[phenixbb] temp files

[Tom Terwilliger]

Hi James,

Not the code (I hope), just any scripts that use these methods. Like this:

mkdir /var/tmp/autosol
phenix.autosol p9.sca 2 se temp_dir=/var/tmp/autosol

Now the temp files go in /var/tmp/autosol and the output files go in
AutoSol_run_xxx/ as usual

All the best,
Tom

All the best,
Tom T

On Sat, Apr 24, 2021 at 11:59 AM James Holton <jmholton at lbl.gov> wrote:

> Thank you Tom!
>
> Ok.  So, in order to change the default I need to go through the code
> looking for "temp_dir" and change things?
>
>
> On 4/24/2021 10:16 AM, Tom Terwilliger wrote:
>
> Hi James,
>
> 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
> 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.
>
> All the best,
> Tom T
>
> On Sat, Apr 24, 2021 at 10:51 AM James Holton <jmholton at lbl.gov> wrote:
>
>> Thank you Li-Wei
>>
>> Definitely not placing blame on one program. Phenix.autobuild is another
>> big temp file producer.  So is XDS. Clearly this ligand run was a case
>> of a misconfigured, runaway task that never finished. However, the files
>> lingered on disk, eating up inodes for 3 years!
>>
>> The reason I'm asking is I think there are significant performance
>> increases to be gained by using fast, local storage for scratch files.
>> This is not just in speed but storage and overall system/cluster
>> performance.  Very few things are more expensive than an NFS write!
>>
>> Does anyone know how to change the default temp file location across
>> phenix ?  Is this a cctbx thing?
>>
>> Thanks
>>
>> -James
>>
>>
>> On 4/23/2021 9:38 PM, Li-Wei Hung wrote:
>> > Hi James,
>> >
>> > I'll leave the global Phenix temp aspect to Billy.
>> > For ligand identification specifically, the working directory is where
>> > all the files are located.  The program will purge most of the
>> > intermediate files upon completion. If the user interrupted the runs
>> > or if the program crashed at certain spots, the purge mechanism might
>> > not kick in. Even so, it'd take many runs to accumulate 20e6 (2e7?)
>> > files. In any case, you've got a point and I'll look into salvaging
>> > intermediate files of ligand identification as soon as they are not
>> > needed in the process.
>> >
>> > Thanks,
>> >
>> > Li-Wei
>> >
>> > On 4/23/2021 7:03 PM, James Holton wrote:
>> >> Hello all,
>> >>
>> >> Is there a way to configure phenix at install time (or perhaps
>> >> post-install) to put temporary files under /tmp ?  I just had to
>> >> delete 20e6 temp files over NFS from a single user's phenix ligand
>> >> identification run.  The delete took almost a month.
>> >>
>> >> Apologies if I am neglecting to look somewhere obvious in the
>> >> documentation,
>> >>
>> >> Happy Weekend!
>> >>
>> >> -James Holton
>> >> MAD Scientist
>> >>
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>>
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>
>
> --
> Thomas C Terwilliger
> Laboratory Fellow, Los Alamos National Laboratory
> Senior Scientist, New Mexico Consortium
> 100 Entrada Dr, Los Alamos, NM 87544
> Email: tterwilliger at newmexicoconsortium.org
> Tel: 505-431-0010
>
>
>

-- 
Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilliger at newmexicoconsortium.org
Tel: 505-431-0010
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