Error when running on HPC

Asked by Jiannan Wang on 2021-01-29

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

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Jiannan Wang
Solved:
2021-02-04
Last query:
2021-02-04
Last reply:
2021-01-29
Robert Caulk (rcaulk) said : #1

Hello,

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

Thankyou,

Robert

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.

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

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

Robert Caulk (rcaulk) said : #5

Thank you for the update :-)