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@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@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@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave@phenix-online.org
>

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@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@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@newmexicoconsortium.org

Tel: 505-431-0010

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org