LinuxQuestions.org
Review your favorite Linux distribution.
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Software
User Name
Password
Linux - Software This forum is for Software issues.
Having a problem installing a new program? Want to know which application is best for the job? Post your question in this forum.

Notices

Reply
 
Search this Thread
Old 07-09-2009, 05:07 PM   #1
synss
Member
 
Registered: Jul 2007
Location: Germany
Distribution: Arch Linux, Mac OS X
Posts: 132

Rep: Reputation: 22
Unhappy Molekel - Molecule visualization


Is anyone using this software on Linux, and if yes, what distro? I may benefit from having a look at the patches or the versions used...

I am trying to install "Molekel", http://molekel.cscs.ch/wiki/pmwiki.php/Main/Build and I have some problems. I think I have all dependencies, including glew, which is not mentioned on the website, but I have a problem compiling:

Code:
/usr/include/Inventor/actions/SoRayPickAction.h: In constructor ‘MoleculeActorPickCommand::MoleculeActorPickCommand()’:
/usr/include/Inventor/actions/SoRayPickAction.h:90: error: ‘SoRayPickAction::SoRayPickAction(const SoRayPickAction&)’ is private
I understand what that means: trying to copy with a private copy-const is forbidden. This Inventor is actually OpenMOIV, which does not seem to have been updated for years: can't be a new problem. So I do not really know what to do...
 
Old 07-28-2009, 09:30 PM   #2
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,625

Rep: Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528
SoRayPickAction.h : is a Coin2 header.

Your problems probably origin from a poor VTK.
These are my notes from July 10' :

VTK........
"cmake_command="
Code:
cmake with-soxt -DBUILD_SHARED_LIBS:BOOL=ON -DBUILD_EXAMPLES:BOOL=ON -DBUILD_TESTING:BOOL=ON -DVTK_USE_GL2PS:BOOL=ON -DVTK_USE_GUISUPPORT:BOOL=ON -DVTK_USE_SYSTEM_EXPAT=ON -DVTK_USE_SYSTEM_FREETYPE=ON -DVTK_USE_SYSTEM_JPEG=ON -DVTK_USE_SYSTEM_PNG=ON -DVTK_USE_SYSTEM_TIFF=ON -DVTK_USE_SYSTEM_ZLIB=ON -DVTK_USE_QVTK=ON -DDESIRED_QT_VERSION=4 ..
And the real problems appear, when you pass 100% compiling :
Problems with linking to libChemKit2.so.
I found no solution.
.....

Google .. libChemKit2.so ..
http://stuff.mit.edu/afs/athena/soft..._glibc2_4/lib/

http://stuff.mit.edu/afs/athena/soft...libChemKit2.so

Google .. molelel ..
http://www.debian.org/devel/debian-m...#official-debs
.....

Last edited by knudfl; 07-28-2009 at 09:31 PM.
 
Old 07-29-2009, 03:20 AM   #3
synss
Member
 
Registered: Jul 2007
Location: Germany
Distribution: Arch Linux, Mac OS X
Posts: 132

Original Poster
Rep: Reputation: 22
Thank you, I managed to compile everything, filed a couple bugs to Molekel, but it still crashes when I start it. It segfaults! And I am not really sure what crashes, Molekel, VTK, some other thing…

So for now, I plot my molecules + vibrations in Matlab. It is better than nothing. Although if anyone managed to get Molekel working, I would appreciate help.

Or pointers to other molecule visualization software than can show IR vibrations with arrows or something similar. I already know Molden and use it for creating animated gifs of the vibrations. But animated gifs are not good for a paper.
 
Old 07-29-2009, 07:54 AM   #4
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,625

Rep: Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528
I used the suggested CentOS 4.2 ( = RH EL 4.x )
for the compiling.
Did you use Arch ? Which version ?

And did you manage to Create libChemKit2.so ?
Or just using one of the pre compiled binaries,
libChemKit2.so ?
.....
 
Old 07-30-2009, 12:37 AM   #5
synss
Member
 
Registered: Jul 2007
Location: Germany
Distribution: Arch Linux, Mac OS X
Posts: 132

Original Poster
Rep: Reputation: 22
I used Arch x86_64, up to date. I pretty much had to compile everything, I also compiled libChemKit2.so. I have been using the AUR where available or wrote the build script otherwise. I tried to compile Molekel from SVN, revision 649. All the dependencies at the latest version available (Coin2.5, etc.).

I will try to recompile VTK. How can I add the debug symbols in cmake? At least I would know whether Molekel or the GUI crashes…

Last edited by synss; 07-30-2009 at 12:46 AM.
 
Old 07-31-2009, 05:44 AM   #6
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,625

Rep: Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528
Quote:
How can I add the debug symbols in cmake?
I sometimes read in the cmake documentation.
( It is huge.) But usually I don't find, what I need.

Examples from other application is often more usable.
And can be found with some luck and some 'Googling'.

This one is from 'kde' and may be what you are looking for :
cmake -DCMAKE_BUILD_TYPE=debugfull ..
http://techbase.kde.org/Development/...ugging_symbols
.....

Molekel : I read somewhere, that it would be replaced
by OpenBabel.
.....
 
Old 08-03-2009, 01:04 AM   #7
knudfl
LQ 5k Club
 
Registered: Jan 2008
Location: Copenhagen, DK
Distribution: pclos2014, Slack14.1 DebWheezy, +50+ other Linux OS, for test only.
Posts: 13,625

Rep: Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528Reputation: 2528
Just saw this : " Linux4Chemistry "

http://www.redbrick.dcu.ie/~noel/linux4chemistry/
 
  


Reply

Tags
cmake, compilation, science, software


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off


Similar Threads
Thread Thread Starter Forum Replies Last Post
cpu visualization binutils General 0 04-23-2008 10:27 AM
font visualization morfeus80 Linux - Newbie 2 04-15-2008 03:56 AM
Molecule screen saver causing system crash in 7:10 POV_Dave Ubuntu 4 01-13-2008 03:22 PM
Molekel Issues kramerz Linux - Software 0 06-13-2006 12:20 AM
Visualization in XMMS? THX1138 Linux - Newbie 4 11-05-2003 12:06 AM


All times are GMT -5. The time now is 07:11 PM.

Main Menu
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
identi.ca: @linuxquestions
Facebook: linuxquestions Google+: linuxquestions
Open Source Consulting | Domain Registration