Re: [gmx-users] mdrun-gpu error

[Mark Abraham]

On 19/01/2012 8:45 PM, aiswarya pawar wrote:
Mark,
THe normal mdrun also hangs thus not generating any output.

OK. It's your problem to solve... keep simplifying stuff until you can 
isolate a small number of possible causes. Top of the list is file 
system availability.

Mark


On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <mark.abra...@anu.edu.au 
<mailto:mark.abra...@anu.edu.au>> wrote:

    On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
    <mailto:aiswarya.pa...@gmail.com> wrote:
    Hi,

    Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.

    No, but you should start trying to simplify what you're doing to
    see where the problem lies. Does normal mdrun work?

    Mark


    Thanks
    Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
it!

    -----Original Message-----
    From: Szilárd Páll<szilard.p...@cbr.su.se>  <mailto:szilard.p...@cbr.su.se>
    Sender:gmx-users-boun...@gromacs.org  <mailto:gmx-users-boun...@gromacs.org>
    Date: Wed, 18 Jan 2012 14:47:59
    To: Discussion list for GROMACS users<gmx-users@gromacs.org>  
<mailto:gmx-users@gromacs.org>
    Reply-To: Discussion list for GROMACS users<gmx-users@gromacs.org>  
<mailto:gmx-users@gromacs.org>
    Subject: Re: [gmx-users] mdrun-gpu error

    Hi,

    Most of those are just warnings, the only error I see there comes from
    the shell, probably an error in your script.

    Cheers,
    --
    Szilárd



    On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
    <aiswarya.pa...@gmail.com>  <mailto:aiswarya.pa...@gmail.com>  wrote:
    Hi users,

    Am running mdrun on gpu . I receive an error such as=

    WARNING: This run will generate roughly 38570 Mb of data


    WARNING: OpenMM does not support leap-frog, will use velocity-verlet
    integrator.


    WARNING: OpenMM supports only Andersen thermostat with the
    md/md-vv/md-vv-avek integrators.


    WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


    WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
    CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
    option.

    /bin/cat: file_loc: No such file or directory


    and the job is running but the nothing written into .xtc, .trr, .edr files .
    What could have gone wrong?

    --
    Aiswarya  B Pawar

    Bioinformatics Dept,
    Indian Institute of Science
    Bangalore



    --
    gmx-users mailing listgmx-us...@gromacs.org  <mailto:gmx-users@gromacs.org>
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at
    http://www.gromacs.org/Support/Mailing_Lists/Search  before posting!
    Please don't post (un)subscribe requests to the list. Use the
    www interface or send it togmx-users-requ...@gromacs.org  
<mailto:gmx-users-requ...@gromacs.org>.
    Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists
    --
    gmx-users mailing listgmx-us...@gromacs.org  <mailto:gmx-users@gromacs.org>
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive 
athttp://www.gromacs.org/Support/Mailing_Lists/Search  before posting!
    Please don't post (un)subscribe requests to the list. Use the
    www interface or send it togmx-users-requ...@gromacs.org  
<mailto:gmx-users-requ...@gromacs.org>.
    Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists




    --
    gmx-users mailing list gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>
    http://lists.gromacs.org/mailman/listinfo/gmx-users
    Please search the archive at
    http://www.gromacs.org/Support/Mailing_Lists/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
    <mailto:gmx-users-requ...@gromacs.org>.
    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore





-- 
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/Support/Mailing_Lists/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/Support/Mailing_Lists