VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 26 2013 - 19:57:36 CDT

On Tue, Aug 27, 2013 at 1:44 AM, Cook, Rich <cook47_at_llnl.gov> wrote:
> Hello,
> I have downloaded and installed the binary release of VMD 1.9.1 on our
> clusters and one of our users pointed out that "python in VMD is broken" on
> our machines.
> There are two symptoms:
> 1) import os,sys fails, as shown by the output below of vmd -python
> ------------------------------------------------------------------------
> rcook_at_rzgpu2 (vmd-1.9.1): vmd -python
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> blah blah blah…
> Info) Starting Python...
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> ValueError: vmdnumpy module not available.
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File "/usr/local/tools/vmd-1.9.1/lib/vmd/scripts/python/Tkinter.py", line
> 59, in <module>
> import _tkinter # If this fails your Python may not be configured for Tk
> ImportError: No module named _tkinter
>>>> import os,sys
> Traceback (most recent call last):
> File "VMD", line 1, in <module>
> ImportError: No module named os
> ------------------------------------------------------------------------
> I've tried fiddling with PYTHONHOME and such and either I'm doing that wrong
> or that's not the right approach. Can anyone solve this?

the python runtime is not bundled with VMD, since it is very large and
not very portable across systems. if you want python support, you are
best off to compile VMD from sources.

> 2) readline does not work in vmd. I.e., up arrow does not get the last
> command, etc. Can this be fixed without a recompile?

there is no readline support in VMD itself. however, the vmd startup
script tries to detect, if the rlwrap utility exists and then uses
that (with all its limitations).

axel.

> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> ☎ (office) (925) 423-9605
> ☎ (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.