Gromacs 4.5.1 installation error

[jimmymisc@…]

Hello all,

I have installed all the dependencies, but when I executed : sudo port install gromacs, I obtained this error (log attached). Can someone help please ?

Thank you

version:1 :debug:main epoch: in tree: 0 installed: 0 :debug:main pkgconfig 0.25_2 exists in the ports tree :debug:main pkgconfig 0.25_2 is the latest installed :debug:main pkgconfig 0.25_2 is active :debug:main Merging existing variants into variants :debug:main new fully merged portvariants: :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/pkgconfig :debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386 :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided :debug:main adding the default universal variant :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf :debug:main No need to upgrade! pkgconfig 0.25_2 >= pkgconfig 0.25_2 :debug:main epoch: in tree: 1 installed: 1 :debug:main gcc44 4.4.5_0 exists in the ports tree :debug:main gcc44 4.4.5_0 is the latest installed :debug:main gcc44 4.4.5_0 is active :debug:main Merging existing variants into variants :debug:main new fully merged portvariants: :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/lang/gcc44 :debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386 :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main No need to upgrade! gcc44 4.4.5_0 >= gcc44 4.4.5_0 :debug:main epoch: in tree: 0 installed: 0 :debug:main gmp 5.0.1_1 exists in the ports tree :debug:main gmp 5.0.1_1 is the latest installed :debug:main gmp 5.0.1_1 is active :debug:main Merging existing variants into variants :debug:main new fully merged portvariants: :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/gmp :debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386 :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided :debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main No need to upgrade! gmp 5.0.1_1 >= gmp 5.0.1_1 :debug:main epoch: in tree: 0 installed: 0 :debug:main mpfr 3.0.1_0 exists in the ports tree :debug:main mpfr 3.0.1_0 is the latest installed :debug:main mpfr 3.0.1_0 is active :debug:main Merging existing variants into variants :debug:main new fully merged portvariants: :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/mpfr :debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386 :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided :debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main No need to upgrade! mpfr 3.0.1_0 >= mpfr 3.0.1_0 :debug:main epoch: in tree: 0 installed: 0 :debug:main libiconv 1.13.1_0 exists in the ports tree :debug:main libiconv 1.13.1_0 is the latest installed :debug:main libiconv 1.13.1_0 is active :debug:main Merging existing variants into variants :debug:main new fully merged portvariants: :debug:main Changing to port directory: /opt/local/var/macports/sources/rsync.macports.org/release/ports/textproc/libiconv :debug:main OS darwin/10.6.0 (Mac OS X 10.6) arch i386 :debug:main org.macports.load registered provides 'load', a pre-existing procedure. Target override will not be provided :debug:main org.macports.unload registered provides 'unload', a pre-existing procedure. Target override will not be provided :debug:main org.macports.distfiles registered provides 'distfiles', a pre-existing procedure. Target override will not be provided :debug:main Using group file /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/muniversal-1.0.tcl :debug:main Reading variant descriptions from /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf :debug:main universal variant already exists, so not adding the default one :debug:main No need to upgrade! libiconv 1.13.1_0 >= libiconv 1.13.1_0 :msg:main ---> Computing dependencies for gromacs:info:main .:debug:main Searching for dependency: pkgconfig :debug:main Found Dependency: receipt exists for pkgconfig :debug:main Searching for dependency: gcc44 :debug:main Found Dependency: receipt exists for gcc44 :msg:main :debug:main Executing org.macports.main (gromacs) :debug:main Skipping completed org.macports.fetch (gromacs) :debug:main Skipping completed org.macports.checksum (gromacs) :debug:main Skipping completed org.macports.extract (gromacs) :debug:main Skipping completed org.macports.patch (gromacs) :msg:main ---> Configuring gromacs :debug:main Using compiler 'MacPorts gcc 4.4' :debug:configure configure phase started at Sun Apr 17 18:17:12 EDT 2011 :debug:configure Executing org.macports.configure (gromacs) :debug:configure Environment: CPATH='/opt/local/include' CFLAGS='-pipe -O2 -m64' CPPFLAGS='-I/opt/local/include' CXXFLAGS='-pipe -O2 -m64' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.6' CXX='/opt/local/bin/g++-mp-4.4' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/.CC_PRINT_OPTIONS' F90FLAGS='-pipe -O2 -m64' LDFLAGS='-L/opt/local/lib' FCFLAGS='-pipe -O2 -m64' OBJC='/opt/local/bin/gcc-mp-4.4' INSTALL='/usr/bin/install -c' F90='/opt/local/bin/gfortran-mp-4.4' FC='/opt/local/bin/gfortran-mp-4.4' FFLAGS='-pipe -O2 -m64' OBJCFLAGS='-pipe -O2 -m64' F77='/opt/local/bin/gfortran-mp-4.4' CC_PRINT_OPTIONS='YES' CC='/opt/local/bin/gcc-mp-4.4' :debug:configure Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/gromacs-4.5.1" && ./configure --prefix=/opt/local --bindir=/opt/local/lib/gromacs/bin --enable-shared --with-x' :info:configure checking build system type... x86_64-apple-darwin10.6.0 :info:configure checking host system type... x86_64-apple-darwin10.6.0 :info:configure checking for a BSD-compatible install... /usr/bin/install -c :info:configure checking whether build environment is sane... yes :info:configure checking for a thread-safe mkdir -p... config/install-sh -c -d :info:configure checking for gawk... no :info:configure checking for mawk... no :info:configure checking for nawk... no :info:configure checking for awk... awk :info:configure checking whether make sets $(MAKE)... yes :info:configure checking how to create a ustar tar archive... gnutar :info:configure checking for C compiler default output file name... a.out :info:configure checking whether the C compiler works... yes :info:configure checking whether we are cross compiling... no :info:configure checking for suffix of executables... :info:configure checking for suffix of object files... o :info:configure checking whether we are using the GNU C compiler... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -g... yes :info:configure checking for /opt/local/bin/gcc-mp-4.4 option to accept ISO C89... none needed :info:configure checking for style of include used by make... GNU :info:configure checking dependency style of /opt/local/bin/gcc-mp-4.4... gcc3 :info:configure checking dependency style of /opt/local/bin/gcc-mp-4.4... gcc3 :info:configure checking how to run the C preprocessor... /opt/local/bin/gcc-mp-4.4 -E :info:configure checking for grep that handles long lines and -e... /usr/bin/grep :info:configure checking for egrep... /usr/bin/grep -E :info:configure checking whether ln -s works... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -O3... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -msse2... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -funroll-all-loops... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -std=gnu99... yes :info:configure checking whether /opt/local/bin/gcc-mp-4.4 accepts -fexcess-precision=fast... no :info:configure :info:configure * Using CFLAGS from environment variable * :info:configure :info:configure checking for ANSI C header files... yes :info:configure checking for sys/types.h... yes :info:configure checking for sys/stat.h... yes :info:configure checking for stdlib.h... yes :info:configure checking for string.h... yes :info:configure checking for memory.h... yes :info:configure checking for strings.h... yes :info:configure checking for inttypes.h... yes :info:configure checking for stdint.h... yes :info:configure checking for unistd.h... yes :info:configure checking for unistd.h... (cached) yes :info:configure checking sys/time.h usability... yes :info:configure checking sys/time.h presence... yes :info:configure checking for sys/time.h... yes :info:configure checking sched.h usability... yes :info:configure checking sched.h presence... yes :info:configure checking for sched.h... yes :info:configure checking for sysconf... yes :info:configure checking for the pthreads library -lpthreads... no :info:configure checking whether pthreads work without any flags... yes :info:configure checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE :info:configure checking if more special flags are required for pthreads... no :info:configure checking for cc_r... /opt/local/bin/gcc-mp-4.4 :info:configure checking if atomic operations are supported... yes :info:configure checking whether byte ordering is bigendian... no :info:configure checking that size_t can hold pointers... yes :info:configure checking for SIGUSR1... yes :info:configure checking for pipes... yes :info:configure checking floating-point format... IEEE754 (little-endian byte and word order) :info:configure checking whether ln -s works... yes :info:configure checking whether make sets $(MAKE)... (cached) yes :info:configure checking for a sed that does not truncate output... /usr/bin/sed :info:configure checking for ld used by /opt/local/bin/gcc-mp-4.4 ... /usr/bin/ld :info:configure checking if the linker (/usr/bin/ld) is GNU ld... no :info:configure checking for /usr/bin/ld option to reload object files... -r :info:configure checking for BSD-compatible nm... /usr/bin/nm :info:configure checking how to recognise dependent libraries... pass_all :info:configure checking dlfcn.h usability... yes :info:configure checking dlfcn.h presence... yes :info:configure checking for dlfcn.h... yes :info:configure checking whether we are using the GNU C++ compiler... yes :info:configure checking whether /opt/local/bin/g++-mp-4.4 accepts -g... yes :info:configure checking dependency style of /opt/local/bin/g++-mp-4.4... gcc3 :info:configure checking how to run the C++ preprocessor... /opt/local/bin/g++-mp-4.4 -E :info:configure checking the maximum length of command line arguments... 196608 :info:configure checking command to parse /usr/bin/nm output from /opt/local/bin/gcc-mp-4.4 object... ok :info:configure checking for objdir... .libs :info:configure checking for ar... ar :info:configure checking for ranlib... ranlib :info:configure checking for strip... strip :info:configure checking if /opt/local/bin/gcc-mp-4.4 supports -fno-rtti -fno-exceptions... no :info:configure checking for /opt/local/bin/gcc-mp-4.4 option to produce PIC... -fno-common :info:configure checking if /opt/local/bin/gcc-mp-4.4 PIC flag -fno-common works... yes :info:configure checking if /opt/local/bin/gcc-mp-4.4 static flag -static works... no :info:configure checking if /opt/local/bin/gcc-mp-4.4 supports -c -o file.o... yes :info:configure checking whether the /opt/local/bin/gcc-mp-4.4 linker (/usr/bin/ld) supports shared libraries... yes :info:configure checking dynamic linker characteristics... darwin10.6.0 dyld :info:configure checking how to hardcode library paths into programs... immediate :info:configure checking whether stripping libraries is possible... yes :info:configure checking if libtool supports shared libraries... yes :info:configure checking whether to build shared libraries... yes :info:configure checking whether to build static libraries... yes :info:configure configure: creating libtool :info:configure appending configuration tag "CXX" to libtool :info:configure checking for ld used by /opt/local/bin/g++-mp-4.4... /usr/bin/ld :info:configure checking if the linker (/usr/bin/ld) is GNU ld... no :info:configure checking whether the /opt/local/bin/g++-mp-4.4 linker (/usr/bin/ld) supports shared libraries... yes :info:configure checking for /opt/local/bin/g++-mp-4.4 option to produce PIC... -fno-common :info:configure checking if /opt/local/bin/g++-mp-4.4 PIC flag -fno-common works... yes :info:configure checking if /opt/local/bin/g++-mp-4.4 static flag -static works... no :info:configure checking if /opt/local/bin/g++-mp-4.4 supports -c -o file.o... yes :info:configure checking whether the /opt/local/bin/g++-mp-4.4 linker (/usr/bin/ld) supports shared libraries... yes :info:configure checking dynamic linker characteristics... darwin10.6.0 dyld :info:configure checking how to hardcode library paths into programs... immediate :info:configure appending configuration tag "F77" to libtool :info:configure checking if libtool supports shared libraries... yes :info:configure checking whether to build shared libraries... yes :info:configure checking whether to build static libraries... yes :info:configure checking for /opt/local/bin/gfortran-mp-4.4 option to produce PIC... -fno-common :info:configure checking if /opt/local/bin/gfortran-mp-4.4 PIC flag -fno-common works... yes :info:configure checking if /opt/local/bin/gfortran-mp-4.4 static flag -static works... no :info:configure checking if /opt/local/bin/gfortran-mp-4.4 supports -c -o file.o... yes :info:configure checking whether the /opt/local/bin/gfortran-mp-4.4 linker (/usr/bin/ld) supports shared libraries... yes :info:configure checking dynamic linker characteristics... darwin10.6.0 dyld :info:configure checking how to hardcode library paths into programs... immediate :info:configure checking for special C compiler options needed for large files... no :info:configure checking for _FILE_OFFSET_BITS value needed for large files... no :info:configure checking for _LARGEFILE_SOURCE value needed for large files... no :info:configure checking for sqrt in -lm... yes :info:configure checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). :info:configure Other alternatives are 'fftw2', or 'mkl' for Intel MKL. :info:configure You are STRONGLY recommended to use one of these - fftw is free. :info:configure :info:configure Use CPPFLAGS and LDFLAGS if the library is installed in a :info:configure non-standard location. (see FAQ at ​http://www.gromacs.org) :info:configure :info:configure If you dont care about performance you can also specify 'fftpack' :info:configure to use a slower set of FFTs built into Gromacs. :info:configure (Just install FFTW3 unless you really know what you are doing). :info:configure :info:configure shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/work/gromacs-4.5.1" && ./configure --prefix=/opt/local --bindir=/opt/local/lib/gromacs/bin --enable-shared --with-x " returned error 1 :error:configure Target org.macports.configure returned: configure failure: shell command failed (see log for details) :debug:configure Backtrace: configure failure: shell command failed (see log for details)

while executing

"$procedure $targetname" :info:configure Warning: the following items did not execute (for gromacs): org.macports.activate org.macports.configure org.macports.build org.macports.destroot org.macports.install :notice:configure Log for gromacs is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_gromacs/main.log