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 <[email protected]>
*To:* Taylor Kaplan <[email protected]>; Discussion list for
GROMACS users <[email protected]>
*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
========================================
--
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