[Wien] Reg: k-point parallel submission of script to the HPC
Eamon McDermott
eamon.mcdermott at usask.ca
Fri Mar 9 16:56:28 CET 2012
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>>
>>> >
>>> >
>>> > _______________________________________________
>>> > Wien mailing list
>>> > Wien at zeus.theochem.tuwien.ac.at <mailto:
>>> 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>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>
>>
>> --
>>
>> 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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