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

[ryandesign (Ryan Carsten Schmidt)]

Please use WikiFormatting for literal output so it doesn't get jumbled together.

Don't forget to fill in the Port and Cc fields.

Don't set Priority to High.

Looks like the relevant error is:

checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3).

gromacs probably needs a dependency on fftw-3 (or possibly fftw-3-single or fftw-3-long; I don't understand the distinction).

[jimmymisc@…]

Thanks, I am new to this, but I will do so in the future.

I installed FFTW-3, but it still did not work, so I installed:

• fftw-3-long --> still did not work
• gromacs-double --> somehow error message did not show up.

However I am confused now on running the program. Typing pdb2gmx yields nothing. Am I doing it wrong ?

[jimmymisc@…]

OK, apologies for the silly comment above. Turns out I just need to install FFTW-3-single for gromacs and FFTW-3-long for gromacs-double. After that, gromacs and gromacs-double can be installed without problem.

What is left now is to figure out how to run gromacs program (pdb2gmx etc) from the directory where my molecules are sitting at.. tips ?

Thank you

[adfernandes (Andrew Fernandes)]

Hmm... you are the second or third time that someone has reported that gromacs did not install fftw-3 as required; it should have been automatic, but was not. I don't understand that one.

As for the binaries: gromacs installs its binaries in a strange place by default. You can always see what files belong to a port with port file [port-name]. You'll see that gromacs puts its binaries in /opt/local/lib/gromacs/bin, so you'll probably need to add that to your $PATH for whatever scripts you have running gromacs.

I'll look into why fftw was not installed under a separate ticket.

[jmroot (Joshua Root)]

All the gcc variants set depends_lib when they should append to it.

[adfernandes (Andrew Fernandes)]

Grr. I can't believe how many times I looked at that and didn't see it. Thanks for the heads-up! Fixed (and updated) in r78014.