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Bryan Lepore

30 Nov 2010 30 Nov '10

9:58 p.m.

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ] i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... oh, hmmm... i seem to have just got this at the packing function : |python: malloc.c:4591: _int_malloc: Assertion `(unsigned long)(size)

= (unsigned long)(nb)' failed.

-Bryan

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Nathaniel Echols

30 Nov 30 Nov

11:24 p.m.

On Tue, Nov 30, 2010 at 1:58 PM, Bryan Lepore wrote:

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ]

i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line....

Which program are you running, phenix.phaser or AutoMR? As far as I know AutoMR does not enable Phaser's parallelism, despite the presence of the nproc keyword - I think this is only there to be passed on to AutoBuild when running on the command line. -Nat

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Bryan Lepore

11:29 p.m.

On Tue, Nov 30, 2010 at 6:24 PM, Nathaniel Echols wrote:

On Tue, Nov 30, 2010 at 1:58 PM, Bryan Lepore wrote:

...
[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ]

i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... Which program are you running, phenix.phaser or AutoMR?

phenix.phaser - it is clearly "Spreading calculation onto 2 threads". just wondering. -Bryan

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Nathaniel Echols

1 Dec 1 Dec

7:29 p.m.

On Tue, Nov 30, 2010 at 3:29 PM, Bryan Lepore wrote:

On Tue, Nov 30, 2010 at 6:24 PM, Nathaniel Echols wrote:

...
On Tue, Nov 30, 2010 at 1:58 PM, Bryan Lepore wrote:

...
[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ]

i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... Which program are you running, phenix.phaser or AutoMR?

phenix.phaser - it is clearly "Spreading calculation onto 2 threads".

Phaser doesn't have an nproc keyword - so it is probably using some default setting. In CCP4 syntax, the directive you want is this: JOBS 4 You could also try setting the environment variable OMP_NUM_THREADS - but I'm not sure if that will have any effect on Phaser. -Nat

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Bryan Lepore
Nathaniel Echols