[phenixbb] temp files
jmholton at lbl.gov
Sat Apr 24 09:50:31 PDT 2021
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?
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.
> 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
>> Happy Weekend!
>> -James Holton
>> MAD Scientist
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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