[gmx-users] mdrun_command_not working in cygwin
Shahid Nayeem
msnayeem at gmail.com
Mon Nov 24 14:23:29 CET 2014
Hi Wahab
I do have Gromacs-4.6.3 installed on my cygwin but there also I am able to
run all commands of gromacs except mdrun. sending the out put and mdlog of
mdrun for 4.6.3.
I do need Gromacs 4.5.4 as I have some comments in my paper where all work
is done on this version. Please help.
Initially with both version of Gromacs I was able to run mdrun but now I
face problem.
For mdrun_4.6.3 which is mdrun_d in my installation the error in running is
as follows
mdrun_d -v -s prot_b4em.tpr
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.6.3 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s prot_b4em.tpr Input Run input file: tpr tpb tpa
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c confout.gro Output Structure file: gro g96 pdb etc.
-e ener.edr Output Energy file
-g md.log Output Log file
-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tabletf tabletf.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo edsam.xvg Output, Opt. xvgr/xmgr file
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-ro rotation.xvg Output, Opt. xvgr/xmgr file
-ra rotangles.log Output, Opt. Log file
-rs rotslabs.log Output, Opt. Log file
-rt rottorque.log Output, Opt. Log file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
-multidir rundir Input, Opt., Mult. Run directory
-membed membed.dat Input, Opt. Generic data file
-mp membed.top Input, Opt. Topology file
-mn membed.ndx Input, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-ddorder enum interleave DD node order: interleave, pp_pme or
cartesian
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-nt int 0 Total number of threads to start (0 is guess)
-ntmpi int 0 Number of thread-MPI threads to start (0 is
guess)
-ntomp int 0 Number of OpenMP threads per MPI process/thread
to start (0 is guess)
-ntomp_pme int 0 Number of OpenMP threads per MPI process/thread
to start (0 is -ntomp)
-pin enum auto Fix threads (or processes) to specific cores:
auto, on or off
-pinoffset int 0 The starting logical core number for pinning to
cores; used to avoid pinning threads from
different mdrun instances to the same core
-pinstride int 0 Pinning distance in logical cores for threads,
use 0 to minimize the number of threads per
physical core
-gpu_id string List of GPU id's to use
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions
with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or
yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-nb enum auto Calculate non-bonded interactions on: auto, cpu,
gpu or gpu_cpu
-[no]tunepme bool yes Optimize PME load between PP/PME nodes or
GPU/CPU
-[no]testverlet bool no Test the Verlet non-bonded scheme
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-nsteps step -2 Run this number of steps, overrides .mdp file
option
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-nex int 0 Number of random exchanges to carry out each
exchange interval (N^3 is one suggestion). -nex
zero or not specified gives neighbor replica
exchange.
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up md.log to ./#md.log.2#
Reading file prot_b4em.tpr, VERSION 4.6.3 (double precision)
tMPI error: I/O or system error: No such file or directory
Aborted (core dumped)
SHAHID NAYEEM at SHAHIDNAYEEM-HP /cygdrive/c/Users/SHAHID NAYEEM/Test_gromacs
md.log file is attached
Shahid
On Mon, Nov 24, 2014 at 2:26 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:
> Almost one year ago, on Sep 11 2013, you started installing
> Gromacs 4.6.3 on cygwin and received some responses regarding
> problems there. What happened with this installation, why
> did you go back to the older Gromacs (4.5.4) version?
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2013-September/084053.html
>
> On 24.11.2014 06:17, Shahid Nayeem wrote:
>
>> I have Gromacs 4.5.4 installed in my cygwin. Initially all the commands
>> were working fine. But now I face problem on running mdrun command. When I
>> run command mdrun_4.5.4 -v -s topol.tpr, this also runs but the output
>> .trr
>> .xtc generated has zero frames. I reinstalled my cygwin in between for
>> some
>> additional packages and I thought this problem might be because of this
>> and
>> so I re installed my gromacs also but there also I face the same problem.
>> I don't get any error message. I am attaching md.log and out put of md
>> command file. Please give me I solution. I dont want to change the version
>> of Gromacs as I have partially completed my work using this version.
>>
>
> BTW, the Gromacs versions below 4.6.7 (iirc) don't work in "normal"
> tMPI mode on cygwin/64. You have to build a "real" MPI executeable
> and run that.
>
> Regards
>
> M.
>
>
>
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