Core Dumped and OpenMC didn't Work

User Support
1

Hi Everyone,

I just installed ‘Enter/Exit Live Reveal Slideshow’ Button using ‘rise’ and it worked. But suddenly when i tried to open anaconda-navigator it show:

Segmentation fault (core dumped)

Then i tried to execute OpenMC but it said:

openmc: Relink /home/guixian/anaconda3/bin/../lib/./libgfortran.so.4' with /lib/x86_64-linux-gnu/librt.so.1’ for IFUNC symbol `clock_gettime’
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 139625625562496:
#000: H5Tarray.c line 115 in H5Tarray_create2(): not an valid base datatype
major: Invalid arguments to routine
minor: Inappropriate type
openmc: symbol lookup error: /home/guixian/anaconda3/bin/…/lib/libopenmc.so: undefined symbol: __h5lib_provisional_MOD_h5offsetof

I search for solution in google but end with updating all conda but still same issue. Really appreciate for any suggestion.

conda info :

active environment : None
user config file : /home/guixian/.condarc
populated config files : /home/guixian/.condarc
conda version : 4.6.7
conda-build version : 3.17.8
python version : 3.6.8.final.0
base environment : /home/guixian/anaconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/guixian/anaconda3/pkgs
/home/guixian/.conda/pkgs
envs directories : /home/guixian/anaconda3/envs
/home/guixian/.conda/envs
platform : linux-64
user-agent : conda/4.6.7 requests/2.21.0 CPython/3.6.8 Linux/4.15.0-45-generic ubuntu/18.04.2 glibc/2.27
UID:GID : 1000:1000
netrc file : None
offline mode : False

conda list :

packages in environment at /home/guixian/anaconda3:

2

Hi Kristina,

It’s hard to say what exactly is going wrong in your environment. One possibility is that OpenMC is looking for HDF5 version 1.8.x and the version you have installed is 1.10.4. You might want to try downgrading HDF5 and see if that fixes the problem. Beyond that, the only thing I can suggest is reinstalling OpenMC or setting up a new conda environment.

Good luck!

Paul

3

Hi Dr. Paul, I'll give it a try. Thanks for you suggestion.