Author Topic: Segmentation Fault when Loading 512 million atoms  (Read 249 times)

bjcowen

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Segmentation Fault when Loading 512 million atoms
« on: July 17, 2018, 07:29:33 PM »
Hello,

I have a couple simulation domains, one 64 million, the other 512 million
The one that is 64 million loads fine, but 512 million loads, then crashes and gives error "Segmentation Fault"

I tried opening OVITO on a full node with 36 cores, and the same error. Does ovito automatically use all the cores of the node, or do I need to specify somehow?

Also, the node as 128 GB of RAM.

Thanks for the help

Alexander Stukowski

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Re: Segmentation Fault when Loading 512 million atoms
« Reply #1 on: July 18, 2018, 09:23:47 AM »
Hi,

Yes, Ovito uses all available processor cores by default for certain analysis algorithms that are parallelized. You can restrict it using the --nthreads command line option if desired.

Are you running the graphical user interface or the script interpreter ("ovitos") on that compute node?

Since this appears to be a bug in the software, it would be great if you would report it in our issue tracker on Gitlab, together with some more detailed information on your Ovito version/operating system/graphics hardware and the operation(s) you were performing:

https://gitlab.com/stuko/ovito/issues

Thank you!

-Alex

bjcowen

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Re: Segmentation Fault when Loading 512 million atoms
« Reply #2 on: July 19, 2018, 09:39:00 PM »
I am running the graphical user interface. Tried running with Ovito/3.0.0 and I get the error. When I run with Ovito/2.9.0, I do not get the error, so seems like some bug in the new release maybe?

The OS is linux, running on 1 node with 121 GB of RAM.
Same error when running on 2 and 4 nodes as well.

I am unsure of the graphics hardware on the system
« Last Edit: July 19, 2018, 09:43:13 PM by bjcowen »

Alexander Stukowski

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Re: Segmentation Fault when Loading 512 million atoms
« Reply #3 on: July 19, 2018, 10:45:15 PM »
So that means you are running Ovito through a VNC remote desktop connection on one of the compute nodes of the cluster, right?

Please go to the Help menu, select "OpenGL Information" and attach the system report generated by Ovito for me. It includes some basic information about the graphics hardware/driver configuration of the machine.

Note that running Ovito on more than 1 node doesn't make much sense. The software doesn't support any distributed type of parallelization. It can only use one node.

bjcowen

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Re: Segmentation Fault when Loading 512 million atoms
« Reply #4 on: July 20, 2018, 04:32:24 PM »
Yes, running on a compute node of a cluster.

Here is the openGl info, when running on Ovito/2.9.0

Note that this version works for 512 million atoms.

Code: [Select]
======= System info =======

Date: Fri Jul 20 08:30:25 2018

Application: Ovito 2.9.0

OS: Linux

uname output: 3.0.101-108.35-default #1 SMP Mon Feb 19 21:13:08 UTC 2018 (251ec24) x86_64 x86_64 GNU/Linux

LSB output:

Architecture: 64 bit

Floating-point size: 32 bit

Qt version: 5.7.0

Command line: ovito

======= OpenGL info =======

Version: 3.3

Profile: core

Alpha: 1

Vendor: VMware, Inc.

Renderer: Gallium 0.4 on llvmpipe (LLVM 3.8, 256 bits)

Version string: 3.3 (Core Profile) Mesa 12.0.2

Swap behavior: other

Depth buffer size: 24

Stencil buffer size: 8

Shading language: 3.30

Geometry shaders supported: yes

Using deprecated functions: no

Using point sprites: yes

Using geometry shaders: yes

Context sharing enabled: yes

When I switch to ovito/3.0.0, I can load 64 millions atoms, but when I try to load 512 million, it crashes with "Segmentation fault"