[Chimera-users] split-map memory use
goddard at cgl.ucsf.edu
Fri Feb 8 10:45:51 PST 2008
I optimized the memory use of split map about 3 weeks ago. You can
try this improved version by downloading the current Chimera daily build:
Still it will need to allocate a full map for each color and that can
use a great deal of memory. If your map is 1 Gbyte and you have several
colors it will not work with a 32-bit version of Chimera. Although you
have 4 Gbytes of memory, some is used by the shared libraries, operating
system, stack, Chimera code, and data. You will be lucky to get 2
Gbytes of data in memory before you run out of address space (32-bit = 4
Gbytes). There simply will be no large enough chunk of the 32-bit
address space to put a copy of the map in. To use more than about 2
Gbyte of data in memory you have to use a 64-bit version of Chimera.
One is available for Linux.
Tom Goddard wrote:
> Hi Thomas,
> The error you got using the Chimera split map command "MemoryError"
> means your machine didn't have enough memory. The split map code is
> quite inefficient, allocating 3 * (number of grid points) floats and
> that allocation failed for you. I've optimized that code a little so
> for maps larger than 16 Mvoxels it works plane by plane avoiding that
> big allocation. You still may run out of memory because each color
> becomes a new full-size map in memory. If you have many colors that
> can be a lot of memory.
> The optimized code will be in tonight's Chimera builds (if they
More information about the Chimera-users