[Chimera-users] Mac 64-bit Chimera version

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 26 14:21:35 PST 2009

Hi Denis,

   Conrad Huang in our lab tried building a 64-bit Mac Chimera several 
months ago.  Many of the third-party packages we rely on failed to 
compile.  We decided to pursue this only after Mac OS 10.6 is released. 
  I believe the rationale of that was that Mac OS 10.5 is the oldest Mac 
OS that supports 64-bit graphical apps.  We still support Mac OS 10.4 
and our current automated build system targets 10.4.  When 10.6 comes 
out we may target our builds to 10.5.

   Currently we only provide 64-bit Chimera on Linux.


Denis Chrétien wrote:
> Dear Thomas,
> We were discussing some time ago about a 64 bit Mac version of Chimera. 
> Did you progress in this project ? (I'm still very limited for 
> visualization of large volumes with my mac, although its not a hardware 
> problem : 16 Gb Ram installed).
> Best regards,
> Denis
> Le 15 mai 08 à 18:41, Thomas Goddard a écrit :
>> Hi Denis,
>>  The Chimera error you reported means there was insufficient memory to 
>> compute the Fourier transform you wanted.  I see from the report that 
>> your Mac has 18 Gbytes (wow).  But our Mac Chimera version is a 32-bit 
>> program so its memory address space is only 4 Gbytes.  In that 4 
>> Gbytes has to fit not only data, but all shared libraries, program 
>> stack and (I think) operating system code.  So really you might have 
>> just 3 Gbytes to work with.  Also my Fourier transform code does a 
>> full complex value FT where it could do a real value FT taking half 
>> the memory.  And the Python library that actually does the FT can only 
>> use double precision, so 16 bytes per complex value.  More memory is 
>> used when Chimera takes just the magnitude of the FT coefficients.  In 
>> short it is using 20 bytes per grid point.  So a 512^3 FT will use 2.5 
>> Gb, about the maximum that will fit in the 32-bit address space 
>> (assuming it isn't already fragmented by other data/libraries since 
>> you need a 2.5 Gb free block).
>>  We plan on fixing this.  We plan on distributing a 64-bit Mac 
>> Chimera, and have tried compiling it.  But some of the ~30 third-party 
>> libraries Chimera depends on did not compile.  So we still need to 
>> work on that -- maybe within 3 months. Also I plan on making the FT 
>> code not such a hog, do a real FT and investigate 32-bit float FT 
>> values for a factor of 4 memory savings.  For now your only option 
>> would be to use one of our 64-bit Chimera versions on Linux or Tru64 
>> operating systems.
>> Tom
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