[phenixbb] temp files

James Holton jmholton at lbl.gov
Sat Apr 24 14:53:07 PDT 2021


What if people are using the GUI ?

On 4/24/2021 2:51 PM, Tom Terwilliger wrote:
> 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 
> <mailto: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
>>     <mailto: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
>>         >>
>>         >> _______________________________________________
>>         >> phenixbb mailing list
>>         >> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>         >> http://phenix-online.org/mailman/listinfo/phenixbb
>>         <http://phenix-online.org/mailman/listinfo/phenixbb>
>>         >> Unsubscribe: phenixbb-leave at phenix-online.org
>>         <mailto:phenixbb-leave at phenix-online.org>
>>         >
>>
>>         _______________________________________________
>>         phenixbb mailing list
>>         phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>         http://phenix-online.org/mailman/listinfo/phenixbb
>>         <http://phenix-online.org/mailman/listinfo/phenixbb>
>>         Unsubscribe: phenixbb-leave at phenix-online.org
>>         <mailto:phenixbb-leave at phenix-online.org>
>>
>>
>>
>>     -- 
>>     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
>>     <mailto: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 
> <mailto:tterwilliger at newmexicoconsortium.org>
> Tel: 505-431-0010
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210424/b48f3f7c/attachment.htm>


More information about the phenixbb mailing list