sci-physics:espresso-3.3.1:20160925-200051.log

sci-physics:espresso-3.3.1:20160925-200051.log (text/plain), 17.71 KB, created by Toralf Förster on 2016-09-25 20:14:51 UTC

 * Package:    sci-physics/espresso-3.3.1
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        X abi_x86_64 amd64 elibc_glibc fftw kernel_linux python_targets_python2_7 userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking espresso-3.3.1.tar.gz to /var/tmp/portage/sci-physics/espresso-3.3.1/work
>>> Source unpacked in /var/tmp/portage/sci-physics/espresso-3.3.1/work
>>> Preparing source in /var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1 ...
 * econf: updating espresso-3.3.1/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating espresso-3.3.1/config/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/espresso-3.3.1 --htmldir=/usr/share/doc/espresso-3.3.1/html --libdir=/usr/lib64 --with-fftw --without-cuda --without-python-interface --without-mpi --without-tk --with-x
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/config/missing: Unknown '--is-lightweight' option
Try '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/config/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '250' is supported by ustar format... yes
checking whether GID '250' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports nested variables... (cached) yes
checking whether we are using development sources... no
****************************************************************
*      Checking compiler characteristics and MPI support       *
****************************************************************
checking for style of include used by make... GNU
checking whether to compile using MPI... no
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 dependency style of x86_64-pc-linux-gnu-g++... none
configure: WARNING: No MPI c++ compiler found, will use fake implementation!
checking whether x86_64-pc-linux-gnu-g++ understands -c and -o together... yes
****************************************************************
*                  Checking for programs                       *
****************************************************************
checking how to print strings... printf
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for sysroot... no
checking for x86_64-pc-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) 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
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gawk... (cached) gawk
checking for egrep... (cached) /bin/grep -E
checking whether ln -s works... yes
checking for doxygen... no
checking for dot... no
checking for pdflatex... no
checking for makeindex... no
checking for bibtex... no
****************************************************************
*               Checking for standard headers                  *
****************************************************************
checking for ANSI C header files... (cached) yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
****************************************************************
*               Checking for standard functions                *
****************************************************************
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/socket.h... (cached) yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking for size_t... yes
checking for working strtod... yes
checking for atexit... yes
checking for floor... yes
checking for getcwd... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... yes
checking for rint... yes
checking for select... yes
checking for socket... yes
checking for sqrt... yes
****************************************************************
*         Checking for required tools and libraries            *
****************************************************************
checking whether to use FFTW... yes
checking for libfftw3... yes
checking for fftw3.h... yes
checking whether to use CUDA... no
checking for nvcc... no
****************************************************************
*                  Checking for Python                         *
****************************************************************
checking for a Python interpreter with version >= 2.5... python
checking for python... /usr/bin/python
checking for python version... 3.4
checking for python platform... linux
checking for python script directory... ${prefix}/lib64/python3.4/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python3.4/site-packages
checking whether python -B works... yes
checking whether the python interface is wanted... no
****************************************************************
*                  Checking for Tcl/Tk                         *
****************************************************************
checking whether to build the Tcl interface... yes
checking for libtcl8.6... yes
checking for tcl.h... yes
checking whether to use Tk... yes
****************************************************************
*                   Other settings                             *
****************************************************************
checking whether to use efence... no
checking whether the variable MYCONFIG is set... no
checking the number of available CPUs... 12 
****************************************************************
*                   Creating output files                      *
****************************************************************
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config/Makefile
config.status: creating config/myconfig-sample-header.hpp
config.status: creating src/Makefile
config.status: creating src/core/Makefile
config.status: creating src/tcl/Makefile
config.status: creating src/python/espressomd/Makefile
config.status: creating tools/Makefile
config.status: creating scripts/Makefile
config.status: creating testsuite/Makefile
config.status: creating doc/Makefile
config.status: creating doc/logo/Makefile
config.status: creating doc/ug/Makefile
config.status: creating doc/dg/Makefile
config.status: creating doc/doxygen/Makefile
config.status: creating doc/tutorials/Makefile
config.status: creating doc/tutorials/01-lennard_jones/Makefile
config.status: creating doc/tutorials/02-charged_system/Makefile
config.status: creating doc/tutorials/03-object_in_fluid/Makefile
config.status: creating doc/latexit.sh
config.status: creating testsuite/runtest.sh
config.status: creating tools/es_mpiexec
config.status: creating src/python/pypresso
config.status: creating src/acconfig.hpp
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing myconfig-sample.hpp commands
****************************************************************
*                   Configuration summary                      *
****************************************************************
platform detected	= x86_64-pc-linux-gnu
package version		= 3.3.1
development sources     = no

Compiler
--------
compiler		= x86_64-pc-linux-gnu-g++
linker			= /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
c++ compiler flags	= -march=native -O2 -pipe
c++ preprocessor flags	= 
linker flags		= -Wl,-O1 -Wl,--as-needed
libraries		= -ltcl8.6 -lfftw3  -lm
using debug flags	= 
using profiling flags	= 

Libraries
---------
FFTW 			= yes
efence			= no


Tcl/Tk
------
Tcl version		= tcl8.6
Tk version		= none

Python
------
python			= /usr/bin/python -B
build python interface  = 

Other settings
--------------
config                  = myconfig.hpp
installation prefix	= /usr
number of test tasks    = 12
mympiexec               = 
mpiexec	     		= 
pdflatex		= no
makeindex		= no
bibtex			= no
doxygen			= no
dot			= no

CUDA disabled or not supported.
WARNING: MPI disabled or not supported! Parallelization turned off.
Not building Python interface.
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1 ...
make -j1 
Making all in config
make[1]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/config'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/config'
Making all in src
make[1]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src'
make  all-recursive
make[2]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src'
Making all in core
make[3]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src/core'
  GEN      myconfig-final.hpp <= ./myconfig-default.hpp
make  all-am
make[4]: Entering directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src/core'
/bin/sh ../../libtool  --tag=CXX   --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src  -I./mpifake   -march=native -O2 -pipe -c -o config-features.lo config-features.cpp
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -I./mpifake -march=native -O2 -pipe -c config-features.cpp  -fPIC -DPIC -o .libs/config-features.o
/bin/sh ../../libtool  --tag=CXX   --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src  -I./mpifake   -march=native -O2 -pipe -c -o cells.lo cells.cpp
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -I./mpifake -march=native -O2 -pipe -c cells.cpp  -fPIC -DPIC -o .libs/cells.o
In file included from cells.cpp:30:0:
utils.hpp:150:16: error: 'std::pmalloc' has not been declared
 #define malloc pmalloc
                ^
utils.hpp:147:17: error: 'std::prealloc' has not been declared
 #define realloc prealloc
                 ^
make[4]: *** [Makefile:878: cells.lo] Error 1
make[4]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src/core'
make[3]: *** [Makefile:638: all] Error 2
make[3]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src/core'
make[2]: *** [Makefile:440: all-recursive] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src'
make[1]: *** [Makefile:378: all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1/src'
make: *** [Makefile:466: all-recursive] Error 1
 * ERROR: sci-physics/espresso-3.3.1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-physics/espresso-3.3.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-physics/espresso-3.3.1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-physics:espresso-3.3.1:20160925-200051.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-physics/espresso-3.3.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-physics/espresso-3.3.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1'
 * S: '/var/tmp/portage/sci-physics/espresso-3.3.1/work/espresso-3.3.1'