[chimerax-users] ChimeraX slower than Chimera at loading maps?

[Tom Goddard]

Hi Brian,

  The map histogram computation will only take a fraction of a second even for large maps.  What is slow is probably what it is doing after that histogram computation, and the status message just stays there because no other message replaces it and the status messages don't automatically disappear until some time delay (30 seconds?).

  When you run ChimeraX on this CentOS 7 system are you remote displaying the graphics to another computer?  That also could be slow.

  We have CentOS 7 servers with a network file system (Beegfs) and ChimeraX can take a phenomenally long time, maybe 60 seconds, to start even in nogui mode, because the file system is horrendously bad at accessing thousands of Python files that are the code of ChimeraX.  Part of that is it is making a network request for each small file, and also our server disks are spinning drives, so accessing all those tiny files at different places on the drive takes time for the disk to spin to the right position.  Most ChimeraX users are on a Mac, Windows, or Linux machine with an SSD drive, which will start 100 times faster.  The speed of disk drives has become a really huge factor in the overall performance of computer systems with modern SSD and NVMe solid state drives being one or two orders of magnitude faster.  Even when accessing a single large file a modern PCIe solid state drive can deliver 30 times the speed of the typical spinning drive (3 GBytes/sec versus 0.1 GBytes/second).

  We like to make ChimeraX as usable as possible for the RCSB so I'd be happy to discuss it further with you.  If you use ChimeraX menu entry Help / Report a Bug... that would be a good way to pursue that discussion.  Ultimately the best solution is to run ChimeraX off a local SSD drive, but I realize that may not be possible (we don't have that on our UCSF servers, but we don't use ChimeraX on those servers).

	Tom



> On Sep 6, 2022, at 10:45 AM, Brian Hudson <hudson at rcsb.rutgers.edu> wrote:
> 
> Hi Tom,
> 
> Thank you for your response.  Since we are on a network file system, it's possible that ChimeraX may not be the best application for the quick visualization that we're looking for.
> 
> One thing that I have since noticed, however, is that step of the map loading process that appears to be taking significantly longer for ChimeraX than Chimera is the "computing histogram" step.
> 
> Thanks,
> 
> Brian
> 
> BRIAN HUDSON, Ph.D.
> Biocurator, RCSB Protein Data Bank
> Assistant Research Professor, Institute for Quantitative Biomedicine
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road, Piscataway NJ 08854
> P: 848.445.4941 | E: brian.hudson at rcsb.org
> 
> On 9/2/2022 5:04 PM, Tom Goddard wrote:
>> Hi Brian,
>>   ChimeraX should be the same speed as Chimera for opening maps.  Opening a 4 GB ccp4 map took 1 second including ChimeraX 1.4 startup time on my Mac.  ChimeraX (and Chimera) only display and read a part of a large map (either single plane or subsampled grid) initially so almost any size map should open quickly.  So I guess the script you are timing actually does other things.  There is no way to advise you without knowing what you are actually timing.  It is also possibly you are on an incredibly slow networked file system.  ChimeraX loads maybe 1000 Python files at startup and on a file system that struggles loading many small files it could take a long time. But I expect Chimera is almost as bad as ChimeraX -- Python based software often loads hundreds of small Python code files.
>> 	Tom
>>> On Sep 2, 2022, at 1:25 PM, Brian Hudson via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> I have a question about map-loading performance in ChimeraX.
>>> 
>>> We use Chimera for the visualization of EM maps, and have recently loaded ChimeraX 1.3 on our Centos 7 workstations.
>>> 
>>> We frequently run a script that opens Chimera (or ChimeraX) and loads one or more maps.  Running the script for the same 2 Gb CCP4-format map in three different programs, I get the following times for program startup + map loading, i.e., the time from when I run the script at the command line to when the map appears onscreen:
>>> 
>>> Chimera 1.12	13 seconds
>>> ChimeraX 0.1	25 seconds
>>> ChimeraX 1.3	66 seconds
>>> 
>>> This isn't exactly the direction I had hoped performance would trend, and was wondering if there was anything that could be done within ChimeraX 1.3 to speed the process along a little.
>>> 
>>> Thanks,
>>> 
>>> Brian
>>> 
>>> -- 
>>> BRIAN HUDSON, Ph.D.
>>> Biocurator, RCSB Protein Data Bank
>>> Assistant Research Professor, Institute for Quantitative Biomedicine
>>> Rutgers, The State University of New Jersey
>>> 174 Frelinghuysen Road, Piscataway NJ 08854
>>> P: 848.445.4941 | E: brian.hudson at rcsb.org
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>