From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Nov 11 2015 - 11:00:21 CST
I would just use the wall-time of a job as reference: if the queue system
won't report it, just add a "date +%s" command to your script to get the
time in seconds before and after running NAMD.
Giacomo
On Tue, Nov 10, 2015 at 9:18 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> Hi Giacomo,
>
> Thanks for your suggestion! I can now run the jobs.
>
> Is there a good way to benchmark the time it takes to run? Unlike a
> regular NAMD job, this does not seem to be generating benchmark times on
> its own.
>
>
> Best regards,
> Chitrak.
>
> On Fri, Nov 6, 2015 at 3:41 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Chitrak: can you perhaps add to the replica.namd a Tcl check the
>> presence of the file before executing NAMD? Something like an error
>> message that gives you the replica number that is showing this error may
>> help you dissect the problem.
>>
>> Giacomo
>>
>> On Thu, Nov 5, 2015 at 5:45 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> I am trying to work through the tutorial of replica exchange umbrella
>>> sampling in NAMD. Somehow, I am getting the following error, although I do
>>> have the colvars.conf file in the folder.
>>>
>>> colvars:
>>> ----------------------------------------------------------------------
>>> colvars: Initializing the collective variables module, version
>>> 2014-10-23.
>>> colvars:
>>> ----------------------------------------------------------------------
>>> colvars: Reading new configuration from file "colvars.conf":
>>> colvars: Error: in opening configuration file "colvars.conf".
>>> colvars: No such file or directory
>>> colvars: If this error message is unclear, try recompiling with
>>> -DCOLVARS_DEBUG.
>>> FATAL ERROR: Error in the collective variables module: No such file or
>>> directory
>>> [0] Stack Traceback:
>>>
>>>
>>>
>>> Has anyone else faced this issue? I saw there was a bug regarding
>>> loading colvars for restarting the simulation, but right now I am just
>>> running the job0.conf file. Also, I am using NAMD 2.10
>>>
>>>
>>> Best regards,
>>> Chitrak.
>>>
>>
>>
>>
>> --
>> Giacomo Fiorin
>> Assistant Professor of Research
>> Institute for Computational Molecular Science (ICMS)
>> College of Science and Technology, Temple University
>> 1925 North 12th Street (035-07), Room 704D
>> Philadelphia, PA 19122-1801
>> Phone: +1-215-204-4213
>> http://goo.gl/Q3TBQU
>> http://giacomofiorin.github.io/
>> https://icms.cst.temple.edu/members.html
>>
>>
>>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 http://goo.gl/Q3TBQU http://giacomofiorin.github.io/ https://icms.cst.temple.edu/members.html
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