VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Apr 14 2008 - 05:16:25 CDT

Hi John, vmd users,

Its clear now .. vmd-1.8.7a21 for LINUX (posted by you on the BIOCORE on
the 3rd of April is compiled with python 2.5)

When I installed this version on my working place (Debian, 32 bits
machine), and I tried gopython it tells me "invalid command name
gopython".. I did add PYTHON and NUMPY to the configure.options before
running configure ...

Is this happening because I do not have python 2.5 installed on my
system (I only have 2.4)?

Best
vlad

Vlad Cojocaru wrote:
> Hi John,
>
> I believe you are right .. It should not matter whether those files
> are executables. I've just thought that the permissions might have
> changed while I checked out the files and that's why I asked. But if
> they were checked in like this and if this is more convenient from
> your side, it should be fine ... There is no reason to affect the
> compilation itself.
>
> Are the latest test version (1.8.7a19) already compiled with python
> 2.5 and tcl 8.5? What Numeric version do you use for compiling ?
>
> Best wishes
> vlad
>
>
>
> John Stone wrote:
>> Hi guys,
>> I believe the source files in public CVS may be marked as executable
>> because we have scripts that copy our internal CVS repository to the externally
>> accessible server. The scripts may do chmod -R ... type operations
>> to make it impossible for CVS permissions to prevent access to the files
>> by the unprivileged CVS server process. I haven't looked at the scripts
>> in years, but that's my vague recollection. It shouldn't harm anything,
>> though it may offend your sense of cleanliness to see all those source
>> files set to be executable. :) I can look into this more closely if
>> people actually care, but thus far it has never mattered to my knowledge,
>> and it has prevented bad permissions in our internal tree from creating
>> problems for external developers working from the public CVS.
>>
>> Cheers,
>> John
>>
>> On Sun, Apr 13, 2008 at 04:00:12PM -0400, Axel Kohlmeyer wrote:
>>
>>> On Sun, 13 Apr 2008, Cojocaru,Vlad wrote:
>>>
>>> VC> Hi Alex,
>>> VC>
>>> VC> Thanks for replying !!
>>> VC>
>>>
>>> VC> I had openSuse 10.0 and upgraded to the new 10.3 (on Athlon 64,
>>> VC> 3500+)... I have just seen that all the checkout files were
>>> VC> executables on my machine after checkout with cvs following exactly
>>> VC> the recipe on the VMD web site ... I cannot explain why all files
>>> VC> were executables if by default the permissions are preserved ...
>>>
>>> probably because they were checked in like this...
>>> i checked my checkout and most, but not all files are executable.
>>> it never made a difference in compiling, so...
>>>
>>> VC> Regarding my second question, I think you misunderstood ... I first
>>> VC> downloaded the binaries for vmd-1.8.7a19 ... And with these binaries
>>> VC> I had the python problem ... After seeing the problem (and having
>>>
>>> well, since you have suse and john is compiling on red hat, i'm not
>>> surprised that there may be (small) differences. you'd have to install
>>> _his_ compile of the python parts. if i remember correctly, he is not
>>> building with tcl 8.5 (not 8.4), on top of that...
>>>
>>> with the diversity of distributions and the ways how people install
>>> (or mutilate) them, the only way to have a binary consistent with your
>>> distribution is to compile yourself. :-(
>>>
>>> VC> the problem so many times before with vmd versions earlier than
>>> VC> 1.8.6) I thought that the simple solution is just to compile vmd and
>>> VC> as I did it before I should be able to do it again ... And that's
>>> VC> when I downloaded the code from CVS
>>> VC>
>>> VC> I did not do the compilation yet ...
>>>
>>> good luck,
>>> axel.
>>>
>>>
>>> VC> bets wishes
>>> VC> vlad
>>> VC>
>>> VC>
>>>
>>> --
>>> =======================================================================
>>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>>> Center for Molecular Modeling -- University of Pennsylvania
>>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>>> =======================================================================
>>> If you make something idiot-proof, the universe creates a better idiot.
>>>
>>
>>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
> 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------