Altro, Thanks for the follow up -- you make some valid points.
As for compilation, the current Makefiles are complex and primarily exist to support automated incremental compilation during development. Use Python's distutils for normal deployments: path-to-your-python/bin/python setup.py build install path-to-your-python/bin/python setup2.py install I don't know whether this approach will mesh with your plan of running multiple platforms out of a single python install, but it just might if distutils is platform aware. Like I said, though this appears to be technically possible, it isn't the normal mode of deployment for Python... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:[email protected] > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Atro > Tossavainen > Sent: Saturday, May 06, 2006 10:12 AM > To: [email protected] > Subject: Re: [PyMOL] That _cmd thing > > Warren, > > Thanks for the quick response. > > > Python as a scripting environment isn't configured for that > style of > > use, where all of the cross-platform components are shared > in common > > and only the platform-specific binaries are separated. > > machine:~/scratch/Python-2.4.2> ./configure --help ... > Fine tuning of the installation directories: > --bindir=DIR user executables [EPREFIX/bin] > --sbindir=DIR system admin executables [EPREFIX/sbin] > --libexecdir=DIR program executables [EPREFIX/libexec] > --datadir=DIR read-only architecture-independent > data [PREFIX/share] > --sysconfdir=DIR read-only single-machine data [PREFIX/etc] > --sharedstatedir=DIR modifiable architecture-independent > data [PREFIX/com] > --localstatedir=DIR modifiable single-machine data [PREFIX/var] > > I have used these features to produce a Python 2.4.2 installation that > does exactly what you say it isn't configured to do. I see no problem > in this respect. Also, having AFS helps for making multi- platform > program installations thanks to the live expansion of "@sys" > to the current value of `sys` in file names by AFS. Witness > > lrwxr-xr-x 1 root root 8 Apr 3 15:31 bin -> @sys/bin > > The machine-dependent files are in `sys`/{bin,lib,include} for all of > the different types of systems that we have. > > > Though it might be possible to pull something like that off, the > > megabytes saved per time spent wouldn't be worth the trouble. > > Perhaps. > > > [Aside: I don't know what prices are like in Europe, but > here in the > > US disk space is running 50-70 cents a GB. > > Disk prices are not the issue. Of course you can replace the current > hard drives in all of the peecees and workstations (>100 of them) with > disks twice or four times the current size, and it won't even cost a > lot to buy the hardware. > There might be other costs, such as having to install them all in the > machines, probably wrecking the Windows installs on them all in the > process and having to redo them all. > > Also, adding more space to a server-grade configuration is often > slightly more expensive than adding a single disk to your peecee. > And when changes are made to a program, I want to make one change, not > n different sets of the same change for n different platforms if I can > avoid it. > > > Thus, a complete platform-specific binary PyMOL install > uses about 2 > > cents worth of disk space, and a complete build with all > dependencies > > from source with object code costs about a quarter (0.25 USD).] > > I believe, perhaps mistakenly, that there might be other advantages to > installing only one copy of each dependency (so that you don't have a > separate zlib for every program that uses it, for example, so that > when zlib security problems come up, you replace one copy instead of > trying to remember to rebuild every package that came with its own). > > > As for the error -- either the _cmd.so binary isn't > installed in the > > right place, or it is for a different platform. > > Since I have only started building Pymol after completing the > installation of all the "ext" packages, and there aren't yet any files > for any of the other platforms but one, it's a case of the former. > > Sure enough, _cmd.so hasn't been built at all. > > "make" continues despite the following command failing in the middle > of the compilation process. I believe Makefiles should be written in > such a way that if any of the commands required to build the end > product fails, the rest of the effort stops there. I only thought I > had it going already because the "make" process went to the end > without failing on an error (that I hadn't seen, and that was > somewhere in the middle of it). > > cc -shared -c */*.o ov/src/*.o -march=i486 -D__i686__ -ffast-math > -Wall -ansi -pedantic -Wno-long-long > -Wmissing-prototypes -g -I{my Python 2.4.2 > install}/include/python2.4 -I{my Python 2.4.2 > install}/@sys/include/python2.4 -I/usr/X11R6/include -D_PYMOL_MODULE > -D_PYMOL_INLINE -D_PYMOL_NO_MAIN > -D_PYMOL_NOPY -L{my Python 2.4.2 install}/@sys/lib > -Wl,-rpath,{my Python 2.4.2 install}/@sys/lib -L{my Tcl/Tk/Tix 8.4.11 > install}/lib -Wl,-rpath,{my Tcl/Tk/Tix > 8.4.11 install}/lib -L/usr/X11R6/lib -lpython2.4 -ltcl8.4 > -ltk8.4 -lTix8.4 -lGL -lGLU -lpng -lXmu -lm > > This command produces a ton of "linker input file unused because > linking not done" messages regarding .o files in layer0/. The command > line makes no sense - "cc -shared -c", "cc -c anything.o", and "-o > something" being missing anyway. > > -- > Atro Tossavainen (Mr.) / The Institute of > Biotechnology at > Systems Analyst, Techno-Amish & / the University of > Helsinki, Finland, > +358-9-19158939 UNIX Dinosaur / employs me, but my > opinions are my own. > < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE > ATTACHMENTS > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; dat=121642 > _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
