Re: [phenixbb] temp files

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 mailto:[email protected]> 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 >> [email protected] mailto:[email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: [email protected] mailto:[email protected] >

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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: [email protected] mailto:[email protected] Tel: 505-431-0010