Hi Justin, Since the manual itself was not sufficient, I asked some other people who are running GROMACS in our group (but they run only on 2 CPUs). Here are the steps I took to compile the parallel version (I have included my notes that they told me as well):
Installation 1. ./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4 This line specifies the installation path 2. Make 3. Make install These two commands will make 'grompp' and analysis functions of GROMACS. 4. Make clean This command will clean some files generated during installation which are not needed anymore. 5. ./configure --enable-mpi --disable-nice --prefix=/global/home/pirzadeh/gromacs-4.0.4 Here we compile the code for parallel version of GROMACS 6. make mdrun 7. make install-mdrun Now the parallel version of mdrun is built. The analysis functions are found in 'bin' folder accompanied by 'GMXRC'. 8. Before running 'grompp' to produce the topology file for simulation, we should use the command source /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the current code. Sorry for tons of e-mails. Payman -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: June 8, 2009 11:12 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Hi, > > I had the chance to run the GROMACS 4.0.4 on another cluster. Same > problem still persists. But what I found is that it can be run on a node > with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . > it will crash. Following are the last lines reported in different files: > > "In the log file of the code": > > > > There are: 1611 Atoms > > There are: 1611 VSites All of your atoms are virtual sites? If so, I would try a simpler test case, to rule out stumbling across some obscure bug. Also: > p2_22627: p4_error: Timeout in establishing connection to remote process: 0 > This is an error message from MPICH, not Gromacs. See, for example: http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html <snip> > To me, it seems that code can not communicate through more than one > node. I am suspicious of doing sth wrong during installation! I tried > wiki, but I can not find the documents as before, and I eally do not > know in which step I might have gone wrong. > If you suspect you have done something wrong, then post the details of the system configuration (hardware, compilers, OS, etc.) as well as a step-by-step record of what you did to compile the software. If your procedure is sound, then it helps rule out the possibility that you messed something up. -Justin > > > Payman > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
