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Thank you Tom!<br>
<br>
Ok. So, in order to change the default I need to go through the
code looking for "temp_dir" and change things?<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/24/2021 10:16 AM, Tom Terwilliger
wrote:<br>
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<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"
moz-do-not-send="true">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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<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" moz-do-not-send="true">tterwilliger@newmexicoconsortium.org</a></div>
<div>Tel: 505-431-0010</div>
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