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.<div><br clear="all">--<br>Eamon McDermott<br>

M.Sc Student<br>Physics and Engineering Physics<br>University of Saskatchewan<br><a href="mailto:eamon.mcdermott@usask.ca" target="_blank">eamon.mcdermott@usask.ca</a><div>Office: +1-306-966-6380</div><div>Scheduling: <span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px"><a href="http://doodle.com/eamon.mcdermott" style="color:rgb(42,93,176)" target="_blank">http://doodle.com/eamon.mcdermott</a></span></div>

<br>
<br><br><div class="gmail_quote">2012/3/9 Gavin Abo <span dir="ltr">&lt;<a href="mailto:gsabo@crimson.ua.edu">gsabo@crimson.ua.edu</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">


  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    In addition to changing the &#39;first&#39; occurrence of<div class="im"><br>
    <br>
    <font color="#000099">echo $WIENROOT run_lapw -p -NI -ec .0000001 -I
    </font><br>
    <br></div>
    to<div class="im"><br>
    <br>
    <font color="#000099">$WIENROOT/run_lapw -p -NI -ec .0000001 -I </font><br>
    <br></div>
    (or <font color="#000099">run_lapw -p -NI -ec .0000001 -I</font>)<br>
    <br>
    Also, check the line:<br>
    <br>
    <font color="#000099">export SCRATCH=`mktemp -d -p
      /tmp/$USER/wien2k/`</font><br>
    <br>
    It might just need to be:<br>
    <br>
    <font color="#000099">export SCRATCH=`/tmp/$USER/wien2k/`</font><br>
    <br>
    because the following in the script might have problems with &quot;mktemp
    -d -p&quot; in the SCRATCH variable:<br>
    <br>
    <font color="#000099">mkdir -p $SCRATCH</font><br>
    <br>
    and<br>
    <br>
    <font color="#000099">rm -rf $SCRATCH</font><div><div class="h5"><br>
    <br>
    On 3/9/2012 2:51 AM, shwetha gummula wrote:
    <blockquote type="cite">Dear Prof. Peter Blaha and Wien2k users,<br>
                Thank you very much for the reply. We will try to do
      this.<br>
            Thanking you<br>
      Regards<br>
      G.Shwetha<br>
      <a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
      <br>
      <br>
      <div class="gmail_quote">On Fri, Mar 9, 2012 at 12:58 PM, Peter
        Blaha <span dir="ltr">&lt;<a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.tuwien.ac.at</a>&gt;</span>
        wrote:<br>
        <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
          You already got the answer previously:<br>
          <br>
          The line:
          <div><br>
             echo $WIENROOT run_lapw -p -NI -ec .0000001 -I<br>
          </div>
          does not execute anything.<br>
          <br>
          Try out such a line in a terminal window.<br>
          <br>
          If you want to use a &quot;supercomputer&quot;, you need to learn some
          basic Linux.<br>
          <br>
          Who wrote the nice script ?   He should be able to teach you
          the meaning<br>
          of each line.<br>
          <br>
          Am 09.03.2012 05:44, schrieb shwetha gummula:<br>
          <blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
            <div>
              Dear Prof. Peter Blaha and Wien2k users,<br>
              <br>
                        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<br>
              mail I posted to wien2k user list earlier also but I
              didn&#39;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<br>
              our HPC. We have Intel 10 version Fortran compiler in our
              machine. Here I am attaching the script file.<br>
              <br>
                       Thanking you<br>
              <br>
               Regards<br>
              G.Shwetha<br>
            </div>
            <a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
            &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>&gt;<br>
            <br>
            <br>
            <br>
            <br>
            On Tue, Mar 6, 2012 at 9:33 PM, shwetha gummula &lt;<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
            &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>&gt;&gt;
            wrote:
            <div>
              <div><br>
                <br>
                <br>
                <br>
                   On Tue, Mar 6, 2012 at 8:01 PM, pascal boulet &lt;<a href="mailto:pascal.boulet@univ-amu.fr" target="_blank">pascal.boulet@univ-amu.fr</a>
                &lt;mailto:<a href="mailto:pascal.boulet@univ-amu.fr" target="_blank">pascal.boulet@univ-amu.fr</a>&gt;&gt;
                wrote:<br>
                <br>
                       Dear G.Shwetha ,<br>
                <br>
                       I might be wrong but the command in TiN.sh to
                submit the calculation<br>
                       looks wrong.<br>
                       My feeling is that you should substitute :<br>
                       $WIENROOT/run_lapw -p -NI -ec .0000001 -I<br>
                       for:<br>
                       echo $WIENROOT run_lapw -p -NI -ec .0000001 -I<br>
                <br>
                       Best regards<br>
                       Pascal<br>
                <br>
                       On 06/03/2012 10:27, shwetha gummula wrote:<br>
                        &gt; Dear P.Blaha and Wien2k Users,<br>
                        &gt;<br>
                        &gt;           We are using WIEN2k 11.1 on Red
                Hat 5.6 version in our HPC.<br>
                        &gt; We have Intel 10 version Fortran compiler
                in our machine. We are<br>
                        &gt; trying to submit the job using the PBS
                 Script file for k-point<br>
                        &gt; parallelization. When we submitting the job
                using qsub case.sh, it is<br>
                        &gt; giving the job ID but in the status it is
                not showing any job ID (when<br>
                        &gt; we give the command qstat). It is creating
                the machine file but it is<br>
                        &gt; not showing any error in the error file and
                output file (it is not<br>
                        &gt; creating any other files). I just want to
                know whether the job is<br>
                        &gt; running or not, or whether it is problem
                with my script file?<br>
                        &gt; But when I submit with the command mode on
                the terminal like : giving<br>
                        &gt; run_lapw -ec 0.00001 it is working and
                creating other files.<br>
                        &gt; Please, Can any one help to solve this
                problem.<br>
                        &gt; Here I&#39;m attaching the script file.<br>
                        &gt;                          Thanking You<br>
                        &gt;<br>
                        &gt;<br>
                        &gt; G.Shwetha<br>
              </div>
            </div>
                    &gt; <a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
            &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>&gt;
            &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
            &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>&gt;&gt;<br>
                    &gt;<br>
                    &gt;<br>
                    &gt; _______________________________________________<br>
                    &gt; Wien mailing list<br>
                    &gt; <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a>
            &lt;mailto:<a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a>&gt;
            <div>
              <br>
                      &gt; <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
              <br>
                     --<br>
                     Pascal Boulet, PhD, computational chemist<br>
                     Aix-Marseille Université<br>
                     Laboratoire MADIREL<br>
                     Avenue Normandie-Niemen<br>
                     13397 Marseille Cedex 20<br>
                     France<br>
                     **********<br>
                     Tel. <a href="tel:%28%2B33%29%20%280%29413.55.18.10" value="+33413551810" target="_blank">(+33) (0)413.55.18.10</a><br>
                     Fax. <a href="tel:%28%2B33%29%20%280%29413.55.18.50" value="+33413551850" target="_blank">(+33) (0)413.55.18.50</a><br>
                     **********<br>
            </div>
                   <a href="mailto:pascal.boulet@univ-amu.fr" target="_blank">pascal.boulet@univ-amu.fr</a>
            &lt;mailto:<a href="mailto:pascal.boulet@univ-amu.fr" target="_blank">pascal.boulet@univ-amu.fr</a>&gt;
            <div>
              <br>
                     **********<br>
                     <a href="https://sites.google.com/a/univ-provence.fr/pb-comput-chem" target="_blank">https://sites.google.com/a/univ-provence.fr/pb-comput-chem</a><br>
                     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
              <br>
                         *<br>
                         * Anglais<br>
                         * Français<br>
              <br>
                         * Anglais<br>
                         * Français<br>
              <br>
                     <a>&lt;javascript:void(0);&gt;</a><br>
                     _______________________________________________<br>
                     Wien mailing list<br>
            </div>
                   <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a>
            &lt;mailto:<a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a>&gt;
            <div>
              <br>
                     <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
              <br>
              <br>
                 Dear Pascal and Wien2k users,<br>
                               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<br>
                 change we observed.<br>
                                                                       
                                  Thanking you<br>
              <br>
              <br>
                 Regards<br>
                 G.Shwetha<br>
            </div>
            <div>    <a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>
              &lt;mailto:<a href="mailto:shwetha.gummula@gmail.com" target="_blank">shwetha.gummula@gmail.com</a>&gt;<br>
              <br>
              <br>
              <br>
              <br>
              _______________________________________________<br>
              Wien mailing list<br>
              <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a><br>
              <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
            </div>
          </blockquote>
          <font color="#888888">
            <br>
            -- <br>
            <br>
                                                 P.Blaha<br>
            --------------------------------------------------------------------------<br>
            Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060
            Vienna<br>
            Phone: <a href="tel:%2B43-1-58801-165300" value="+43158801165300" target="_blank">+43-1-58801-165300</a>             FAX:
            <a href="tel:%2B43-1-58801-165982" value="+43158801165982" target="_blank">+43-1-58801-165982</a><br>
            Email: <a href="mailto:blaha@theochem.tuwien.ac.at" target="_blank">blaha@theochem.tuwien.ac.at</a>
               WWW: <a href="http://info.tuwien.ac.at/theochem/" target="_blank">http://info.tuwien.ac.at/theochem/</a><br>
            --------------------------------------------------------------------------</font>
          <div>
            <div><br>
              <br>
              _______________________________________________<br>
              Wien mailing list<br>
              <a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a><br>
              <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
            </div>
          </div>
        </blockquote>
      </div>
      <br>
      <br>
      <fieldset></fieldset>
      <br>
      <pre>_______________________________________________
Wien mailing list
<a href="mailto:Wien@zeus.theochem.tuwien.ac.at" target="_blank">Wien@zeus.theochem.tuwien.ac.at</a>
<a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a>
</pre>
    </blockquote>
    <br>
  </div></div></div>

<br>_______________________________________________<br>
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<a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a><br>
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<br></blockquote></div><br></div>