Hi Tom,
thank so much you for your answer. I uploaded the nigthtly build and it worked far better (a couple of hours) and ended correctly.
I noticed that the gain was due to the fact the only about 2400 boxes were calculated (in place of more than 40000 in my slow previous calculation, likely explaining the gain of a factor 20). As i have a very large map, i wonder how this affects the quality of the LocalResolutionMap. And i also wonder if there is a mean to define this parameter to study this effect.
Thank you so much for your help.
Best regards.
Philippe.
-----------------------------------------------
Philippe Cuniasse, PhD/HDR.
Institut de Biologie Integrative de la cellule.
UMR 9198 CNRS-CEA-Univ Paris Sud
Bat 144 CE-Saclay
91191 Gif-sur-Yvette Cedex
France
Tel: (33) 1 69 08 56 35
Fax: (33) 1 69 08 47 12
Email: [email protected]mailto:[email protected]
Web: http://biodev.cea.fr/rasmot3d/
-----------------------------------------------
________________________________
De : Tom Terwilliger
Envoyé : vendredi 27 octobre 2023 11:04:52
À : CUNIASSE Philippe
Cc : [email protected]; Tom Terwilliger
Objet : Re: [phenixbb] Pb LocalResolutionMap calculation
Hi Philippe,
I'm sorry for the slow calculation...the problem is the number of boxes is too high. If you download a nightly build like this one:
https://phenix-online.org/download/phenix/nightly/?version=1.21rc1-5130
then it should be a lot faster (still not quick, but in your case should be 20x faster).
All the best,
Tom T
On Fri, Oct 27, 2023 at 2:16 AM CUNIASSE Philippe mailto:[email protected]> wrote:
Dear all,
i try to calculate local resolution maps with phenix since a couple of days. It turns out that the calculation seems very slow and i suspect that there is a problem because i even cannot stop the calculation with the abort button in the gui. In my last run (still running), i use 2 half-maps and the program can read them correctly, start the calculation by returning that 42875 boxes are considered. I run it on my MacBook pro (M1 running OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs. However, with this calculation (and also a smaller map with about 17000 boxes on 1CPU), the calculations run more than 24 hours without finishing. I wonder if there coud be a problem and if no, what could be the duration of such calculation.
Thanks in advance for your help.
Best regards.
Philippe Cuniasse.
-----------------------------------------------
Philippe Cuniasse, PhD/HDR.
Institute for Integrative Biology of the Cell (I2BC)
UMR 9198 CNRS-CEA-Univ Paris Sud
Bat 144 CE-Saclay
91191 Gif-sur-Yvette Cedex, France
Tel: (33) 1 69 08 56 35
Fax: (33) 1 69 08 47 12
Email: [email protected]mailto:[email protected]
Web: http://biodev.cea.fr/rasmot3d/
Web: https://www.i2bc.paris-saclay.fr
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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
