<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 "temp_dir=xxxx" 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 <<a href="mailto:jmholton@lbl.gov">jmholton@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid 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'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>
> Hi James,<br>
><br>
> I'll leave the global Phenix temp aspect to Billy.<br>
> For ligand identification specifically, the working directory is where <br>
> all the files are located. The program will purge most of the <br>
> intermediate files upon completion. If the user interrupted the runs <br>
> or if the program crashed at certain spots, the purge mechanism might <br>
> not kick in. Even so, it'd take many runs to accumulate 20e6 (2e7?) <br>
> files. In any case, you've got a point and I'll look into salvaging <br>
> intermediate files of ligand identification as soon as they are not <br>
> needed in the process.<br>
><br>
> Thanks,<br>
><br>
> Li-Wei<br>
><br>
> On 4/23/2021 7:03 PM, James Holton wrote:<br>
>> Hello all,<br>
>><br>
>> Is there a way to configure phenix at install time (or perhaps <br>
>> post-install) to put temporary files under /tmp ? I just had to <br>
>> delete 20e6 temp files over NFS from a single user's phenix ligand <br>
>> identification run. The delete took almost a month.<br>
>><br>
>> Apologies if I am neglecting to look somewhere obvious in the <br>
>> documentation,<br>
>><br>
>> Happy Weekend!<br>
>><br>
>> -James Holton<br>
>> MAD Scientist<br>
>><br>
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<br>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><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></div></div></div></div></div></div>