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Dear Ansgar,<div><br></div><div>I had already installed Xcode which includes all the compilers for Mac. </div><div><br>As you can see in my /usr/bin, I have:</div><div>lrwxr-xr-x 1 root wheel 7 Jul 19 07:52 gcc -> gcc-4.2</div><div><div>lrwxr-xr-x 1 root wheel 7 Jul 19 07:53 g++ -> g++-4.2</div><div>lrwxr-xr-x 1 root wheel 7 Jul 20 09:14 c++-3.3 -> g++-3.3</div><div>Macintosh:bin alikachmar$ pwd</div><div>/usr/bin</div><div>Macintosh:bin alikachmar$ </div><div><br></div><div>and I have gcc as well:</div><div><br></div><div><div>Macintosh:bin alikachmar$ cd /usr/local/lib</div><div>Macintosh:lib alikachmar$ ls -lrt</div><div>total 18960</div><div>-rwxr-xr-x@ 1 root wheel 735 Mar 21 2007 libgmp.la</div><div>-rw-r--r--@ 1 root wheel 448148 Mar 21 2007 libgmp.a</div><div>-rwxr-xr-x@ 1 root wheel 781 Dec 22 2008 libmpfr.la</div><div>-rw-r--r--@ 1 root wheel 1342688 Dec 22 2008 libmpfr.a</div><div>drwxr-xr-x@ 3 root wheel 102 Jun 26 2009 gcc</div><div>-rwxr-xr-x@ 1 root wheel 906 Jun 26 2009 libssp.la</div><div>-rw-r--r--@ 1 root wheel 49612 Jun 26 2009 libssp.a</div><div>-rwxr-xr-x@ 1 root wheel 17040 Jun 26 2009 libssp.0.dylib</div><div>-rwxr-xr-x@ 1 root wheel 895 Jun 26 2009 libssp_nonshared.la</div><div>-rw-r--r--@ 1 root wheel 2160 Jun 26 2009 libssp_nonshared.a</div><div>-rw-r--r--@ 1 root wheel 17500 Jun 26 2009 libgcc_s.10.5.dylib</div><div>-rw-r--r--@ 1 root wheel 17372 Jun 26 2009 libgcc_s.10.4.dylib</div><div>-rw-r--r--@ 1 root wheel 261384 Jun 26 2009 libgcc_s.1.dylib</div><div>-rwxr-xr-x@ 1 root wheel 940 Jun 26 2009 libgfortran.la</div><div>-rw-r--r--@ 1 root wheel 5079684 Jun 26 2009 libgfortran.a</div><div>-rwxr-xr-x@ 1 root wheel 996600 Jun 26 2009 libgfortran.3.dylib</div><div>drwxr-xr-x@ 18 root wheel 612 Jun 26 2009 x86_64</div><div>-rw-r--r--@ 1 root wheel 768188 Jun 26 2009 libiberty.a</div><div>-rw-r--r--@ 1 root wheel 165 Jun 26 2009 libgomp.spec</div><div>-rwxr-xr-x@ 1 root wheel 912 Jun 26 2009 libgomp.la</div><div>-rw-r--r--@ 1 root wheel 348956 Jun 26 2009 libgomp.a</div><div>-rwxr-xr-x@ 1 root wheel 76948 Jun 26 2009 libgomp.1.dylib</div><div>drwxr-xr-x 4 root wheel 136 Dec 15 2009 ImageMagick-6.5.8</div><div>lrwxrwxrwx 1 root wheel 14 Jul 16 22:09 libssp.dylib -> libssp.0.dylib</div><div>lrwxrwxrwx 1 root wheel 15 Jul 16 22:09 libgomp.dylib -> libgomp.1.dylib</div><div>lrwxrwxrwx 1 root wheel 19 Jul 16 22:09 libgfortran.dylib -> libgfortran.3.dylib</div><div>lrwxrwxrwx 1 root wheel 16 Jul 16 22:09 libgcc_s_x86_64.1.dylib -> libgcc_s.1.dylib</div><div>lrwxrwxrwx 1 root wheel 16 Jul 16 22:09 libgcc_s_ppc64.1.dylib -> libgcc_s.1.dylib</div><div>-rw-r--r-- 1 root wheel 197248 Jul 17 00:28 libf2c.a</div><div>Macintosh:lib alikachmar$ </div></div><div><br></div><div><br></div><div>I add in my .bash_profile: export PATH=$PATH:/usr/bin/gcc and still I have the same error.</div><div><br></div><div><br></div><div>Thanks.</div><div><br></div><div>Ali</div>> From: Ansgar.Esztermann@mpi-bpc.mpg.de<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 22 Jul 2010 10:38:02 +0200<br>> Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard<br>> <br>> [This should have gone to the list]<br>> <br>> Dear Ali,<br>> <br>> 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).<br>> <br>> <br>> Regards,<br>> <br>> A.<br>> <br>> <br>> On Jul 22, 2010, at 8:30 , KACHMAR Ali wrote:<br>> > Dear Ansgar,<br>> <br>> > <br>> > the config.log reads:<br>> > <br>> > configure:3845: checking for cc option to accept ISO C89<br>> > configure:3919: cc -c -g -O2 -I/Users/alikachmar/software/include conftest.c >&5<br>> > configure:3925: $? = 0<br>> > configure:3948: result: none needed<br>> > configure:3977: checking for style of include used by make<br>> > configure:4005: result: GNU<br>> > configure:4030: checking dependency style of cc<br>> > configure:4121: result: gcc3<br>> > configure:4419: checking dependency style of cc<br>> > configure:4510: result: gcc3<br>> > configure:4535: checking for mpxlc<br>> > configure:4565: result: no<br>> > configure:4535: checking for mpicc<br>> > configure:4551: found /usr/bin/mpicc<br>> > configure:4562: result: mpicc<br>> > configure:4576: checking whether the MPI cc command works<br>> > configure:4600: mpicc -o conftest -g -O2 -I/Users/alikachmar/software/include -L/Users/alikachmar/software/lib conftest.c >&5<br>> > --------------------------------------------------------------------------<br>> > The Open MPI wrapper compiler was unable to find the specified compiler<br>> > gcc in your PATH.<br>> > <br>> > Note that this compiler was either specified at configure time or in<br>> > one of several possible environment variables.<br>> > <br>> > --------------------------------------------------------------------------<br>> > configure:4606: $? = 1<br>> > configure: failed program was:<br>> > | /* confdefs.h. */<br>> > | #define PACKAGE_NAME "gromacs"<br>> > | #define PACKAGE_TARNAME "gromacs"<br>> > | #define PACKAGE_VERSION "4.0.5"<br>> > | #define PACKAGE_STRING "gromacs 4.0.5"<br>> > | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"<br>> > | #define PACKAGE "gromacs"<br>> > | #define VERSION "4.0.5"<br>> > | #define GMX_SOFTWARE_SQRT<br>> > | #define GMX_QMMM_GAUSSIAN<br>> > | #define BUILD_TIME "Thu Jul 22 07:52:36 CEST 2010"<br>> > | #define BUILD_USER "alikachmar@Macintosh.local"<br>> > | #define BUILD_MACHINE "Darwin 9.8.0 i386"<br>> > | /* end confdefs.h. */<br>> > | #include <mpi.h><br>> > | int<br>> > | main ()<br>> > | {<br>> > | int argc; char **argv; MPI_Init(&argc,&argv);<br>> > | ;<br>> > | return 0;<br>> > | }<br>> > configure:4618: error: Cannot compile and link MPI code with mpicc<br>> > <br>> > <br>> > my .bash_profile:<br>> > <br>> > <br>> > # Setting PATH for Python 2.7<br>> > # The orginal version is saved in .bash_profile.pysave<br>> > PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"<br>> > export PATH<br>> > <br>> > # Setting PATH for MacPython 2.6<br>> > # The orginal version is saved in .bash_profile.pysave<br>> > PATH="/Library/Frameworks/Python.framework/Versions/2.6/bin:${PATH}"<br>> > export PATH<br>> > <br>> > export PATH=$PATH:/usr/local/lib<br>> > export PATH=$PATH: /usr/bin/mpicc<br>> > export PATH=$PATH:/usr/local/lam/bin/<br>> > <br>> > source /usr/local/gromacs/bin/GMXRC<br>> > <br>> > export CPPFLAGS=-I/usr/local/openmpi/include<br>> > <br>> > <br>> > PS: the gcc is under the directory: /usr/local/lib or /usr/lib.<br>> > <br>> > Thanks.<br>> > <br>> > Ali<br>> > <br>> > <br>> > <br>> > > From: Ansgar.Esztermann@mpi-bpc.mpg.de<br>> > > To: gmx-users@gromacs.org<br>> > > Date: Wed, 21 Jul 2010 12:15:25 +0200<br>> > > Subject: Re: [gmx-users] installation: gromacs on Mac.10.5.8 leopard<br>> > > <br>> > > <br>> > > On Jul 21, 2010, at 11:07 , KACHMAR Ali wrote:<br>> > > <br>> > > > checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc<br>> > > <br>> > > <br>> > > 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). <br>> > > <br>> > > Regards,<br>> > > <br>> > > A.<br>> > > -- <br>> > > Ansgar Esztermann<br>> > > DV-Systemadministration<br>> > > Max-Planck-Institut für biophysikalische Chemie, Abteilung 105<br>> > > <br>> > > -- <br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > De nouvelles Emoticones sur Messenger ? Téléchargez gratuitement les émoticônes Summer !<br>> <br>> -- <br>> Ansgar Esztermann<br>> DV-Systemadministration<br>> Max-Planck-Institut für biophysikalische Chemie, Abteilung 105<br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></div> <br /><hr />Le nouveau Messenger arrive ! <a href='http://clk.atdmt.com/FRM/go/244627952/direct/01/' target='_new'>Téléchargez-le gratuitement et découvrez ses nouvelles fonctionnalités</a></body>
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