From: Jessica MJ Swanson <jswanson@mc...>  20060126 20:49:28

Hi all, Just wondering if the updated version of psize.py could use a fix. The previous version gave the mesh spacing for the single (nonparallel execution) grid, but the new version only gives spacings for the grids parced out in a parallel run (see example below). Both would be ideal. Can we either change it back or add the single to the parallel? Thanks, Jessica version 0.4.0 $APBSTOOLS/psize.py SPACE=0.10 cramhelix1abt.pqr ############## GENERAL CALCULATION INFO ############# Coarse grid dims = 33.109 x 16.199 x 15.609 A Fine grid dims = 33.109 x 16.199 x 15.609 A Num. fine grid pts. = 321 x 161 x 129 Parallel solve required (1271.601 MB > 400.000 MB) Total processors required = 4 Proc. grid = 2 x 2 x 1 Grid pts. on each proc. = 97 x 129 x 129 Fine mesh spacing = 0.205647 x 0.0760531 x 0.121948 A Estimated mem. required for parallel solve = 307.880 MB/proc. Number of focusing operations = 2 version 0.3.2 $APBSTOOLS/psize.py SPACE=0.10 cramhelix1abt.pqr ################# CALCULATION INFO #################### Coarse grid dims = 33.109 x 16.199 x 15.609 A Fine grid dims = 33.109 x 16.199 x 15.609 A Num. fine grid pts. = 321 x 161 x 129 Fine mesh spacing = 0.103466 x 0.101246 x 0.121948 A Estimated mem. required for sequential solve = 1017.280 MB Parallel solve required (1017.280 MB > 400.000 MB) Proc. grid = 2 x 2 x 1 Grid pts. on each proc. = 129 x 129 x 129 Estimated mem. required for parallel solve = 327.559 MB/proc. Number of focusing operations = 2 
From: Todd Dolinsky <todd@cc...>  20060126 22:30:33
Attachments:
Message as HTML

Hi Jessica  The change was originally part of a bug fix. In the past we had more than = a handful of users try to use finelyspaced sequential grids on machines that lacked the available memory, so we switched to only displaying grids that would fit on a standard machine (with a default memory ceiling of 400 MB). With that in mind, you should be able to generate sequentialgrid spacings by increasing the memory ceiling with the GMEMCEIL flag  since it looks like the suggested memory ceiling for your PQR file was ~ 1300 MB, passing in the GMEMCEIL flag like python psize.py SPACE=3D0.10 GMEMCEIL=3D2000 cramhelix1abt.pqr should allow you to make a sequential grid. Similarly, if you use inputgen.py and use the METHOD=3Dauto flag it will ensure that the example input file is sequential and not parallel. See the inputgen help (python intputgen.py help) for more info. I think that answers your question  if not, please let me know. Todd On 1/26/06, Jessica MJ Swanson <jswanson@...> wrote: > > Hi all, > > Just wondering if the updated version of psize.py could use a fix. The > previous version gave the mesh spacing for the single (nonparallel > execution) grid, but the new version only gives spacings for the grids > parced out in a parallel run (see example below). Both would be ideal. > Can we either change it back or add the single to the parallel? > > Thanks, > Jessica > > > version 0.4.0 > $APBSTOOLS/psize.py SPACE=3D0.10 cramhelix1abt.pqr > > ############## GENERAL CALCULATION INFO ############# > Coarse grid dims =3D 33.109 x 16.199 x 15.609 A > Fine grid dims =3D 33.109 x 16.199 x 15.609 A > Num. fine grid pts. =3D 321 x 161 x 129 > Parallel solve required (1271.601 MB > 400.000 MB) > Total processors required =3D 4 > Proc. grid =3D 2 x 2 x 1 > Grid pts. on each proc. =3D 97 x 129 x 129 > Fine mesh spacing =3D 0.205647 x 0.0760531 x 0.121948 A > Estimated mem. required for parallel solve =3D 307.880 MB/proc. > Number of focusing operations =3D 2 > > version 0.3.2 > $APBSTOOLS/psize.py SPACE=3D0.10 cramhelix1abt.pqr > > ################# CALCULATION INFO #################### > Coarse grid dims =3D 33.109 x 16.199 x 15.609 A > Fine grid dims =3D 33.109 x 16.199 x 15.609 A > Num. fine grid pts. =3D 321 x 161 x 129 > Fine mesh spacing =3D 0.103466 x 0.101246 x 0.121948 A > Estimated mem. required for sequential solve =3D 1017.280 MB > Parallel solve required (1017.280 MB > 400.000 MB) > Proc. grid =3D 2 x 2 x 1 > Grid pts. on each proc. =3D 129 x 129 x 129 > Estimated mem. required for parallel solve =3D 327.559 MB/proc. > Number of focusing operations =3D 2 > > > >  > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.asus.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > _______________________________________________ > apbsusers mailing list > apbsusers@... > https://lists.sourceforge.net/lists/listinfo/apbsusers > 
From: David Zhang <zhang.q@gm...>  20060127 02:21:16
Attachments:
Message as HTML

Hi Jess, If it's always what you want, you can add an alias to your .cshrc file to make it default: alias psize "$APBSTOOLS/psize.py GMEMCEIL=3D2000" David On 1/26/06, Todd Dolinsky <todd@...> wrote: > > Hi Jessica  > > The change was originally part of a bug fix. In the past we had more tha= n > a handful of users try to use finelyspaced sequential grids on machines > that lacked the available memory, so we switched to only displaying grids > that would fit on a standard machine (with a default memory ceiling of 40= 0 > MB). > > With that in mind, you should be able to generate sequentialgrid spacing= s > by increasing the memory ceiling with the GMEMCEIL flag  since it look= s > like the suggested memory ceiling for your PQR file was ~ 1300 MB, passin= g > in the GMEMCEIL flag like > > python psize.py SPACE=3D0.10 GMEMCEIL=3D2000 cramhelix1abt.pqr > > should allow you to make a sequential grid. > > Similarly, if you use inputgen.py and use the METHOD=3Dauto flag it wil= l > ensure that the example input file is sequential and not parallel. See t= he > inputgen help (python intputgen.py help) for more info. > > I think that answers your question  if not, please let me know. > > Todd > > On 1/26/06, Jessica MJ Swanson < jswanson@...> wrote: > > > > Hi all, > > > > Just wondering if the updated version of psize.py could use a fix. The > > previous version gave the mesh spacing for the single (nonparallel > > execution) grid, but the new version only gives spacings for the grids > > parced out in a parallel run (see example below). Both would be ideal. > > Can we either change it back or add the single to the parallel? > > > > Thanks, > > Jessica > > > > > > version 0.4.0 > > $APBSTOOLS/psize.py SPACE=3D 0.10 cramhelix1abt.pqr > > > > ############## GENERAL CALCULATION INFO ############# > > Coarse grid dims =3D 33.109 x 16.199 x 15.609 A > > Fine grid dims =3D 33.109 x 16.199 x 15.609 A > > Num. fine grid pts. =3D 321 x 161 x 129 > > Parallel solve required (1271.601 MB > 400.000 MB) > > Total processors required =3D 4 > > Proc. grid =3D 2 x 2 x 1 > > Grid pts. on each proc. =3D 97 x 129 x 129 > > Fine mesh spacing =3D 0.205647 x 0.0760531 x 0.121948 A > > Estimated mem. required for parallel solve =3D 307.880 MB/proc. > > Number of focusing operations =3D 2 > > > > version 0.3.2 > > $APBSTOOLS/psize.py SPACE=3D0.10 cramhelix1abt.pqr > > > > ################# CALCULATION INFO #################### > > Coarse grid dims =3D 33.109 x 16.199 x 15.609 A > > Fine grid dims =3D 33.109 x 16.199 x 15.609 A > > Num. fine grid pts. =3D 321 x 161 x 129 > > Fine mesh spacing =3D 0.103466 x 0.101246 x 0.121948 A > > Estimated mem. required for sequential solve =3D 1017.280 MB > > Parallel solve required (1017.280 MB > 400.000 MB) > > Proc. grid =3D 2 x 2 x 1 > > Grid pts. on each proc. =3D 129 x 129 x 129 > > Estimated mem. required for parallel solve =3D 327.559 MB/proc. > > Number of focusing operations =3D 2 > > > > > > > >  > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > > files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > > http://sel.asus.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat= =3D121642 > > > > _______________________________________________ > > apbsusers mailing list > > apbsusers@... > > https://lists.sourceforge.net/lists/listinfo/apbsusers > > > > 