[gmx-users] cannot open file
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 3 00:53:49 CEST 2011
Taylor Kaplan wrote:
> Hi Justin,
>
> I'm running em.sh file as nohup em.sh &. Below is the code in my
> em.sh file.
>
> mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s
> etExcited.tpr -o etExcited.trr -c etExcited.gro -e etExcited.edr -g
> etExcited.log -pd &.
>
> I've double checked my directory, all the file names are right and I've
> checked my nve.mdp file that I was running which I've posted below as well.
>
> title = production-dynamics
> ;warnings = 10
> cpp = /lib/cpp
> ;DEFINE = -DPOSRES
> DEFINE = -DFLEXIBLE
> ;constraints = hbonds
> ;constraint_algorithm = shake
> integrator = md
> dt = 0.0005 ;
> nsteps = 1000000 ;
> ;nstcomm = 1 ; reset c.o.m motion
> nstlist = 10
> ns_type = grid
> nstenergy = 1 ; print energies
> nstlog = 1 ; print to logfile
> nstvout = 100000 ; write velocities
> nstxout = 100000 ; collect data in fs (write coords)
> ;nstxtcout = 0 ; to print corrdinates to xtc trajectory
> energygrps = Protein HC4 r_42 r_46 r_50 r_52 r_68 r_69 r_70 SOL
> nstfout = 0
> coulombtype = PME-Switch
> fourierspacing = 0.12
> pme_order = 4
> vdwtype = switch
> rvdw = 1.0
> rlist = 1.2
> rcoulomb = 1.0
> pbc = xyz
> ;dispcorr = Ener
> continuation = yes
> ;Berendsen temperature coupling is on
> Tcoupl = no ; temperature bath (yes, no)
> ;tau_t = 0.1
> ;tc-grps = system
> ;ref_t = 300
> ;Berendsen Pressure coupling is on
> pcoupl = no ; pressure bath (yes, no)
> ;pcoupltype = isotropic
> ;tau_p = 0.5
> ;compressibility = 4.5e-05
> ;ref_p = 1.0
> ;Generate velocities is on at 300
> gen_vel = no ; generate initial velocities
> ;gen_temp = 300.0 ; initial temperature
> ;gen_seed = 173529 ; random seeD
>
> Lastly I used the command " grompp -f nve.mdp -c etExcited.gro -p
> etExcited.top -n res.ndx -o etExcited " to generate my .tpr file and I
> had no errors. To show that I have all the correct files in my directory
> below I have printed the files from ls command.
>
> nalysis etSimulation.gro #mdout.mdp.2# posre_Protein.itp
> E46QT50V.pdb etSimulation.log #mdout.mdp.3# resE.ndx
> em.mdp etSimulation.top nohup.out res.ndx
> em.sh etSimulation.trr npt.mdp Save
> etExcited.gro et.tpr nve.mdp state_prev.cpt
> etExcited.top machine nvt.mdp stateSimulation.cpt
> etExcited.tpr mdout.mdp posre_Ion2.itp topol.top
> #etExcited.tpr.1# #mdout.mdp.1# posre.itp
>
> I have no idea why this stopped working for me, its just very recent.
>
If things used to work and now don't, and everything else is constant with
respect to Gromacs (i.e. the version and specific installation you're using),
then this is a problem for your sysadmin. Sudden, unexpected changes mean
someone is messing with your system.
-Justin
> Thanks,
>
> Taylor
>
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Taylor Kaplan <taylor_kaplan at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at gromacs.org>
> *Sent:* Friday, July 29, 2011 4:17 PM
> *Subject:* Re: [gmx-users] cannot open file
>
>
>
> Taylor Kaplan wrote:
> > Hi gromacs users,
> >
> > I'm running a simulation but I keep getting the following errors.
> >
> > rogram mdrun_mpi, VERSION 4.5.1
> > Source code file: gmxfio.c, line: 537
> >
> > Can not open file:
> > taExcited.tpr
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > "That Was Cool" (Beavis and Butthead)
> >
> > Error on node 0, will try to stop all the nodes
> > Halting parallel program mdrun_mpi on CPU 0 out of 4
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode -1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> --------------------------------------------------------------------------
> >
> > gcq#182: "That Was Cool" (Beavis and Butthead)
> >
> >
> --------------------------------------------------------------------------
> > mpirun has exited due to process rank 0 with PID 9680 on
> > node compute-0-10 exiting without calling "finalize". This may
> > have caused other processes in the application to be
> > terminated by signals sent by mpirun (as reported here).
> >
> > I don't know why gromacs cannot find my taExcited.tpr file, since it
> does exist in my working directory. However I noticed that when gromacs
> makes copies of my log files, its putting it in my home directory. This
> leads me to believe that it must be looking into the wrong path. This
> problem is only recent since gromacs knows where to looking when i
> reference my other working files, such as when i run grompp, but mdrun
> does not want to open up my .tpr file. Any ideas?
> >
>
> Are you submitting the job to a queue? If so, please provide the entire
> script you're using to execute mdrun. Does the problem persist in newer
> versions of Gromacs? It's always best to start from the newest
> available version, rather than troubleshoot an old one, just to find out
> the problem has already been resolved.
>
> -Justin
>
> -- ========================================
>
> 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
>
> ========================================
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list