OK! I tested your suggestion about frequent output. As you had predicted, it crashed immediately. But the message I got from the cluster was
PBS Job Id: 94865.orca1.ibb Job Name: AFPIII_NVT275test job deleted Job deleted at request of r...@elder2.ibb MOAB_INFO: job was rejected - job violates qos configuration 'job '94865' violates MINPROC policy of 4 (R: 1, U: 0)' This is despite the fact that in my submission script, the number of CPUs are 8! As I had mentioned earlier, same script is used for my water systems. Regards, Payman On Fri, 2009-09-04 at 19:29 -0400, Justin A. Lemkul wrote: > Have you tried my suggestion from the last message of setting frequent > output? > Could your system just be collapsing at the outset of the simulation? > Setting > nstxout = 1 would catch something like this. > > There is nothing special about treating a protein in parallel vs. a system of > water. Since a system of water runs just fine, it seems even more likely to > me > that your system is simply crashing immediately, rather than a problem with > Gromacs or the MPI implementation. > > -Justin > > Paymon Pirzadeh wrote: > > Regarding the problems I have on running protein system in parallel > > (runs without output), When I run pure water system, everything is fine, > > I have tested pure water systems 8 times larger than my protein system. > > while the former runs fine, the latter has problems. I have also tested > > pure water systems with approximately same number of sites in .gro file > > as in my protein .gro file, and with the same input file in terms of > > spitting outputs; they are fine.I would like to know what happens to > > GROMACS when a protein is added to the system. The cluster admin has not > > get back to me, but I still want to check there is no problem with my > > setup! (although my system runs fine in serial mode). > > Regards, > > > > Payman > > > > > > > > On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote: > >> Payman Pirzadeh wrote: > >>> There is sth strange about this problem which I suspect it might be due to > >>> the mdp file and input. I can run the energy minimization without any > >>> problems (I submit the job and it apparently works using the same > >>> submission > >>> script)! But as soon as I prepare the tpr file for MD run, then I run into > >>> this run-without-output trouble. > >>> Again I paste my mdp file below (I want to run an NVT run): > >>> > >> There isn't anything in the .mdp file that suggests you wouldn't get any > >> output. > >> The output of mdrun is buffered, so depending on your settings, you may > >> have > >> more frequent output during energy minimization. There may be some > >> problem with > >> the MPI implementation in buffering and communicating data properly. > >> That's a > >> bit of a guess, but it could be happening. > >> > >> Definitely check with the cluster admin to see if there are any error > >> messages > >> reported for the jobs you submitted. > >> > >> Another test you could do to force a huge amount of data would be to set > >> all of > >> your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter > >> simulation (to > >> prevent massive data output!); this would force more continuous data > >> through the > >> buffer. > >> > >> -Justin > >> > >>> cpp = cpp > >>> include = -I../top > >>> define = -DPOSRES > >>> > >>> ; Run control > >>> > >>> integrator = md > >>> dt = 0.001 ;1 fs > >>> nsteps = 3000000 ;3 ns > >>> comm_mode = linear > >>> nstcomm = 1 > >>> > >>> ;Output control > >>> > >>> nstxout = 5000 > >>> nstlog = 5000 > >>> nstenergy = 5000 > >>> nstxtcout = 1500 > >>> nstvout = 5000 > >>> nstfout = 5000 > >>> xtc_grps = > >>> energygrps = > >>> > >>> ; Neighbour Searching > >>> > >>> nstlist = 10 > >>> ns_type = grid > >>> rlist = 0.9 > >>> pbc = xyz > >>> > >>> ; Electrostatistics > >>> > >>> coulombtype = PME > >>> rcoulomb = 0.9 > >>> ;epsilon_r = 1 > >>> > >>> ; Vdw > >>> > >>> vdwtype = cut-off > >>> rvdw = 1.2 > >>> DispCorr = EnerPres > >>> > >>> ;Ewald > >>> > >>> fourierspacing = 0.12 > >>> pme_order = 4 > >>> ewald_rtol = 1e-6 > >>> optimize_fft = yes > >>> > >>> ; Temperature coupling > >>> > >>> tcoupl = v-rescale > >>> ld_seed = -1 > >>> tc-grps = System > >>> tau_t = 0.1 > >>> ref_t = 275 > >>> > >>> ; Pressure Coupling > >>> > >>> Pcoupl = no > >>> ;Pcoupltype = isotropic > >>> ;tau_p = 1.0 > >>> ;compressibility = 5.5e-5 > >>> ;ref_p = 1.0 > >>> gen_vel = yes > >>> gen_temp = 275 > >>> gen_seed = 173529 > >>> constraint-algorithm = Lincs > >>> constraints = all-bonds > >>> lincs-order = 4 > >>> > >>> Regards, > >>> > >>> Payman > >>> > >>> > >>> -----Original Message----- > >>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > >>> On Behalf Of Mark Abraham > >>> Sent: August 27, 2009 3:32 PM > >>> To: Discussion list for GROMACS users > >>> Subject: Re: [gmx-users] Re: wierd behavior of mdrun > >>> > >>> Vitaly V. Chaban wrote: > >>>> Then I believe you have problems with MPI. > >>>> > >>>> Before I experienced something alike on our old system - serial > >>>> version worked OK but parallel one failed. The same issue was with > >>>> CPMD by the way. Another programs worked fine. I didn't correct that > >>>> problem... > >>>> > >>>> On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh<ppirz...@ucalgary.ca> > >>> wrote: > >>>>> Yes, > >>>>> it works when it is run on one processor interactively! > >>> That's fine, but it doesn't mean the problem is with the parallelism, as > >>> Vitaly suggests. If your cluster filesystem isn't configured properly, > >>> you will observe these symptoms. Since the submission script was the > >>> same, MPI worked previously, so isn't likely to be the problem... > >>> > >>> Mark > >>> > >>>>> On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote: > >>>>>>> I made a .tpr file for my md run without any problems (using the > >>>>>>> bottom > >>>>>>> mdp file). My job submission script is also the same thing I used for > >>>>>>> other jobs which had no problems. But now when I submit this .tpr > >>>>>>> file, > >>>>>>> only an empty log file is generated! The qstat of the cluster shows > >>> that > >>>>>>> the job is running, also the processors are 100% engaged while I have > >>> no > >>>>>>> outputs! > >>>>>> A standard guess: what about trying to run the single-processor job on > >>>>>> the same cluster? Does it run OK? > >>>>>> > >>>>>> > >>>> _______________________________________________ > >>>> 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 > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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
