I'm running it on a CIFS-mounted disk. Phenix and the data are located on the same disk, though.<div><br></div><div>I'll give a newer build a try. Thanks. :)</div><div><br></div><div>Eric<br><br><div class="gmail_quote">
On Mon, Sep 10, 2012 at 3:20 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5">On Mon, Sep 10, 2012 at 7:38 AM, Eric Williams <<a href="mailto:ericwilliams@pobox.com">ericwilliams@pobox.com</a>> wrote:<br>
> I'm currently running cif_as_mtz and model_vs_data on the whole PDB as part<br>
> of my dissertation. Time has become a critical concern, and cif_as_mtz<br>
> (dev-1141) is running very, very slowly (1-4 minutes per entry).<br>
><br>
> Here's how I'm calling it:<br>
><br>
> phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge<br>
> --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn><br>
> --output-file-name=<sf_mtz_fn><br>
><br>
> I'm hoping that perhaps someone could help me determine which command line<br>
> argument(s) could be removed to provide maximum speed-up.<br>
<br>
</div></div>Are you running this on NFS-mounted disks by any chance?<br>
<br>
None of these should be especially time-consuming - the only big<br>
bottleneck in the program is "--use-model". �I just tried running the<br>
command above on a reasonably large structure (1zy8) and it was very<br>
quick (< 15s). �On the off chance that something big changed in the<br>
last couple of weeks, can you update to the latest nightly build and<br>
see if it's still running slowly? �If so, send us some IDs that take a<br>
particularly long time and we'll see if we can reproduce the problem.<br>
<br>
thanks,<br>
Nat<br>
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