[phenixbb] temp files

James Holton 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.
> 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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