[gmx-users] installation: gromacs on Mac.10.5.8 leopard
KACHMAR Ali
kachmar_ali at hotmail.fr
Thu Jul 22 11:00:46 CEST 2010
Dear Ansgar,
I had already installed Xcode which includes all the compilers for Mac.
As you can see in my /usr/bin, I have:lrwxr-xr-x 1 root wheel 7 Jul 19 07:52 gcc -> gcc-4.2lrwxr-xr-x 1 root wheel 7 Jul 19 07:53 g++ -> g++-4.2lrwxr-xr-x 1 root wheel 7 Jul 20 09:14 c++-3.3 -> g++-3.3Macintosh:bin alikachmar$ pwd/usr/binMacintosh:bin alikachmar$
and I have gcc as well:
Macintosh:bin alikachmar$ cd /usr/local/libMacintosh:lib alikachmar$ ls -lrttotal 18960-rwxr-xr-x@ 1 root wheel 735 Mar 21 2007 libgmp.la-rw-r--r--@ 1 root wheel 448148 Mar 21 2007 libgmp.a-rwxr-xr-x@ 1 root wheel 781 Dec 22 2008 libmpfr.la-rw-r--r--@ 1 root wheel 1342688 Dec 22 2008 libmpfr.adrwxr-xr-x@ 3 root wheel 102 Jun 26 2009 gcc-rwxr-xr-x@ 1 root wheel 906 Jun 26 2009 libssp.la-rw-r--r--@ 1 root wheel 49612 Jun 26 2009 libssp.a-rwxr-xr-x@ 1 root wheel 17040 Jun 26 2009 libssp.0.dylib-rwxr-xr-x@ 1 root wheel 895 Jun 26 2009 libssp_nonshared.la-rw-r--r--@ 1 root wheel 2160 Jun 26 2009 libssp_nonshared.a-rw-r--r--@ 1 root wheel 17500 Jun 26 2009 libgcc_s.10.5.dylib-rw-r--r--@ 1 root wheel 17372 Jun 26 2009 libgcc_s.10.4.dylib-rw-r--r--@ 1 root wheel 261384 Jun 26 2009 libgcc_s.1.dylib-rwxr-xr-x@ 1 root wheel 940 Jun 26 2009 libgfortran.la-rw-r--r--@ 1 root wheel 5079684 Jun 26 2009 libgfortran.a-rwxr-xr-x@ 1 root wheel 996600 Jun 26 2009 libgfortran.3.dylibdrwxr-xr-x@ 18 root wheel 612 Jun 26 2009 x86_64-rw-r--r--@ 1 root wheel 768188 Jun 26 2009 libiberty.a-rw-r--r--@ 1 root wheel 165 Jun 26 2009 libgomp.spec-rwxr-xr-x@ 1 root wheel 912 Jun 26 2009 libgomp.la-rw-r--r--@ 1 root wheel 348956 Jun 26 2009 libgomp.a-rwxr-xr-x@ 1 root wheel 76948 Jun 26 2009 libgomp.1.dylibdrwxr-xr-x 4 root wheel 136 Dec 15 2009 ImageMagick-6.5.8lrwxrwxrwx 1 root wheel 14 Jul 16 22:09 libssp.dylib -> libssp.0.dyliblrwxrwxrwx 1 root wheel 15 Jul 16 22:09 libgomp.dylib -> libgomp.1.dyliblrwxrwxrwx 1 root wheel 19 Jul 16 22:09 libgfortran.dylib -> libgfortran.3.dyliblrwxrwxrwx 1 root wheel 16 Jul 16 22:09 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dyliblrwxrwxrwx 1 root wheel 16 Jul 16 22:09 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib-rw-r--r-- 1 root wheel 197248 Jul 17 00:28 libf2c.aMacintosh:lib alikachmar$
I add in my .bash_profile: export PATH=$PATH:/usr/bin/gcc and still I have the same error.
Thanks.
Ali> From: Ansgar.Esztermann at mpi-bpc.mpg.de
> To: gmx-users at gromacs.org
> Date: Thu, 22 Jul 2010 10:38:02 +0200
> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
>
> [This should have gone to the list]
>
> Dear Ali,
>
> gcc should be in /usr/bin (or some other bin, if you do not use Apple's compiler), not in /usr/lib nor /usr/local/lib. Do you have the developer tools installed? If not, get them from http://developer.apple.com/mac/ (they should also be on the OS DVDs, albeit in an older version).
>
>
> Regards,
>
> A.
>
>
> On Jul 22, 2010, at 8:30 , KACHMAR Ali wrote:
> > Dear Ansgar,
>
> >
> > the config.log reads:
> >
> > configure:3845: checking for cc option to accept ISO C89
> > configure:3919: cc -c -g -O2 -I/Users/alikachmar/software/include conftest.c >&5
> > configure:3925: $? = 0
> > configure:3948: result: none needed
> > configure:3977: checking for style of include used by make
> > configure:4005: result: GNU
> > configure:4030: checking dependency style of cc
> > configure:4121: result: gcc3
> > configure:4419: checking dependency style of cc
> > configure:4510: result: gcc3
> > configure:4535: checking for mpxlc
> > configure:4565: result: no
> > configure:4535: checking for mpicc
> > configure:4551: found /usr/bin/mpicc
> > configure:4562: result: mpicc
> > configure:4576: checking whether the MPI cc command works
> > configure:4600: mpicc -o conftest -g -O2 -I/Users/alikachmar/software/include -L/Users/alikachmar/software/lib conftest.c >&5
> > --------------------------------------------------------------------------
> > The Open MPI wrapper compiler was unable to find the specified compiler
> > gcc in your PATH.
> >
> > Note that this compiler was either specified at configure time or in
> > one of several possible environment variables.
> >
> > --------------------------------------------------------------------------
> > configure:4606: $? = 1
> > configure: failed program was:
> > | /* confdefs.h. */
> > | #define PACKAGE_NAME "gromacs"
> > | #define PACKAGE_TARNAME "gromacs"
> > | #define PACKAGE_VERSION "4.0.5"
> > | #define PACKAGE_STRING "gromacs 4.0.5"
> > | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> > | #define PACKAGE "gromacs"
> > | #define VERSION "4.0.5"
> > | #define GMX_SOFTWARE_SQRT
> > | #define GMX_QMMM_GAUSSIAN
> > | #define BUILD_TIME "Thu Jul 22 07:52:36 CEST 2010"
> > | #define BUILD_USER "alikachmar at Macintosh.local"
> > | #define BUILD_MACHINE "Darwin 9.8.0 i386"
> > | /* end confdefs.h. */
> > | #include <mpi.h>
> > | int
> > | main ()
> > | {
> > | int argc; char **argv; MPI_Init(&argc,&argv);
> > | ;
> > | return 0;
> > | }
> > configure:4618: error: Cannot compile and link MPI code with mpicc
> >
> >
> > my .bash_profile:
> >
> >
> > # Setting PATH for Python 2.7
> > # The orginal version is saved in .bash_profile.pysave
> > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
> > export PATH
> >
> > # Setting PATH for MacPython 2.6
> > # The orginal version is saved in .bash_profile.pysave
> > PATH="/Library/Frameworks/Python.framework/Versions/2.6/bin:${PATH}"
> > export PATH
> >
> > export PATH=$PATH:/usr/local/lib
> > export PATH=$PATH: /usr/bin/mpicc
> > export PATH=$PATH:/usr/local/lam/bin/
> >
> > source /usr/local/gromacs/bin/GMXRC
> >
> > export CPPFLAGS=-I/usr/local/openmpi/include
> >
> >
> > PS: the gcc is under the directory: /usr/local/lib or /usr/lib.
> >
> > Thanks.
> >
> > Ali
> >
> >
> >
> > > From: Ansgar.Esztermann at mpi-bpc.mpg.de
> > > To: gmx-users at gromacs.org
> > > Date: Wed, 21 Jul 2010 12:15:25 +0200
> > > Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard
> > >
> > >
> > > On Jul 21, 2010, at 11:07 , KACHMAR Ali wrote:
> > >
> > > > checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc
> > >
> > >
> > > This is the immediate problem: something goes wrong when compiling a test program with mpicc. If you look into the configure log, you should find a more detailed explanation of what went wrong (somewhere near the end).
> > >
> > > Regards,
> > >
> > > A.
> > > --
> > > Ansgar Esztermann
> > > DV-Systemadministration
> > > Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
> > >
> > > --
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
> --
> Ansgar Esztermann
> DV-Systemadministration
> Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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