Error when running on HPC

Asked by Jiannan Wang

Hello,

I'm trying to run Yade on HPC. Our IT helped me set up a singularity under my account. It seems to be OK with launching Yade. But when I actually tried to run the script same as the one in the thermal coupling example [1] (omitted the graphic plot part), the following error occurred after 6000 iterations:

<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
CGAL ERROR: assertion violation!
Expr: dexp != 2047
File: /usr/include/CGAL/Mpzf.h
Line: 448
Explanation: Creating an Mpzf from infinity or NaN.

I tried to typed printAllVersions(), I got the following:

```
Yade version : 2021.01a
Yade features : BoostLog PrecisionDouble Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV TWOPHASEFLOW SPH FEMLIKE GL2PS LBMFLOW THERMAL PARTIALSAT PotentialParticles
Yade config dir: ~/.yade
Yade precision : 53 bits, 15 decimal places, without mpmath
```

Libraries used :

| library | cmake | C++ |
| ------------- | --------------------- | ------------------- |
| boost | 1.74.0 | 1.74.0 |
| cgal | | 5.2 |
| cmake | 3.18.4 | |
| compiler | /usr/bin/c++ 10.2.1 | gcc 10.2.1 |
| eigen | 3.3.9 | 3.3.9 |
| freeglut | 2.8.1 | |
| gl | | 20190805 |
| ipython | 7.19.0 | |
| metis | | 5.1.0 |
| openblas | | OpenBLAS 0.3.10 |
| python | 3.9.1 | 3.9.1 |
| qglviewer | | 2.6.3 |
| qt | | 5.15.2 |
| sqlite | | 3.34.0 |
| suitesparse | 5.8.1 | 5.8.1 |
| vtk | 9.0.1 | 9.0.1 |

```
Linux version : Ubuntu Hirsute Hippo (development branch)
Architecture : amd64
Little endian : True
```
I'm wondering where it may go wrong? What is missing from the installation that cause this problem. Thank you.

Best
Jiannan

[1]: https://gitlab.com/yade-dev/trunk/-/blob/master/examples/ThermalEngine/thermoHydroMechanical_coupling.py

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Jiannan Wang
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Revision history for this message
Robert Caulk (rcaulk) said :
#1

Hello,

Can you confirm that the same error does not appear on a standard desktop computer?

Thankyou,

Robert

Revision history for this message
Robert Caulk (rcaulk) said :
#2

I should also point out that you appear to be using a development branch of linux that is not explicitly supported by Yade. I am a bit surprised an HPC is using this type of distro...did they install ubuntu 21.04 just for you? If so, ask them to install a stable release like 18.04 or 20.04. Both versions are supported by Yade.

Revision history for this message
Jiannan Wang (jnwang) said :
#3

Hello Robert,

Yes, the same error dose not appear on my standard desktop.

I think they installed Yade inside a ubuntu 21.04 singularity container just for me. I'll ask them for a new installation. Thank you.

Best regards
Jiannan

Revision history for this message
Jiannan Wang (jnwang) said :
#4

Hello Robert,

Just an update: they install the 20.04 on my account and now Yade and yadedaily seems to be working well. Thank you for the help.

Best regards
Jiannan

Revision history for this message
Robert Caulk (rcaulk) said :
#5

Thank you for the update :-)