Random crashes

[justin.ditrani@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-03-08)
Description
ChimeraX randomly crashes durign use. Even more so when doing simulations on ISOLDE. Is there hardware/drivers that are not compatible with ChimeraX? Thanks. 

Log:
UCSF ChimeraX version: 0.92 (2020-03-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 445.75
OpenGL renderer: GeForce RTX 2070 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

Is there anything you can think of that you were doing that might be correlated to the crashes? I do know of one (extremely) intermittent crash that can happen when first preparing a model for ISOLDE, but so far I've been unable to track down the cause (every time I do anything to try to catch and analyse it, the crash never happens). But that doesn't sound like what you're experiencing here.

[Tom Goddard]

I do not encounter crashes using Windows ChimeraX. There are three possibilities 1) your graphics driver is unstable, 2) your data (atomic model) is unusual in some way hitting a bug in ChimeraX, 3) you are using some unusual ChimeraX capability that is buggy. I put those in order of likelihood. Getting a newer or older graphics driver is the solution for 1. For 2 or 3 we need more clues.

[Tom Goddard]

If you have CUDA installed for ISOLDE to do MD on your Nvidia GPU then bugs in that driver could also be the cause.

[justin.ditrani@…]

Hello,

Thanks for the quick reply. The crashes are occurring during the ISOLDE
cryoEM tutorial. The crashes seemed random but now are always happening
when I open the ramachandran plot for the model. Do I need CUDA in order to
run these features; I don't think I have that. I will try different drivers
for now.

Thanks,
Justin Di Trani

On Sat, Mar 28, 2020 at 1:13 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[goddard@…]

CUDA is not needed.  It makes the MD run faster.

[justin.ditrani@…]

Hello,

Thanks again for your help. I have tried different drivers and none of them
seem to work. Is there a specific driver for my video card that has been
shown to work well. If this
isn't the problem what other things can I try?

On Sat, Mar 28, 2020 at 8:47 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Could you follow the instructions at https://helgeklein.com/blog/2018/10/creating-an-application-crash-dump/ to get a crash dump file next time it crashes, and send that?
 

 

[justin.ditrani@…]

  Hello,

Here is the crashdump report from the crash I reproduced by opening the
ramachandran plot in ChimeraX.

Thank you
 ChimeraX.exe.14504.dmp
<https://drive.google.com/file/d/1gcfWGuecShV6mWqtOVLCnnhCVRdiODQn/view?usp=drive_web>

On Sun, Mar 29, 2020 at 1:11 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Something a bit weird here. Your bug report lists the ChimeraX version 
as 0.92, but the crash dump lists the ChimeraX.exe module version as 
0.91.0.0. Eric? Tom? Any thoughts on how that could occur?

On 2020-03-29 18:33, ChimeraX wrote:

[justin.ditrani@…]

According to the ISOLDE install page in the more tools section of ChimeraX
ISOLDE is only compatible with chimeraX 0.91 so I tried 0.91 when I was
trying to get it working. It seems the same as 0.92. Should I switch back
to 0.91?

Thanks,
JDT

On Sun, Mar 29, 2020 at 1:59 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

The actual crash is happening in Qt5WebEngineCore, so it's highly 
unlikely to be your graphics driver causing it. I'll have to leave it to 
the ChimeraX team to help you further, I think - this looks like an 
environment/installation problem rather than something specific to 
ISOLDE, and I'm afraid I'm not well enough versed in the mechanics of 
Windows builds to dig much further.

On 2020-03-29 18:58, ChimeraX wrote:

[justin.ditrani@…]

Great. Thanks so much for your help.

On Sun, Mar 29, 2020 at 2:08 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Where did you get the idea that ISOLDE is only compatible with ChimeraX 0.91? "According to the ISOLDE install page in the more tools section of ChimeraX ISOLDE is only compatible with chimeraX 0.91" I don't see anything that says that on the web pages. The current ISOLDE is for ChimeraX 0.92 and that is the best to use.

Tristan, thanks for looking into this. If you have a stack trace from the ChimeraX.exe.14504.dmp file could you attach it to this ticket?

QtWebEngineCore is part of the Qt window toolkit ChimeraX uses. We do not develop it (and it is millions of lines of code). We have seen many (20?) ChimeraX crash reports on macOS in QtWebEngineCore. It could be some feature ChimeraX is using in Qt that is unstable, or maybe is being used wrong. But we have no case we can reproduce so we have not been able to track it down.

Could you give more details. Does the crash happen every time you try to use ISOLDE? How long does it take using ISOLDE before it crashes (1 minute? 5 minutes?)? Is it always after you started a simulation? When is the earliest it crashes -- what is the fewest steps you had to do, what were those steps? Without more clues we won't be able to help.

[Tom Goddard]

Do you have any other Windows machine you can test on? Does it crash o that machine? This would help clarify if it is your specific Windows machine (if only one machine crashes), or maybe it is some specific sequence of steps you do in ChimeraX (would happen on both machines).

[Tristan Croll]

It *was* actually still saying that on the webpage (I edited it 
yesterday). Along the lines of "use ChimeraX 0.91 to get the ISOLDE 
release, or 0.92 to get the dev builds"). I've changed it to just say to 
use 0.92.

I'm afraid I wasn't able to get much more out of the dump file than that 
(perhaps because I lack experience dealing with them in Windows). Is the 
file still available at the link Justin provided?

On 2020-03-30 18:12, ChimeraX wrote:

[goddard@…]

I can try looking at the *.dmp file when I am next on Windows (probably later today).

[justin.ditrani@…]

Hello all,

The crash happened when I try to open the ramachandran plot.

On this same computer (my desktop) I have my hard drive partitioned with
ubuntu installed on one of the partitions. Even on ubuntu it doesn't seem
to want to work. In this case the
simulation just doesn't seem to run. It starts then doesn't move for hours.
Is this easier to troubleshoot?

I also tried running it on my laptop (windows 10) and it works well.
Perhaps there is something wrong with the graphics card on my desktop? It
seems like a machine specific problem so
it might not be worth your time to try to fix. Unless there is obvious
things I can troubleshoot on ubuntu I don't want to take up more of your
time.

Thanks again for all of your help. Love the program and look forward to
getting into it more.

Best,
Justin Di Trani



On Mon, Mar 30, 2020 at 1:38 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

Which version of ChimeraX are you using for the Ubuntu machine? ISOLDE
is currently only properly compatible with the CentOS 7 and "Generic
Linux" version of ChimeraX. It *might* sort-of work with the Ubuntu
16.04 build, but you should use the generic Linux build to make sure. 

Is it crashing for *any* model, or just yours? I.e. if you do "open 3io0
structureFactors true" and open the Ramachandran plot, does it still
crash? If it's specific to a model, could you send me that model so I
can troubleshoot?

On 2020-03-30 18:55, Justin Di Trani wrote:

[goddard@…]

Thanks for the additional info!  Since it crashes on your desktop but not your laptop, I suspect the desktop graphics driver is a factor.  But it could just be that the desktop graphics is much faster and that makes some timing race condition happen which leads to the crash.  But I believe many ISOLDE users have used it on fast graphics (like your Nvidia RTX 2070), so simply running faster is probably not the cause.  So I will stick with the theory that the graphics driver has some issue.

Running ISOLDE on Ubuntu is a totally different issue.  There it is not crashing, the simulation just seems hung or extremely slow.  Tristan can advise on that.  ISOLDE certainly can work well on Linux, since Tristan (the developer of ISOLDE) mostly uses Linux.  Maybe you don't have a graphics driver or CUDA on Linux and it is simply very very slow.

[justin.ditrani@…]

Hello,

I am just going trough the tutorial right now so I am using the map and
model from the tutorial. ie using the command -
cxcmd:isolde%20demo%20cryo_em%20modelOnly%20true%20startIsolde%20false.
When I open the ramachandran plot for this model it crashes. I will stick
with ubuntu since it s

On ubuntu I am using the Generic Linux 64-bit however I am using Ubuntu
18.04.3. Right now I am using the NVIDIA driver metapackage (see picture
below). Is this good? I will install CUDA and see if it stops hanging.

Best,
JDT

[image: image.png]


On Mon, Mar 30, 2020 at 2:14 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[justin.ditrani@…]

Added by email2trac

[Tristan Croll]

That's really strange! I know of another user running it on a laptop 
with a GTX 2060 with good performance and stability, so it does seem to 
be something specific to your system. As a quick double-check, could you 
set the "Experience level" menu (drop-down at bottom right of the ISOLDE 
panel) to "advanced" and tell me what options become available in the 
"Computational Platform" drop-down that appears on the Sim settings tab?

On 2020-03-30 19:20, ChimeraX wrote:

[justin.ditrani@…]

Only CPU and reference. Maybe its not recognizing my GPU?

On Mon, Mar 30, 2020 at 2:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tristan Croll]

That means you don't have CUDA installed... you should see the following 
warning telling you that in the log:

                 'WARNING: no OpenCL or compatible CUDA '
                 'drivers detected! While it is theoretically possible to 
run '
                 'ISOLDE using CPU only, in practice it is prohibitively 
slow. '
                 'If you have a suitable GPU in your machine, please 
check that you '
                 'have the recommended drivers from the manufacturer 
installed. '
                 'The current required CUDA version is 10.1 - if 
installed, please '
                 'make sure this is on your library path before starting 
ChimeraX.'

At least that's an easy enough fix: just install CUDA.

On 2020-03-30 19:41, ChimeraX wrote:

[justin.ditrani@…]

Works like a charm now. Thanks so much for all your help!!!!!

On Mon, Mar 30, 2020 at 2:45 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Do you mean it now works on Ubuntu or on Windows after installing CUDA?

[justin.ditrani@…]

Only Ubuntu, on Windows it still doesnt work. Even with cuda.

On Mon., Mar. 30, 2020, 4:25 p.m. ChimeraX, <
ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

[Tom Goddard]

Justin has ISOLDE working on Linux. The crashes using ISOLDE on Windows seem to be graphics driver related since he does not see crashes on a different Windows machine looking at the same data.