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Hi,<br><br>You don't need MPI within one machine.<br>Gromacs 4.5 has a built in thread-mpi library that gets built automatically.<br><br>Berk<br><br>> Date: Tue, 28 Sep 2010 10:22:30 +0200<br>> From: dommert@icp.uni-stuttgart.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] MPI and dual-core laptop<br>> <br>> -----BEGIN PGP SIGNED MESSAGE-----<br>> Hash: SHA1<br>> <br>> On 09/27/2010 08:42 PM, simon sham wrote:<br>> > Hi,<br>> > I wanted to test the GROMACS MPI version in my dual-processors laptop. I<br>> > have installed openmpi 1.4.2 version. However, when I tried to configure<br>> > GROMACS 4.5.1 with --enable-mpi option, I got the following<br>> > configuration problem:<br>> > <br>> > "checking whether the MPI cc command works... configure: error: Cannot<br>> > compile and link MPI code with mpicc"<br>> > <br>> > <br>> > mpicc is in my /usr/local/bin directory.<br>> > <br>> > Questions:<br>> > 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?<br>> > 2. If yes, how should I configure the software?<br>> > <br>> > Thanks in advance for your insight.<br>> > <br>> > Best,<br>> > <br>> > Simon Sham<br>> > <br>> > <br>> <br>> Hi,<br>> <br>> it seems the mpicc compiler does not find the necessary libraries to<br>> link or doesn't even find the compiler. Check if mpicc is in your path.<br>> <br>> To include the missing libraries in the GROMACS configuration use the<br>> LDFLAGS and CPPFLAGS variables to set the corresponding pathes.<br>> <br>> CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ...<br>> <br>> If you have to add further include and library directories you have to<br>> add a further -I/... and/or -L/... and put the whole expression after<br>> the = into quotes, e.g CPPFLAGS="-I/usr/local/lib<br>> - -I/home/user/local/fftw3/include" and so on.<br>> <br>> However if you use Gromacs 4.5 I would use and get common with the CMake<br>> system, which really works fine and also a GUI is available that allows<br>> you to easy set your variables options.<br>> <br>> /Flo<br>> <br>> <br>> - -- <br>> Florian Dommert<br>> Dipl.-Phys.<br>> <br>> Institute for Computational Physics<br>> <br>> University Stuttgart<br>> <br>> Pfaffenwaldring 27<br>> 70569 Stuttgart<br>> <br>> Phone: +49(0)711/685-6-3613<br>> Fax: +49-(0)711/685-6-3658<br>> <br>> EMail: dommert@icp.uni-stuttgart.de<br>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<br>> -----BEGIN PGP SIGNATURE-----<br>> Version: GnuPG v1.4.10 (GNU/Linux)<br>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/<br>> <br>> iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o<br>> tC0AoJRxehKCtgYNSq8qa5fqbEagde8a<br>> =YCG5<br>> -----END PGP SIGNATURE-----<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/Support/Mailing_Lists/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/Support/Mailing_Lists<br> </body>
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