thanks, Tim. It's good to have a "power Mac" user on the team. Take your
time. My finding both in Linux and Windows now is that the applet starts
at about 40Mb required memory allocation and then goes from there. One
large protein (1p84, 32000+ atoms) can push it to 64Mb instantly. The
colleague who debugged this with me on Linux had his limit set at 50 Mb
and, sure enough, as soon as the allocated memory got to 50.001 Mb the
browser was history.
The same enzyme brought Opera to 58Mb on my PC and, interestingly, when
Opera had the focus, Firefox went back down to 43Mb. MSIE meanwhile went
to 62Mb and stayed there.
http://fusion.stolaf.edu/bh/confchem/jmol/demo.htm (Jmol 10.2)
browser opened/Mb +page/Mb +1p84.pdb/Mb
MSIE6.0... 19 44 63
Firefox1.5.0.3 18 43 64-->43
Opera8.51 14 35 57
http://fusion.stolaf.edu/bh/confchem/jmol/demo.htm?demo=12 (Jmol 10.x)
browser opened/Mb +page/Mb +1p84.pdb/Mb
MSIE6.0... 19 43 62
Firefox1.5.0.3 18 42 65-->47
Opera8.51 14 37 57
So I would have to say that Opera is doing something right here, and
Firefox has some way of reducing its memory footprint that the other
browsers don't have. [Later: Opera and MSIE both slowly dropped down
about 10 Mb as well.]
Ah, now the behavior at http://fusion.stolaf.edu/chemistry/jmol/xtalx
(jmol 10.x) is quite different. In that case, loading up maleic.cif,
which has 18 crystals, and displaying the {1 1 1} unit cell produces an
interesting effect. Firefox is cycling on about a 20-second cycle
between 58 and 88 Mb memory usage, picking up about 2 Mb per second
until it gets to 88, then dropping again suddenly to 58 Mb. MSIE is just
sitting at 63 Mb; Opera is just sitting at 56 Mb. I wonder what in the
world is going on with Firefox? Note that this is whith repeating
setTimeout loop of 10 ms. When I change that to 100 ms, the cycling is
still there, just quite sow and not hardly to the same extent.
Wow, here's something interesting: I do a getProperty auxiliaryInfo,
which gives me the information shown below for each of those 18 models,
and Firefox just shot up to 107 Mb and continues to climb to 115 Mb --
cycling now down to 50 Mb and climbing rapidly again. What could that
be about?
auxiliaryinfo=new Array()
auxiliaryinfo.modelSetAuxiliaryInfo=new Array()
auxiliaryinfo.modelSetAuxiliaryInfo.someModelsHaveFractionalCoordinates=true
auxiliaryinfo.modelSetAuxiliaryInfo.someModelsHaveSymmetry=true
auxiliaryinfo.modelSetAuxiliaryInfo.someModelsHaveUnitcells=true
auxiliaryinfo.models=new Array()
auxiliaryinfo.models[0]=new Array()
auxiliaryinfo.models[0].num=1
auxiliaryinfo.models[0].modelAuxiliaryInfo=new Array()
auxiliaryinfo.models[0].modelAuxiliaryInfo.spaceGroup="P c"
auxiliaryinfo.models[0].modelAuxiliaryInfo.symmetryCount=1
auxiliaryinfo.models[0].modelAuxiliaryInfo.presymmetryAtomIndex=0
auxiliaryinfo.models[0].modelAuxiliaryInfo.presymmetryAtomCount=24
auxiliaryinfo.models[0].modelAuxiliaryInfo.coordinatesAreFractional=true
auxiliaryinfo.models[0].modelAuxiliaryInfo.symmetryOperations=new Array()
auxiliaryinfo.models[0].modelAuxiliaryInfo.symmetryOperations[0]="x,y,z"
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell=new Array()
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[0]=3.8051
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[1]=7.4961004
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[2]=8.3524
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[3]=90
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[4]=98.84901
auxiliaryinfo.models[0].modelAuxiliaryInfo.notionalUnitcell[5]=90
auxiliaryinfo.models[0].modelAuxiliaryInfo.latticeDesignation="0: (0)"
auxiliaryinfo.models[0]._ipt=0
auxiliaryinfo.models[1]=new Array()
Miguel, I'd be interested in knowing, if you can't even get past loading
the applet, what your maximum memory allocation is set at, or at least
what your process report says for the amount of memory used by Mozilla
right after the crash.
Timothy Driscoll wrote:
On May 10, 2006, at 6:15 p, Bob Hanson wrote:
Well, that must be it. Sitting here at my PC I see the Opera memory
usage zoom to 76Mb as I build 27 crystals in the maleic.cif
collection up to 3x3x2, and Netscape is at 126Mb from similar use.
I'm certain these would have crashed that Linux browser long ago,
and my guess is that's the issue with the Macs as well.
I am in unfamiliar territory here, and trying to finish up the
semester so I'm pressed for time as well. but...
OS X has a utility called Java Preferences which allows you to fiddle
with cache and memory, at least at some level. mine is set to use
Unlimited Disk Space for the Java cache, but of course, that can not
be true - because I consistently see Java heap errors after opening
many Jmol applets consecutively.
I will be happy to help test these issues and research among the
Apple developer material - just not at this very minute. :-( next
week will be *so* much better for me.
tim
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