Re: [PyMOL] pymol crashes with large pdb files

[<an...@bi...>]

Limited physical memory might indeed be the problem.
When I ray-trace under WinXP, memory usage increases sharply (to about
500MB) and after a second or so, pymol crashes.
When I ray-trace under linux, almost all physical memory (1GB) is being
used. Barely 40MB available.

We should be getting new computers next week. We'll see if 2GB will do the
trick for Windows.


Andreas


>> Now there is a twist to the story. We also run linux (redhat with 2.4.18
>> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working
>> speed is much slower but no crashes when ray-tracing from the exact same
>> pml script.
>> Can it be that linux makes better use of its physical memory or that the
>> 2GB of swap make the difference?
>
> When you ray-trace an image, PyMOL will tell you exactly how much memory
> it's using.  My suspicion is that this is painfully close to the physical
> memory limit.  From what I understand, swap space does not give you more
> memory but Linux will transfer idle programs to swap, freeing up more
> RAM for PyMOL.  I have no idea how Windows works (other than "badly").
>
> 'top' in Linux or the Task Manager in WinXP should tell you how much
> physical memory is being used at any time.
>
> ----------------------------------------------------------------------------
> Nathaniel Echols
> Programmer
> na...@bi...                                        Gerstein
> Lab
> 203-589-6765                                                 Yale
> University
> ----------------------------------------------------------------------------