[phenixbb] v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)

Nathaniel Echols nechols at lbl.gov
Tue Jul 10 15:22:24 PDT 2012

On Tue, Jul 10, 2012 at 2:46 PM, Phil Jeffrey <pjeffrey at princeton.edu> wrote:
> This is in F432 in a=b=c=340A at 2.85A resolution.  Mac OSX 10.5.8, the
> machine has 8Gb memory of which something like 6Gb is hanging around begging
> to be used.
> 1,327,104,000 if that's in bytes doesn't seem all that excessive.
> On the other hand, 340*340*340= 39,419,600 so it's perhaps a little greedy.

Forgot to address this - in fact the formula for map size in bytes is
something vaguely like this (I am totally guessing here):

map_size = 8 * a * b * c / (d_min/resolution_factor)^3

resolution_factor is 0.25 in this context.  The multiplier of 8 is
because we're using double-precision floating point numbers, which are
64 bits each.  This comes out to 868,250,664 bytes for your structure,
but I'm probably missing some essential details, and I think the grid
size will be adjusted to behave well in the FFT.

It's hard to guess exactly why this crashes in your case; it doesn't
seem like something that should run out of memory, but this particular
routine may be a bit of a bottleneck.


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