[gmx-users] gromacs on glacier.westgrid.ca

[Justin A. Lemkul]

Payman Pirzadeh wrote:
> Dear Tsjerk,
> Thanks for your e-mail. The message that cluster sends is:
> 
> "Running on 4 processors.
> Starting run at: Sat May 16 17:13:28 PDT 2009
> Warning: Command line arguments for program should be given
> after the program name.  Assuming that
> ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a
> command line argument for the program.
> Warning: Command line arguments for program should be given
> after the program name.  Assuming that -s is a
> command line argument for the program.
> Warning: Command line arguments for program should be given
> after the program name.  Assuming that npttest is a
> command line argument for the program.
> Missing: program name
> Program -path either does not exist, is not
> executable, or is an erroneous argument to mpirun.
> Job finished at: Sat May 16 17:13:28 PDT 2009"
> 
> The message that GROMACS has in log file is:
> 
> "Program mdrun, VERSION 3.3.1
> Source code file: gmxfio.c, line: 706
> 
> Can not open file:
> topol.tpr"
> 
> This is while I have the topology file in the same folder.
> 

It might be useful to post the script you're using to submit the job.  There's 
something (or several things) fundamentally wrong.  Your path points to Gromacs 
version 4.0.4, but the executable that's being called is version 3.3.1.

-Justin

> Payman
> 
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Tsjerk Wassenaar
> Sent: May 19, 2009 12:25 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] gromacs on glacier.westgrid.ca
> 
> Hi Payman,
> 
> That is probably not the only grid facility on which Gromacs may be
> run and it would be helpful if you could give specifications of it
> (WMS software e.g.), which could give you more response. Also, it
> would be helpful if you'd be able to give more information regarding
> the output. Then you'd also have to ask the question whether your
> problem is grid related or gromacs related. In the former case you'd
> better consult support from the facility you're trying to use.
> 
> Cheers,
> 
> Tsjerk
> 
> On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh <ppirzade at ucalgary.ca>
> wrote:
>> Hi All,
>>
>> Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
>> yes, I will be appreciated if he/she can tell me how to run gmx on this
>> facility. I either get error messages which says either the executable or
>> the topology file can not be found.
>>
>> Regards,
>>
>>
>>
>> Payman
>>
>>
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================