Re: [gmx-users] MPI and dual-core laptop
Hi, if you only want to use the two processors of you laptop you can simple leave away the --enable-mpi flag. Then it will work in parallel using threads. Use mdrun -nt 2 -s ... to specify two threads. If you anyhow want to compile with MPI, take a look at the config.log file (search for 'Cannot compile and link MPI code') to check the actual cause of your problem, probably some library was not found. Carsten On Sep 27, 2010, at 8:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI and dual-core laptop
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/27/2010 08:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham Hi, it seems the mpicc compiler does not find the necessary libraries to link or doesn't even find the compiler. Check if mpicc is in your path. To include the missing libraries in the GROMACS configuration use the LDFLAGS and CPPFLAGS variables to set the corresponding pathes. CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ... If you have to add further include and library directories you have to add a further -I/... and/or -L/... and put the whole expression after the = into quotes, e.g CPPFLAGS=-I/usr/local/lib - -I/home/user/local/fftw3/include and so on. However if you use Gromacs 4.5 I would use and get common with the CMake system, which really works fine and also a GUI is available that allows you to easy set your variables options. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o tC0AoJRxehKCtgYNSq8qa5fqbEagde8a =YCG5 -END PGP SIGNATURE- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] MPI and dual-core laptop
Hi, You don't need MPI within one machine. Gromacs 4.5 has a built in thread-mpi library that gets built automatically. Berk Date: Tue, 28 Sep 2010 10:22:30 +0200 From: domm...@icp.uni-stuttgart.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] MPI and dual-core laptop -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/27/2010 08:42 PM, simon sham wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham Hi, it seems the mpicc compiler does not find the necessary libraries to link or doesn't even find the compiler. Check if mpicc is in your path. To include the missing libraries in the GROMACS configuration use the LDFLAGS and CPPFLAGS variables to set the corresponding pathes. CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure ... If you have to add further include and library directories you have to add a further -I/... and/or -L/... and put the whole expression after the = into quotes, e.g CPPFLAGS=-I/usr/local/lib - -I/home/user/local/fftw3/include and so on. However if you use Gromacs 4.5 I would use and get common with the CMake system, which really works fine and also a GUI is available that allows you to easy set your variables options. /Flo - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkyhpcYACgkQLpNNBb9GiPm1AgCfWcXsF7zs+fGV2gGFiGgG1H4o tC0AoJRxehKCtgYNSq8qa5fqbEagde8a =YCG5 -END PGP SIGNATURE- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MPI and dual-core laptop
Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI and dual-core laptop
Hi, My 2 cents on your problem: I've been running gromacs on nearly everything, from one to six cores. It works. Besides mpi being in your /usr/local/bin, is it on the path of your system? You can do, in the terminal export PATH=$PATH:/usr/local/bin Or, for a more permanent solution, go to your ~/.bashrc file, find a line which already has some PATH folders in it, and add the :/usr/local/bin and then just retry the configure command on a new terminal. Sometimes I need to use different mpi implementations - apparently at random. Building OpenMPI from source has been the most sucessfully approach. Don't know what system you're running, but there any many linux distros which already include gromacs in the repos. Hope it helps, Gonçalo On 27 September 2010 19:42, simon sham ssha...@yahoo.com wrote: Hi, I wanted to test the GROMACS MPI version in my dual-processors laptop. I have installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 4.5.1 with --enable-mpi option, I got the following configuration problem: checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpicc mpicc is in my /usr/local/bin directory. Questions: 1. Can I run GROMACS 4.5.1 in a dual-processor laptop? 2. If yes, how should I configure the software? Thanks in advance for your insight. Best, Simon Sham -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
