VMD-L Mailing List

From: Cook, Rich (cook47_at_llnl.gov)
Date: Mon Aug 26 2013 - 20:06:20 CDT

OK, then from sources it is… on to my next questions in a separate email! :-)

On Aug 26, 2013, at 5:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
 wrote:

> 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. 

-- 
✐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)