Author Topic: TmoleX visualization not working on Ubuntu 14.04  (Read 2378 times)

pski

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TmoleX visualization not working on Ubuntu 14.04
« on: March 24, 2015, 07:45:06 pm »
I have installed TmoleX on my machine running Ubuntu 64-bit 14.04. There were no issues during installation, but I am unable to visualize any molecules in the TmoleX visualization window. I have tried the following, but nothing appears in the window:
1) File->Open/Import Molecule
2) Adding individual atoms from the Draw Tool

Thank you for any help you can provide.

pski

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Re: TmoleX visualization not working on Ubuntu 14.04
« Reply #1 on: March 24, 2015, 11:13:58 pm »
This turned out to be a problem with my nvidia drivers and linux environment. I solved it by updating to the latest nvidia drivers, updating bumblebee (a Debian package), and then running TmoleX with my GPU. My machine is a Thinkpad T520.

tonyst

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Re: TmoleX visualization not working on Ubuntu 14.04
« Reply #2 on: May 06, 2016, 02:28:48 pm »
Hi

I have the same problem.

Running arch linux with 4.5.1 kernel. Java environments:

Available Java environments:
  java-7-openjdk/jre
  java-8-openjdk/jre (default)

I tried with both versions. System is up to date. Running with intel gpu (i5 haswell).

Any ideas how to fix this?

uwe

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Re: TmoleX visualization not working on Ubuntu 14.04
« Reply #3 on: May 06, 2016, 04:46:02 pm »
Hi,

open a shell (terminal) and enter:

export MESA_GL_VERSION_OVERRIDE=2.1
export LIBGL_ALWAYS_SOFTWARE=1

then go to the installation directory and start TmoleX, e.g.:

cd ~/COSMOlogic/TmoleX15/TmoleX
./TmoleX15

if you can see the molecules, add the two lines (export ...) to the TmoleX15 script. If you open it in an editor, it starts with:

Quote
#!/bin/sh

# Uncomment the following line to override the JVM search sequence
# INSTALL4J_JAVA_HOME_OVERRIDE=
# Uncomment the following line to add additional VM parameters
# INSTALL4J_ADD_VM_PARAMS=


INSTALL4J_JAVA_PREFIX=""
GREP_OPTIONS=""

change that to

Quote
#!/bin/sh

# Uncomment the following line to override the JVM search sequence
# INSTALL4J_JAVA_HOME_OVERRIDE=
# Uncomment the following line to add additional VM parameters
# INSTALL4J_ADD_VM_PARAMS=

export MESA_GL_VERSION_OVERRIDE=2.1
export LIBGL_ALWAYS_SOFTWARE=1

INSTALL4J_JAVA_PREFIX=""
GREP_OPTIONS=""

Then you should be able to start TmoleX15 directly using the icon on the desktop.

Regards,

Uwe