Hi Justin, Regarding your suggestion using spc216, when I tried the energetically minimize spc216 with grompp,I got the following error:
Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File spce.itp, line 1 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype Same thing happened when I tried TIP4P. Where is the problem? I did not have this issue with my own model. Regards, 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 1:53 PM To: Gromacs Users' List Subject: Re: [gmx-users] gromacs on glacier Payman Pirzadeh wrote: > Dear Justin, > Here is the mpich version: > MPICH Version: 1.2.7p1 > MPICH Release date: $Date: 2005/11/04 11:54:51$ > MPICH Patches applied: none > MPICH configure: -prefix=/share/apps/intel/mpich/ > MPICH Device: ch_p4 > Well, I think that MPICH is your problem then. There are several reports of sporadic bugs (the one that you're seeing!) with that version. Since it's several years old, getting a fix is probably a bit unlikely :) Perhaps you can sort out with the sysadmins what you can do. Like I said before, probably OpenMPI is a better bet - we've never had a problem with it. You can probably install it yourself in your home directory, and point to mpicc with environment variables during the Gromacs installation. > Also the gcc compiler: > gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9) > Copyright (C) 2006 Free Software Foundation, Inc. > > About the system, I have water model with 3 atom sites and 3 virtual sites. > Probably not a very good test case for diagnosing problems, but I think it's unrelated in this case. When testing, keep it simple - run a simulation with spc216.gro from the Gromacs installation, it should pretty much always work :) -Justin > 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 11:56 AM > To: Gromacs Users' List > Subject: Re: [gmx-users] gromacs on glacier > > > > Payman Pirzadeh wrote: >> 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. >> > > This is pretty much the standard installation procedure. What we also need > to > know are the compilers used, etc. for the installation. The error you're > getting is from MPICH. Which version is installed on the cluster? It may > be > old and buggy. In any case, you can try to install something newer, like a > recent version of OpenMPI (which we have on our cluster); it may be more > reliable. Only a random thought, means nothing unless we know what you have > > installed :) > > What about the contents of your system, as I asked before? Do you really > have a > 100% virtual site system? > > -Justin > >> 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! 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