[chimerax-users] Memory problems with Orbital Viewer

[Michael Patzschke]

Hello Tony,

Thank you very much. This fixed the problem.

Kind regards,
Michael

P.S. Thank you for mentioning the race condition. I sm aware of the problem and use 5.0.3 for production runs. This is an older serial calculation.

> On 24. Jan 2023, at 09:09, Tony Schaefer <tony.schaefer.chem at gmail.com> wrote:
> 
> Michael,
> 
> I've released an updated version of SEQCROW to the toolshed (Tools -> More Tools... on the menu). This just has a different method for determining available memory, which will hopefully fix this. If memory is still an issue, I can try to change how the orbitals are calculated to reduce memory usage. 
> 
> As a side note, ORCA 5.0.1 has a race condition bug, so it might give you bogus energies if you run it in parallel. There's more details on the ORCA forum, but the developers recommend updating to a newer version. 
> 
> Best,
> 
> Tony
> 
> On Tue, Jan 24, 2023 at 12:50 AM Michael Patzschke <m.patzschke at hzdr.de <mailto:m.patzschke at hzdr.de>> wrote:
> Hello Tony,
> 
> Thank you very much for your quick reply.Can I first say, that the orbital viewer is a very useful tool and that I appreciate your work and effort. Now to your questions. The message is copy and pated from the screen. It does indeed say 0.0GB. The orca version used for the calculation is 5.0.1, the settings are the standard settings in orbital viewer. Padding 3.0 Å, resolution 0.1 and IsoSurfaces 0.01.
> 
> I just started ChimeraX (version 1.5) again and tried the same visualisation, now the message says "Estimated peak memory usage (0.1GB)” The molecule is acetonitrile.
> 
> Kind regards,
> Michael
> 
> 
> 
>> On 24. Jan 2023, at 08:39, Tony Schaefer <tony.schaefer.chem at gmail.com <mailto:tony.schaefer.chem at gmail.com>> wrote:
>> 
>> Michael,
>> 
>> I develop the Orbital Viewer tool. Does it really say 0.0GB for both estimated peak memory usage and available memory? I've looked into it a bit, and it looks like the way I'm determining available memory is not the best. I'll release a patch for that soon. You might also have other applications open that are taking up memory.
>> 
>> I do not expect the estimated memory usage to be 0 GB. That's calculated directly from the grid size, number of threads, and number of atoms. If this does say 0.0 GB, I'd be interested in your orbital settings, basis set, and ORCA version. 
>> 
>> As the message suggests, you can decrease the memory required by adjusting the resolution, padding, or number of threads on the 'orbital settings' tab of the Orbital Viewer tool. If you are able to load an orbital (with the resolution set to 0.75 A to be quick/safe), you can see how much extra padding you have by running the command `volume showOutlineBox true`. This will show the total volume where the orbital values were calculated, even though only the isosurface is shown. A smaller box (i.e. less padding) will require less memory at a given resolution. 
>> 
>> The warning is there because exceeding the available memory could crash ChimeraX or force you to restart your computer. It's not meant to be a nuisance, so I'd like to make sure it's working properly. 
>> 
>> Best,
>> 
>> Tony
>> 
>> On Mon, Jan 23, 2023 at 11:25 PM Michael Patzschke via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> Dear colleagues,
>> 
>> I am using ChimeraX mostly for small molecular complexes, typically up to 100 atoms. I am running the code on a MacBook Pro with 16 GB of memory under macOS 11.8.8. When I try to render molecular orbitals from an orca calculation I get even for very small molecules the warning message:
>> 
>> Estimated peak memory usage (0.0GB) is above or close to
>> the available memory (0.0GB).
>> Exceeding available memory might affect the stability of your
>> computer. You may attempt to continue, but it is recommended
>> that you lower your resolution, decrease padding, or use
>> fewer threads.
>> 
>> Press "Ok" to continue or "Abort" to cancel
>> 
>> Is there any way to fix this problem?
>> 
>> Kind regards,
>> Michael Patzschke
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