[Wien] Reg: k-point parallel submission of script to the HPC

Gavin Abo gsabo at crimson.ua.edu
Fri Mar 9 16:43:07 CET 2012


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 <mailto:shwetha.gummula at gmail.com>
>
> On Fri, Mar 9, 2012 at 12:58 PM, Peter Blaha 
> <pblaha at theochem.tuwien.ac.at <mailto: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>
>         <mailto: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>
>         <mailto: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>
>         <mailto: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>>
>         <mailto: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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>                --
>                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>
>         <mailto:pascal.boulet at univ-amu.fr
>         <mailto:pascal.boulet at univ-amu.fr>>
>
>                **********
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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>
>         <mailto: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
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