[Wien] Reg: k-point parallel submission of script to the HPC
shwetha gummula
shwetha.gummula at gmail.com
Fri Mar 9 18:17:41 CET 2012
Dear Wien2k users,
Thank you Gavin Abo, Eamon McDermott for the valuable reply.
Thanking you
Regards
G. Shwetha
shwetha.gummula at gmail.com
On Fri, Mar 9, 2012 at 9:26 PM, Eamon McDermott <eamon.mcdermott at usask.ca>wrote:
> The SCRATCH line is fine. The backticks cause the shell to execute the
> command contained within them and load the output (a full path to a new
> temporary directory) into the environment variable.
>
> --
> Eamon McDermott
> M.Sc Student
> Physics and Engineering Physics
> University of Saskatchewan
> eamon.mcdermott at usask.ca
> Office: +1-306-966-6380
> Scheduling: http://doodle.com/eamon.mcdermott
>
>
>
> 2012/3/9 Gavin Abo <gsabo at crimson.ua.edu>
>
>> In addition to changing the 'first' occurrence of
>>
>>
>> echo $WIENROOT run_lapw -p -NI -ec .0000001 -I
>>
>> to
>>
>>
>> $WIENROOT/run_lapw -p -NI -ec .0000001 -I
>>
>> (or run_lapw -p -NI -ec .0000001 -I)
>>
>> Also, check the line:
>>
>> export SCRATCH=`mktemp -d -p /tmp/$USER/wien2k/`
>>
>> It might just need to be:
>>
>> export SCRATCH=`/tmp/$USER/wien2k/`
>>
>> because the following in the script might have problems with "mktemp -d
>> -p" in the SCRATCH variable:
>>
>> mkdir -p $SCRATCH
>>
>> and
>>
>> rm -rf $SCRATCH
>>
>>
>> On 3/9/2012 2:51 AM, shwetha gummula wrote:
>>
>> Dear Prof. Peter Blaha and Wien2k users,
>> Thank you very much for the reply. We will try to do this.
>> Thanking you
>> Regards
>> G.Shwetha
>> shwetha.gummula at gmail.com
>>
>> On Fri, Mar 9, 2012 at 12:58 PM, Peter Blaha <
>> pblaha at theochem.tuwien.ac.at> wrote:
>>
>>> You already got the answer previously:
>>>
>>> The line:
>>>
>>> echo $WIENROOT run_lapw -p -NI -ec .0000001 -I
>>> does not execute anything.
>>>
>>> Try out such a line in a terminal window.
>>>
>>> If you want to use a "supercomputer", you need to learn some basic Linux.
>>>
>>> Who wrote the nice script ? He should be able to teach you the meaning
>>> of each line.
>>>
>>> Am 09.03.2012 05:44, schrieb shwetha gummula:
>>>
>>>> Dear Prof. Peter Blaha and Wien2k users,
>>>>
>>>> We are trying to submit k-point parallelization jobs to HPC
>>>> through script file (qsub case.sh). It is showing job ID but it is not
>>>> running (not showing any error). This
>>>> mail I posted to wien2k user list earlier also but I didn't solved the
>>>> problem yet. Please can any one help me regarding this. We are using WIEN2k
>>>> 11.1 on Red Hat 5.6 version in
>>>> our HPC. We have Intel 10 version Fortran compiler in our machine. Here
>>>> I am attaching the script file.
>>>>
>>>> Thanking you
>>>>
>>>> Regards
>>>> G.Shwetha
>>>> shwetha.gummula at gmail.com <mailto:shwetha.gummula at gmail.com>
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Mar 6, 2012 at 9:33 PM, shwetha gummula <
>>>> shwetha.gummula at gmail.com <mailto:shwetha.gummula at gmail.com>> wrote:
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Mar 6, 2012 at 8:01 PM, pascal boulet <
>>>> pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>> wrote:
>>>>
>>>> Dear G.Shwetha ,
>>>>
>>>> I might be wrong but the command in TiN.sh to submit the
>>>> calculation
>>>> looks wrong.
>>>> My feeling is that you should substitute :
>>>> $WIENROOT/run_lapw -p -NI -ec .0000001 -I
>>>> for:
>>>> echo $WIENROOT run_lapw -p -NI -ec .0000001 -I
>>>>
>>>> Best regards
>>>> Pascal
>>>>
>>>> On 06/03/2012 10:27, shwetha gummula wrote:
>>>> > Dear P.Blaha and Wien2k Users,
>>>> >
>>>> > We are using WIEN2k 11.1 on Red Hat 5.6 version in
>>>> our HPC.
>>>> > We have Intel 10 version Fortran compiler in our machine. We
>>>> are
>>>> > trying to submit the job using the PBS Script file for
>>>> k-point
>>>> > parallelization. When we submitting the job using qsub
>>>> case.sh, it is
>>>> > giving the job ID but in the status it is not showing any job
>>>> ID (when
>>>> > we give the command qstat). It is creating the machine file
>>>> but it is
>>>> > not showing any error in the error file and output file (it
>>>> is not
>>>> > creating any other files). I just want to know whether the
>>>> job is
>>>> > running or not, or whether it is problem with my script file?
>>>> > But when I submit with the command mode on the terminal like
>>>> : giving
>>>> > run_lapw -ec 0.00001 it is working and creating other files.
>>>> > Please, Can any one help to solve this problem.
>>>> > Here I'm attaching the script file.
>>>> > Thanking You
>>>> >
>>>> >
>>>> > G.Shwetha
>>>> > shwetha.gummula at gmail.com <mailto:shwetha.gummula at gmail.com>
>>>> <mailto:shwetha.gummula at gmail.com <mailto:shwetha.gummula at gmail.com>>
>>>> >
>>>> >
>>>> > _______________________________________________
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>>>> Wien at zeus.theochem.tuwien.ac.at>
>>>>
>>>> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>
>>>> --
>>>> Pascal Boulet, PhD, computational chemist
>>>> Aix-Marseille Université
>>>> Laboratoire MADIREL
>>>> Avenue Normandie-Niemen
>>>> 13397 Marseille Cedex 20
>>>> France
>>>> **********
>>>> Tel. (+33) (0)413.55.18.10
>>>> Fax. (+33) (0)413.55.18.50
>>>> **********
>>>> pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
>>>>
>>>> **********
>>>> https://sites.google.com/a/univ-provence.fr/pb-comput-chem
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>
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>>>>
>>>>
>>>> Dear Pascal and Wien2k users,
>>>> Thank you for your reply. We already tried by
>>>> substituting echo $WIENROOT run_lapw -p -NI -ec .0000001 by
>>>> $WIENROOT/run_lapw -p -NI -ec .0000001 -I but no
>>>> change we observed.
>>>>
>>>> Thanking you
>>>>
>>>>
>>>> Regards
>>>> G.Shwetha
>>>> shwetha.gummula at gmail.com <mailto:shwetha.gummula at gmail.com>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
>>> --
>>>
>>> P.Blaha
>>>
>>> --------------------------------------------------------------------------
>>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>>> Email: blaha at theochem.tuwien.ac.at WWW:
>>> http://info.tuwien.ac.at/theochem/
>>>
>>> --------------------------------------------------------------------------
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>>
>>
>>
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