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):
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