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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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PyMOL failed to start #178

Open fabioatuib opened 3 years ago

fabioatuib commented 3 years ago

Hello! Sorry in advance if this is not the right place for this type of issue. Do you know why pymol a failed to start? Thank you in advance!

PyMOL failed to start, dumping diagnostics... pymol-2.4.1-py37h913975d_0.json conda build: py37h913975d_0 https://conda.anaconda.org/schrodinger/linux-64

Operating System: Linux-5.4.0-72-generic-x86_64-with-debian-buster-sid

80~18.04.1-Ubuntu SMP Mon Apr 12 23:26:25 UTC 2021

PyQt5 5.12.3 (Qt 5.12.5)

Python: 3.7.8 | packaged by conda-forge | (default, Jul 31 2020, 02:25:08) [GCC 7.5.0] prefix=/home/fol007/anaconda3/envs/py37_rdkit executable=/home/fol007/anaconda3/envs/py37_rdkit/bin/python filesystemencoding=utf-8

Qt, Python and PyMOL Environment Variables: LANG=en_US.UTF-8 LANGUAGE= PYMOL_DATA=/home/fol007/anaconda3/envs/py37_rdkit/share/pymol/data PYMOL_PATH=/home/fol007/anaconda3/envs/py37_rdkit/share/pymol PYTHONPATH=/home/fol007/PhD_Project/Template_Based_Docking_Project_GitRepo/cross_free_docking_cluster_run QT4_IM_MODULE=xim QT_ACCESSIBILITY=1 QT_API=pyqt5 QT_IM_MODULE=xim QT_XKB_CONFIG_ROOT=/home/fol007/anaconda3/envs/py37_rdkit/lib

PATH: /home/fol007/anaconda3/envs/py37_rdkit/bin:/home/fol007/anaconda3/condabin:/us r/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/loca l/games:/snap/bin:/opt/puppetlabs/bin:/home/fol007/Desktop/pycharm-2020.3.4/bi n:/home/fol007/Desktop/pymol:/home/fol007/Zotero_linux-x86_64

ImportError Traceback (most recent call last)

in 6 from rdkit import Chem 7 from rdkit.Chem import AllChem ----> 8 from pymol import cmd 9 ~/anaconda3/envs/py37_rdkit/lib/python3.7/site-packages/pymol/__init__.py in 647 648 try: --> 649 import pymol._cmd 650 except ImportError: 651 _report_cmd_DLL_problem() ImportError: /home/fol007/anaconda3/envs/py37_rdkit/lib/python3.7/site-packages/pymol/../../../libnetcdf.so: undefined symbol: H5Pset_fapl_ros3
JarrettSJohnson commented 3 years ago

Is this using the latest libnetcdf?

conda install -c conda-forge libnetcdf

and then try a clean build

thorstenwagner commented 2 years ago

I had a similar problem with the latest pymol version (fresh conda insallation). I needed to download libnetcdf to get it working:

conda install -c conda-forge libnetcdf==4.7.3