SYS_TYPES_H
-- Looking for include files HAVE_SYS_TYPES_H - found
-- Looking for include files HAVE_SYS_STAT_H
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-- Looking for include files HAVE_RPC_XDR_H - found
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-- Looking for include files HAVE_SMMINTRIN_H - found
-- Looking for include files HAVE_IO_H
-- Looking for include files HAVE_IO_H - not found.
-- Looking for strcasecmp
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-- Looking for _commit
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-- Looking for sqrt in m
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-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of bool
-- Check size of bool - failed
-- Check size of int
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-- Check size of long int
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-- Check if the system is big endian
-- Searching 16 bit integer
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- checking for module 'libxml-2.0'
--   found libxml-2.0, version 2.7.8
-- Found LibXml2: /usr/lib64/libxml2.so 
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found
-- Looking for gethostbyname
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-- Looking for remove
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-- Looking for shmat
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-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib64/libX11.so
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Looking for include files HAVE_SCHED_H
-- Looking for include files HAVE_SCHED_H - found
-- Looking for sysconf
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-- Atomics found
-- Setting build user & time
-- Setting build user & time - OK
-- Checking floating point format
-- Checking floating point format - unknown
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for return type of signals
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-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for inline keyword
-- Checking for inline keyword - inline
-- Checking for inline keyword
-- Checking for inline keyword - inline
-- Checking for pipe support
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Checking for MSVC x86 inline asm
-- Checking for MSVC x86 inline asm - not supported
-- Checking for system XDR support
-- Checking for system XDR support - present
-- Found FFTW3: /usr/lib64/libfftw3.so 
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- checking for module 'blas'
--   found blas, version 5.1.0
-- checking for module 'lapack'
--   found lapack, version 5.1.0
-- The ASM-ATT compiler identification is GNU
-- Found assembler: /usr/bin/as
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C                -O2 -pipe -march=native -mtune=native 
C++              -O2 -pipe -march=native -mtune=native 
Linker flags:
Executable        -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common
Module           -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common
Shared           -Wl,-O1 -Wl,--as-needed,--hash-style=gnu,--sort-common

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5 ...
 * Compiling for double precision
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5_double"
make -j17 
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/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/scatter.c:70:25: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c: В функции «tMPI_Gather»:
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/gather.c:69:25: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/list.c.o
[ 44%] [ 44%] [ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/type.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/lock.c.o
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/group.c: В функции «tMPI_In_group»:
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/group.c:68:8: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/numa_malloc.c.o
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/tmpi_init.c: В функции «tMPI_Thread_init»:
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/tmpi_init.c:269:28: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
[ 44%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/once.c.o
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c: В функции «tMPI_Cart_get»:
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/topology.c:105:42: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/once.c: В функции «tMPI_Once»:
/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5/src/gmxlib/thread_mpi/once.c:75:38: замечание: The ABI for passing parameters with 64-byte alignment has changed in GCC 4.6
Linking C shared library libgmx.so
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lacml
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lacml
collect2: выполнение ld завершилось с кодом возврата 1
make[2]: *** [src/gmxlib/libgmx.so.6] Ошибка 1
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Ошибка 2
make: *** [all] Ошибка 2
 * ERROR: sci-chemistry/gromacs-4.5.5-r1 failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.5.5-r1',
 * the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.5.5-r1'.
 * The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/temp/environment'.
 * S: '/var/tmp/portage/sci-chemistry/gromacs-4.5.5-r1/work/gromacs-4.5.5'