ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory

[universvm]

I'm out of luck installing pymol. For various reasons I won't go into, I cannot use conda. I have been trying to install with apt-get or using the precompiled binaries. I have been stuck at this error and cannot seem to find anything on google:

"ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory"

I tried looking it up in the repository here as well and yet I cannot find anything. Here's the full dump:

PyMOL failed to start, dumping diagnostics...

Operating System:
Linux-5.4.0-1104-azure-x86_64-with-glibc2.35
#110~18.04.1-Ubuntu SMP Sat Feb 11 17:41:21 UTC 2023
PyQt5 5.15.9 (Qt 5.15.2)

Python:
3.10.6 (main, May 29 2023, 11:10:38) [GCC 11.3.0]
prefix=/opt/{REDACTED}/.venv
executable=/opt/{REDACTED}/.venv/bin/python
filesystemencoding=utf-8

Qt, Python and PyMOL Environment Variables:
LANG=C.UTF-8
PYDEVD_USE_FRAME_EVAL=NO
PYMOL_DATA=/opt/pymol/share/pymol/data
PYMOL_PATH=/opt/pymol/share/pymol
PYTORCH_NVML_BASED_CUDA_CHECK=1
QT_API=pyqt5
QT_XKB_CONFIG_ROOT=/opt/{REDACTED}/.venv/lib

PATH:
/opt/{REDACTED}/.venv/bin:/opt/{REDACTED}/bin:/opt/c
onda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/root/.local/bin:/usr/local
/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

Traceback (most recent call last):
  File "/opt/pymol/lib/python3.10/site-packages/pymol/__init__.py", line 72, in <module>
    import pymol
  File "/opt/pymol/lib/python3.10/site-packages/pymol/__init__.py", line 620, in <module>
    import pymol._cmd
ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory

Things that I've tried:

• !apt-get install -y -q python3-vtk7
• !pip install vtk

[JarrettSJohnson]

Do you need VTK-m? If not, then you can add --use-vtkm="no" to your setup arguments.

Edit: Also make sure that you're specifically installing vtkm version 1.5 if your flag is set to "1.5"

[minsu1794]

I also have same problem, and tried --use-vtkm="no" but still same error occur.

[JarrettSJohnson]

I also have same problem, and tried --use-vtkm="no" but still same error occur.

I can't seem to reproduce this error. And this is with a clean build? --use-vtkm is also no by default.

[minsu1794]

I have used : conda install -c schrodinger pymol to setup the conda environment.

So here`s my log: PyMOL failed to start, dumping diagnostics... pymol-2.5.7-py39had9a3ec_0.json conda build: py39had9a3ec_0 https://conda.anaconda.org/schrodinger/linux-64

Operating System: Linux-3.10.0-1127.10.1.el7.x86_64-x86_64-with-glibc2.17

1 SMP Wed Jun 3 14:28:03 UTC 2020

PyQt5 5.15.10 (Qt 5.15.2)

Python: 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:49:32) [GCC 12.3.0] prefix=/home/mcho43/anaconda3/envs/crispro executable=/home/mcho43/anaconda3/envs/crispro/bin/python filesystemencoding=utf-8

Qt, Python and PyMOL Environment Variables: LANG=en_US.UTF-8 PYMOL_DATA=/home/mcho43/anaconda3/envs/crispro/share/pymol/data PYMOL_PATH=/home/mcho43/anaconda3/envs/crispro/share/pymol QT_API=pyqt5 QT_XKB_CONFIG_ROOT=/home/mcho43/anaconda3/envs/crispro/lib

PATH: /home/mcho43/anaconda3/envs/crispro/bin:/home/mcho43/anaconda3/condabin:/home/ mcho43/cellranger/cellranger-5.0.1:/home/mcho43/bin:/usr/local/bin:/usr/bin:/u sr/local/sbin:/usr/sbin:/home/mcho43/.local/bin:/home/mcho43/bin

Traceback (most recent call last): File "/home/mcho43/anaconda3/envs/crispro/bin/crispro", line 4, in import('pkg_resources').run_script('crispro==1.0.2', 'crispro') File "/home/mcho43/anaconda3/envs/crispro/lib/python3.9/site-packages/pkg_resources/init.py", line 722, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/mcho43/anaconda3/envs/crispro/lib/python3.9/site-packages/pkg_resources/init.py", line 1561, in run_script exec(code, namespace, namespace) File "/home/mcho43/anaconda3/envs/crispro/lib/python3.9/site-packages/crispro-1.0.2-py3.9.egg/EGG-INFO/scripts/crispro", line 27, in import crispro.crispro_structures as crispro_structures File "/home/mcho43/anaconda3/envs/crispro/lib/python3.9/site-packages/crispro-1.0.2-py3.9.egg/crispro/crispro_structures.py", line 21, in import pymol File "/home/mcho43/anaconda3/envs/crispro/lib/python3.9/site-packages/pymol/init.py", line 620, in import pymol._cmd ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory

I`ve been trying to install vtkm 1.5 through this link : https://gitlab.kitware.com/vtk/vtk-m/-/releases?after=eyJyZWxlYXNlZF9hdCI6IjIwMjEtMTItMDggMTM6NDg6MTUuNjI2MjkwMDAwIC0wNTAwIiwiaWQiOiIxMjUyIn0

All the 1.5 version I tried however didn`t have specific libvtkm_cont-1.5.so.1.

[JarrettSJohnson]

conda install -c schrodinger pymol

installs Incentive PyMOL (improperly), which is a separate python package from this repo's open-source. Use a new environment and try either:

conda install -c conda-forge pymol-open-source if you need to install open source

or

conda install -c conda-forge -c schrodinger pymol (note the inclusion of conda-forge channel first) if you need to install the Incentive PyMOL conda package. See https://pymol.org/conda/ for more info.

[skrhakv]

I had a similar issue:

ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory

It was resolved by using conda install -c conda-forge pymol-open-source which @JarrettSJohnson suggested.

Thanks!

[minsu1794]

Thank you! The suggestion did resolve my issue.

[JarrettSJohnson]

No worries. I assume that the OP's issue will be solved with this too. Closing.

[iland24]

Thank you, I was facing the same issue but conda install -c conda-forge pymol-open-source worked.

[universvm]

Hi @JarrettSJohnson

As I mentioned in the post, I cannot use conda or apt-get, so unfortunately the issue is not solved. Is there an easier way to install PyMol?

[JarrettSJohnson]

Can you inform which method you installed PyMOL to get the error above? Was this from the installers from the website? If so, there may be a fix coming for it this week.

[universvm]

Can you inform which method you installed PyMOL to get the error above? Was this from the installers from the website? If so, there may be a fix coming for it this week.

This was from compiling from source

[JarrettSJohnson]

If I'm not mistaken, diagnostics dumping upon opening PyMOL only occurs from our incentive product (which is not abled to be compiled from source). So even if you're compiling open-source, it may be trying to open incentive? Can you try uninstalling this incentive PyMOL version?

[universvm]

Apologies, I'm not sure what the incentive product is and perhaps I mistakenly remembered that I got that error installing this repository (pymol-open-source).

From your message it sounds like this should not be happening using this repository but rather only when using another version (perhaps a pre-compiled one)?

[JarrettSJohnson]

Incentive products come from either the installers found on pymol.org or from the schrodinger conda channel when installing pymol. Pre-installed Open-Source PyMOL comes from various package managers such homebrew, apt, and even conda but from the conda-forge channel under the pymol-open-source package name.

This repository only provides the raw source and users can build PyMOL on their own via setup.py and getting their own dependencies in some way.

Correct, if you're compiling strictly from source from this repository, you shouldn't see that error message. Those who have installed the incentive version (e.g. pymol -c schrodinger conda) will see that error.