Hi, Our system system administrator configured the software with --MPI option according to the installation instructions. He told me there were lots of warning messages when he did it. My related question is that since there is LAM/MPI out there as well, can GROMACS 4.5 be configured with OPENMPI? Thanks in advance, Simon Sham
Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi, I got all sorts of error message such as "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol `ompi_mpi_byte' has different size in shared object, consider re-linking", and many others. My questions: 1. When I prepare my system for simulations, do I have to consistently use *_mpi functions in gromacs_4.5.1_mpi directory? 2. Are there any details that I need to pay attention when I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924/2a671694/attachment-0001.html ------------------------------ Message: 3 Date: Fri, 24 Sep 2010 15:18:27 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] MPI To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4c9cf983.7010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Guess my reply never hit the list, either, but it's in the archive: http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html -Justin simon sham wrote: > Hi, > This is the same email that I'd sent yesterday but has not got posted? > Hi, > I have some questions about installation of GROMACS with MPI. > Our system administrator has installed the 4.5.1 version in our system. > When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" > with mdrun_mpi, I got all sorts of error message such as > "opt/apps/gromacs/gromacs-4.5.1-mpi/bin/mdrun_mpi: Symbol > `ompi_mpi_byte' has different size in shared object, consider > re-linking", and many others. > > My questions: > 1. When I prepare my system for simulations, do I have to consistently > use *_mpi functions in gromacs_4.5.1_mpi directory? > 2. Are there any details that I need to pay attention when I configure > the software with openmpi? > > Thanks for your help in advance. > > Best, > > Simon Sham > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================
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