<div dir="ltr">Hi James,<div><br></div><div>By default, the GUI should try to delete AutoBuild temporary files. However, if the jobs crash, the cleaning up might not take place. In that case, the deletion of temporary files can be manually run by selecting &quot;Projects&quot; in the menu bar, then &quot;Clean up large files&quot;, and then selecting the project directory.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Apr 24, 2021 at 2:56 PM James Holton &lt;<a href="mailto:jmholton@lbl.gov">jmholton@lbl.gov</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
  
    
  
  <div>
    What if people are using the GUI ?<br>
    <br>
    <div>On 4/24/2021 2:51 PM, Tom Terwilliger
      wrote:<br>
    </div>
    <blockquote type="cite">
      
      <div dir="ltr">Hi James,
        <div><br>
          <div>Not the code (I hope), just any scripts that use these
            methods. Like this:</div>
          <div><br>
          </div>
          <div>mkdir /var/tmp/autosol</div>
          <div>phenix.autosol p9.sca 2 se temp_dir=/var/tmp/autosol</div>
          <div><br>
          </div>
          <div>Now the temp files go in /var/tmp/autosol and the output
            files go in AutoSol_run_xxx/ as usual</div>
          <div><br>
          </div>
          <div>All the best,</div>
          <div>Tom</div>
          <div><br>
          </div>
          <div>All the best,</div>
          <div>Tom T</div>
        </div>
      </div>
      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Sat, Apr 24, 2021 at 11:59
          AM James Holton &lt;<a href="mailto:jmholton@lbl.gov" target="_blank">jmholton@lbl.gov</a>&gt;
          wrote:<br>
        </div>
        <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
          <div> Thank you Tom!<br>
            <br>
            Ok.  So, in order to change the default I need to go through
            the code looking for &quot;temp_dir&quot; and change things?<br>
            <br>
            <br>
            <div>On 4/24/2021 10:16 AM, Tom Terwilliger wrote:<br>
            </div>
            <blockquote type="cite">
              <div dir="ltr">Hi James,
                <div><br>
                </div>
                <div>There is no overall Phenix temp directory
                  specification, but most of the temp_dir usage is from
                  autosol/autobuild/ligandfit/map_to_model.  Each of
                  these has the keyword &quot;temp_dir=xxxx&quot; which you should
                  be</div>
                <div>able to set to any directory you want (and local is
                  better as you note).  Most programs using a temp_dir
                  also have a keyword clean_up=True as well.</div>
                <div><br>
                </div>
                <div>All the best,</div>
                <div>Tom T</div>
              </div>
              <br>
              <div class="gmail_quote">
                <div dir="ltr" class="gmail_attr">On Sat, Apr 24, 2021
                  at 10:51 AM James Holton &lt;<a href="mailto:jmholton@lbl.gov" target="_blank">jmholton@lbl.gov</a>&gt;
                  wrote:<br>
                </div>
                <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Thank you Li-Wei<br>
                  <br>
                  Definitely not placing blame on one program.
                  Phenix.autobuild is another <br>
                  big temp file producer.  So is XDS. Clearly this
                  ligand run was a case <br>
                  of a misconfigured, runaway task that never finished.
                  However, the files <br>
                  lingered on disk, eating up inodes for 3 years!<br>
                  <br>
                  The reason I&#39;m asking is I think there are significant
                  performance <br>
                  increases to be gained by using fast, local storage
                  for scratch files. <br>
                  This is not just in speed but storage and overall
                  system/cluster <br>
                  performance.  Very few things are more expensive than
                  an NFS write!<br>
                  <br>
                  Does anyone know how to change the default temp file
                  location across <br>
                  phenix ?  Is this a cctbx thing?<br>
                  <br>
                  Thanks<br>
                  <br>
                  -James<br>
                  <br>
                  <br>
                  On 4/23/2021 9:38 PM, Li-Wei Hung wrote:<br>
                  &gt; Hi James,<br>
                  &gt;<br>
                  &gt; I&#39;ll leave the global Phenix temp aspect to
                  Billy.<br>
                  &gt; For ligand identification specifically, the
                  working directory is where <br>
                  &gt; all the files are located.  The program will
                  purge most of the <br>
                  &gt; intermediate files upon completion. If the user
                  interrupted the runs <br>
                  &gt; or if the program crashed at certain spots, the
                  purge mechanism might <br>
                  &gt; not kick in. Even so, it&#39;d take many runs to
                  accumulate 20e6 (2e7?) <br>
                  &gt; files. In any case, you&#39;ve got a point and I&#39;ll
                  look into salvaging <br>
                  &gt; intermediate files of ligand identification as
                  soon as they are not <br>
                  &gt; needed in the process.<br>
                  &gt;<br>
                  &gt; Thanks,<br>
                  &gt;<br>
                  &gt; Li-Wei<br>
                  &gt;<br>
                  &gt; On 4/23/2021 7:03 PM, James Holton wrote:<br>
                  &gt;&gt; Hello all,<br>
                  &gt;&gt;<br>
                  &gt;&gt; Is there a way to configure phenix at install
                  time (or perhaps <br>
                  &gt;&gt; post-install) to put temporary files under
                  /tmp ?  I just had to <br>
                  &gt;&gt; delete 20e6 temp files over NFS from a single
                  user&#39;s phenix ligand <br>
                  &gt;&gt; identification run.  The delete took almost a
                  month.<br>
                  &gt;&gt;<br>
                  &gt;&gt; Apologies if I am neglecting to look
                  somewhere obvious in the <br>
                  &gt;&gt; documentation,<br>
                  &gt;&gt;<br>
                  &gt;&gt; Happy Weekend!<br>
                  &gt;&gt;<br>
                  &gt;&gt; -James Holton<br>
                  &gt;&gt; MAD Scientist<br>
                  &gt;&gt;<br>
                  &gt;&gt;
                  _______________________________________________<br>
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                          <div>
                            <div dir="ltr">
                              <div dir="ltr">Thomas C Terwilliger
                                <div>Laboratory Fellow, Los Alamos
                                  National Laboratory</div>
                                <div>Senior Scientist, New Mexico
                                  Consortium</div>
                                <div>100 Entrada Dr, Los Alamos, NM
                                  87544</div>
                                <div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div>
                                <div>Tel: 505-431-0010</div>
                                <div><br>
                                </div>
                              </div>
                            </div>
                          </div>
                        </div>
                      </div>
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                  </div>
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            </blockquote>
            <br>
          </div>
        </blockquote>
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              <div>
                <div dir="ltr">
                  <div>
                    <div dir="ltr">
                      <div dir="ltr">Thomas C Terwilliger
                        <div>Laboratory Fellow, Los Alamos National
                          Laboratory</div>
                        <div>Senior Scientist, New Mexico Consortium</div>
                        <div>100 Entrada Dr, Los Alamos, NM 87544</div>
                        <div>Email: <a href="mailto:tterwilliger@newmexicoconsortium.org" target="_blank">tterwilliger@newmexicoconsortium.org</a></div>
                        <div>Tel: 505-431-0010</div>
                        <div><br>
                        </div>
                      </div>
                    </div>
                  </div>
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          </div>
        </div>
      </div>
    </blockquote>
    <br>
  </div>

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