[Chimera-users] Memory requirements for Chimera

Tom Goddard goddard at cgl.ucsf.edu
Wed Feb 21 10:17:11 PST 2007

Hi Christopher,

  I think it starts making sense to use a 64-bit machine if you are 
loading data that requires >= 1 Gbyte.  In general, 32-bit linux 
binaries will run on a 64-bit machine.  Currently we only provide a 
32-bit linux Chimera distribution though we plan on adding 64-bit Linux 
as a standard Chimera platform in the next 6 months.  The 32-bit Chimera 
runs fine on 64-bit linux.  The advantage of a 64-bit version is that it 
uses memory pointers that are 64 bits so they can address more than 4 
Gbytes.   On a 32-bit system the operating system and the many libraries 
that Chimera uses (~50) may occupy a significant portion of the 4 Gbyte 
address space.  Even if you have less than 4 Gbytes of physical memory 
the operating system can and does use the full 32-bit 4 Gbyte address 
space and swap data to disk when there is not enough physical memory.  
But if a program asks for a 512 Mbyte block of memory and there is no 
available segment of that size in the address space then it will fail.

  Graphics drivers use the computer's main memory for data that will not 
fit on the card.  Either 256 or 512 Mbytes on the graphics card should 
give good performance even for large systems.  Unless you are using the 
volume "solid" rendering mode the rendering speed will slow to much less 
than 1 frame per second before you use up 256 Mbytes.

  For reference, the machines I currently use for developing Chimera and 
looking at large volume data sets are: 1) Mac dual G5 desktop with 1.5 
Gbyte memory and 128 Mb ATI Radeon 9800 Pro graphics, and 2) MacBook 
Pro, Intel Core 2 duo, 2 Gbyte memory, 256 Mb ATI X1600 graphics.

  Thanks for the apoptosome papers -- interesting work.


Christopher Akey wrote:
> Tom-
> ok, I will keep notes on what is not working and send them to you, as 
> we go through making figures this week.
> Will chimera run fine on a 64 bit Linux box? The other option is 32 
> bits, but if I buy a high end workstation it should probably be 64 bit 
> yes?
> Also, about making Chimera able to handle big sessions: is the rate 
> limiting factor the RAM or the memory on the Graphics Card. We have a 
> 512 Mb cache on our current graphics card and still have problems, so 
> I presume we are RAM limited.
> When buying a new machine, should I invest in a 512 Mb Nvidia card or 
> is 256 fine, as long as there is enough RAM?
> By the way, I am attaching two pdfs of papers published using Chimera 
> graphics.
> thanks.
> Tom Goddard wrote:
>> Hi Christopher,
>>  I'm not sure what causes crashes in Chimera when you are working 
>> close to the available memory limit.  If a memory allocation fails in 
>> C++ it should produce an error message in Chimera indicating that 
>> memory could not be allocated because we catch those exceptions.  
>> Memory allocations in C (not C++) libraries that Chimera uses are 
>> likely to cause a crash though.
>>  It would help us to know what Chimera is doing when the crashes 
>> occur.  We may be able to put some safety checks in our C++ where C 
>> library allocations are known to fail.  Do I understand correctly 
>> that crashes happen while you are saving an image (individual tiles 
>> being displayed on screen)?  Chimera by default makes an image 3 
>> times larger then requested to make a smoother image.  That can take 
>> a good bit of memory.  Are there other actions that cause crashes?
>>    Tom

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