Error when running on HPC
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::ThreadRun
CGAL ERROR: assertion violation!
Expr: dexp != 2047
File: /usr/include/
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
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 :-)