VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 14 2008 - 10:26:18 CDT

Hi,
  Sorry for the delayed reply, trying to finish a paper submission... :)
Only the LINUXAMD64 test builds should have Python 2.5 compiled in
at the moment, but I'll be expanding that over the next few weeks as
time allows.

  John

On Mon, Apr 14, 2008 at 12:43:00PM +0200, Vlad Cojocaru wrote:
> Thanks Alex,
>
> Sorry ... of course ... its logical since the binaries are already
> compiled .... This means that the 1.8.7a21 version was actually compiled
> without python ...
>
> vlad
>
> Axel Kohlmeyer wrote:
> >On Mon, 14 Apr 2008, Vlad Cojocaru wrote:
> >
> >VC> Hi John, vmd users,
> >VC>
> >VC> Its clear now .. vmd-1.8.7a21 for LINUX (posted by you on the BIOCORE
> >on the
> >VC> 3rd of April is compiled with python 2.5)
> >VC>
> >VC> When I installed this version on my working place (Debian, 32 bits
> >machine),
> >VC> and I tried gopython it tells me "invalid command name gopython".. I
> >did add
> >VC> PYTHON and NUMPY to the configure.options before running configure ...
> >
> >if you download and install a binary version, changing configure.options
> >hast _no_ effect. this only applies to compilations.
> >
> >axel.
> >
> >VC>
> >VC> Is this happening because I do not have python 2.5 installed on my
> >system (I
> >VC> only have 2.4)?
> >VC>
> >VC> Best
> >VC> vlad
> >VC>
> >VC>
> >VC> Vlad Cojocaru wrote:
> >VC> > Hi John,
> >VC> >
> >VC> > I believe you are right .. It should not matter whether those files
> >are
> >VC> > executables. I've just thought that the permissions might have
> >changed
> >VC> > while I checked out the files and that's why I asked. But if they
> >were
> >VC> > checked in like this and if this is more convenient from your side,
> >it
> >VC> > should be fine ... There is no reason to affect the compilation
> >itself.
> >VC> >
> >VC> > Are the latest test version (1.8.7a19) already compiled with python
> >2.5
> >VC> > and tcl 8.5? What Numeric version do you use for compiling ?
> >VC> >
> >VC> > Best wishes
> >VC> > vlad
> >VC> >
> >VC> >
> >VC> >
> >VC> > John Stone wrote:
> >VC> > > Hi guys,
> >VC> > > I believe the source files in public CVS may be marked as
> >executable
> >VC> > > because we have scripts that copy our internal CVS repository to
> >the
> >VC> > > externally
> >VC> > > accessible server. The scripts may do chmod -R ... type operations
> >VC> > > to make it impossible for CVS permissions to prevent access to the
> >files
> >VC> > > by the unprivileged CVS server process. I haven't looked at the
> >scripts
> >VC> > > in years, but that's my vague recollection. It shouldn't harm
> >anything,
> >VC> > > though it may offend your sense of cleanliness to see all those
> >source
> >VC> > > files set to be executable. :) I can look into this more closely
> >if
> >VC> > > people actually care, but thus far it has never mattered to my
> >VC> > > knowledge,
> >VC> > > and it has prevented bad permissions in our internal tree from
> >creating
> >VC> > > problems for external developers working from the public CVS.
> >VC> > >
> >VC> > > Cheers,
> >VC> > > John
> >VC> > >
> >VC> > > On Sun, Apr 13, 2008 at 04:00:12PM -0400, Axel Kohlmeyer wrote:
> >VC> > >
> >VC> > > > On Sun, 13 Apr 2008, Cojocaru,Vlad wrote:
> >VC> > > >
> >VC> > > > VC> Hi Alex,
> >VC> > > > VC>
> >VC> > > > VC> Thanks for replying !!
> >VC> > > > VC>
> >VC> > > >
> >VC> > > > VC> I had openSuse 10.0 and upgraded to the new 10.3 (on Athlon
> >64,
> >VC> > > > VC> 3500+)... I have just seen that all the checkout files were
> >VC> > > > VC> executables on my machine after checkout with cvs following
> >VC> > > > VC> exactly the recipe on the VMD web site ... I cannot explain
> >why
> >VC> > > > VC> all files were executables if by default the permissions are
> >VC> > > > VC> preserved ...
> >VC> > > >
> >VC> > > > probably because they were checked in like this...
> >VC> > > > i checked my checkout and most, but not all files are executable.
> >VC> > > > it never made a difference in compiling, so...
> >VC> > > >
> >VC> > > > VC> Regarding my second question, I think you misunderstood ... I
> >VC> > > > VC> first downloaded the binaries for vmd-1.8.7a19 ... And with
> >these
> >VC> > > > VC> binaries I had the python problem ... After seeing the
> >problem
> >VC> > > > VC> (and having
> >VC> > > >
> >VC> > > > well, since you have suse and john is compiling on red hat, i'm
> >not
> >VC> > > > surprised that there may be (small) differences. you'd have to
> >install
> >VC> >>> _his_ compile of the python parts. if i remember correctly, he is
> >not
> >VC> > > > building with tcl 8.5 (not 8.4), on top of that...
> >VC> > > >
> >VC> > > > with the diversity of distributions and the ways how people
> >install
> >VC> > > > (or mutilate) them, the only way to have a binary consistent
> >with your
> >VC> > > > distribution is to compile yourself. :-(
> >VC> > > >
> >VC> > > > VC> the problem so many times before with vmd versions earlier
> >than
> >VC> > > > VC> 1.8.6) I thought that the simple solution is just to compile
> >vmd
> >VC> > > > VC> and as I did it before I should be able to do it again ...
> >And
> >VC> > > > VC> that's when I downloaded the code from CVS
> >VC> > > > VC>
> >VC> > > > VC> I did not do the compilation yet ...
> >VC> > > >
> >VC> > > > good luck,
> >VC> > > > axel.
> >VC> > > >
> >VC> > > >
> >VC> > > > VC> bets wishes
> >VC> > > > VC> vlad
> >VC> > > > VC>
> >VC> > > > VC>
> >VC> > > >
> >VC> > > > --
> >VC> > > >
> >=======================================================================
> >VC> > > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> >VC> > > > http://www.cmm.upenn.edu
> >VC> > > > Center for Molecular Modeling -- University of
> >Pennsylvania
> >VC> > > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> >VC> > > > 19104-6323
> >VC> > > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> >1-215-898-5425
> >VC> > > >
> >=======================================================================
> >VC> > > > If you make something idiot-proof, the universe creates a better
> >VC> > > > idiot.
> >VC> > > >
> >VC> > >
> >VC> > >
> >VC> >
> >VC> > --
> >VC> >
> >----------------------------------------------------------------------------
> >VC> > Dr. Vlad Cojocaru
> >VC> >
> >VC> > EML Research gGmbH
> >VC> > Schloss-Wolfsbrunnenweg 33
> >VC> > 69118 Heidelberg
> >VC> >
> >VC> > Tel: ++49-6221-533266
> >VC> > Fax: ++49-6221-533298
> >VC> >
> >VC> > e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> >VC> >
> >VC> > http://projects.villa-bosch.de/mcm/people/cojocaru/
> >VC> >
> >VC> >
> >----------------------------------------------------------------------------
> >VC> > EML Research gGmbH
> >VC> > Amtgericht Mannheim / HRB 337446
> >VC> > Managing Partner: Dr. h.c. Klaus Tschira
> >VC> > Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> >VC> > http://www.eml-r.org
> >VC> >
> >----------------------------------------------------------------------------
> >VC> >
> >VC> >
> >VC>
> >VC>
> >
> >
>
> --
> ----------------------------------------------------------------------------
> 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
> ----------------------------------------------------------------------------
> 

-- 
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