VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 01 2009 - 18:31:54 CST

On Tue, 2009-12-01 at 15:50 -0800, Rich Cook wrote:
> I guess I should share that I'm building from source because the
> binary installation did not work for me. We install on our clusters,
> and when I display back to my Mac workstation, it crashed my entire
> machine, quite an impressive feat! I'm hoping a source build changes
> things, as I can then pick and choose which modules to include.

rich,
that sounds much more like your mac is to blame than anything else.
i don't think that building from source will help much. for the most
part it is either the remote machine sending garbage or the local
machine crashing on being handed garbage that would be the reason.

as an additional option to john's effort, you can perhaps take some
hints from the attached fedora .spec file as to how you could build
VMD from source using the locally installed libraries.

cheers,
   axel.

>
> On Dec 1, 2009, at 12:03 PM, John Stone wrote:
>
> >
> > Rich,
> > I'll go ahead and add new environment variables for the Python stuff
> > since a lot of people end up building from source in order to
> > integrate
> > VMD with their favorite Python version and Python library
> > installation.
> >
> > Are you doing your builds from CVS, or from the source tarballs for
> > the
> > official release? I can send you a note when I've modified the
> > configure
> > script to enable the environment variable overrides and committed it
> > to CVS.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Dec 01, 2009 at 11:59:29AM -0800, Rich Cook wrote:
> >> Thanks, that's helpful. It would be great if this stuff could be
> >> done
> >> from the command line, as you can see I automate things to deploy on
> >> more than one machine, and hand-editing files is a non-starter in
> >> this
> >> environment -- I end up writing sed scripts to take care of it.
> >>
> >> But thanks again for the information.
> >>
> >> On Dec 1, 2009, at 8:05 AM, John Stone wrote:
> >>
> >>>
> >>> Hi,
> >>> The standard VMD 'configure' script expects all of the libraries
> >>> to be found in vmd/lib rather than in /usr/local or other locations.
> >>> We do this because when we build VMD here we have to have strict
> >>> control
> >>> over which versions of the various libraries we are linking against,
> >>> and
> >>> this prevents us from accidentally picking up a bad version of Tcl,
> >>> Python,
> >>> or FLTK from the /usr/local tree on system we're compiling on.
> >>>
> >>> You can redirect the VMD compilation to use whatever directory
> >>> structure
> >>> you like by editing the appropriate lines in the 'configure' script
> >>> prior to generating the makefiles etc. Look in the 'configure'
> >>> script
> >>> starting on line 1027 and you'll see where the default Python
> >>> include
> >>> and linkage paths are set. You can simply edit those directory
> >>> paths
> >>> and you should be in business. This is often simpler than manually
> >>> editing
> >>> the makefile that the configure script generates, although that
> >>> approach
> >>> would work equally well if you're more comfortable with it.
> >>>
> >>> For Tcl/Tk we allow overriding default paths with the use of a few
> >>> environment variables (see line 22-31 in the 'configure' script).
> >>> If people would find it helpful, I could add logic to allow the same
> >>> kinds of overrides for Python and other libraries that are often
> >>> part
> >>> of the default OS install.
> >>>
> >>> Let me know if you have more questions.
> >>>
> >>> Cheers,
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>
> >>> On Mon, Nov 30, 2009 at 03:49:23PM -0800, Rich Cook wrote:
> >>>> Hello,
> >>>>
> >>>> I am using the below script to install VMD 1.8.7. I'm almost
> >>>> there,
> >>>> but the build seems to be unable to find the python library. Can
> >>>> some
> >>>> wise person here help me? I find the build instructions to be
> >>>> confusing and incomplete. Thanks for any help or pointers to
> >>>> additional info.
> >>>>
> >>>> Here is my machine info:
> >>>> rcook_at_zeus287 (src): uname -a
> >>>> Linux zeus287 2.6.18-76chaos #1 SMP Fri Aug 14 13:22:06 EDT 2009
> >>>> x86_64 x86_64 x86_64 GNU/Linux
> >>>>
> >>>> Do I need to download and install Python 2.5 in the vmd-1.8.7
> >>>> directory to get it in there?
> >>>> Here is the installation script:
> >>>> #
> >>>> =
> >>>> =
> >>>> ===================================================================
> >>>> # begin installation script for vmd
> >>>> #!/usr/bin/env bash
> >>>> if ! . $HOME/RC_bash_lib/shellfuncs.sh; then
> >>>> echo "need shellfuncs, time to exit, bye bye"
> >>>> exit 1
> >>>> fi
> >>>>
> >>>> set -x
> >>>> cd /usr/global/tools/vmd/1.8.7
> >>>>
> >>>> rm -rf $SYS_TYPE/{src,bin,lib}
> >>>> mkdir -p $SYS_TYPE/src
> >>>> cd $SYS_TYPE
> >>>> [ -d Tcl ] || errexit "You must have Tcl installed in $(pwd)/Tcl"
> >>>>
> >>>> cd src
> >>>> tar -xvzf /usr/global/tools/vmd/1.8.7/tarballs/vmd-1.8.7.src.tar.gz
> >>>>
> >>>> echo "============================================================"
> >>>> echo "First the plugins have to be built"
> >>>> cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/plugins
> >>>> gmake LINUXAMD64 TCLINC=-I/usr/global/tools/vmd/1.8.7/$SYS_TYPE/
> >>>> Tcl/
> >>>> include TCLLIB=-L/usr/global/tools/vmd/1.8.7/$SYS_TYPE/Tcl/lib/
> >>>> export PLUGINDIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/
> >>>> vmd-1.8.7/
> >>>> plugins
> >>>> gmake distrib
> >>>>
> >>>> echo "============================================================"
> >>>> echo "Now build SURF"
> >>>> cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/vmd-1.8.7/lib/surf
> >>>> uncompress surf.tar.Z -c | tar -xv || errexit "could not untar surf
> >>>> library"
> >>>> gmake depend
> >>>> gmake
> >>>> mv surf surf_LINUXAMD64
> >>>>
> >>>> echo "============================================================"
> >>>> echo "Now make Fltk"
> >>>> cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/
> >>>> tar -xvzf /usr/global/tools/vmd/1.8.7/tarballs/fltk-1.1.10rc3-
> >>>> source.tar.gz
> >>>> cd fltk-1.1.10rc3 || errexit "cannot cd to fltk directory"
> >>>> ./configure --prefix=/usr/global/tools/vmd/1.8.7/$SYS_TYPE
> >>>> gmake
> >>>> gmake install || errexit "Cannot build Fltk library"
> >>>>
> >>>> echo "============================================================"
> >>>> echo "Now the main thing can be built"
> >>>> cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/vmd-1.8.7
> >>>> sedfiles -e "s:install_bin_dir=\"/usr/local/bin\":install_bin_dir=
> >>>> \"/
> >>>> usr/global/tools/vmd/1.8.7/$SYS_TYPE/bin\":" -e
> >>>> "s:install_library_dir=
> >>>> \"/usr/local/lib:install_library_dir=\"/usr/global/tools/vmd/
> >>>> 1.8.7/$SYS_TYPE/lib:" configure
> >>>> chmod 775 configure
> >>>> export TCL_INCLUDE_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//
> >>>> include
> >>>> export TCL_LIBRARY_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//lib
> >>>> export TK_INCLUDE_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//
> >>>> include
> >>>> export TK_LIBRARY_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//lib
> >>>>
> >>>> ./configure LINUXAMD64 OPENGL FLTK ACTC NETCDF TK TCL PYTHON NUMPY
> >>>> PTHREADS LP64 PTHREADS NOSILENT
> >>>> cd src
> >>>> gmake # <--------- this fails
> >>>> gmake install
> >>>>
> >>>> # end vmd installation script
> >>>> #=============================================================
> >>>> Here is the error:
> >>>>
> >>>> g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-
> >>>> math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDGRAPHICS -DVMDACTC -
> >>>> DVMDPYTHON -DVMDTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -DVMDNUMPY -
> >>>> DVMDORBITALS -DVMDWITHORBITALS -DVMDWITHCARBS -DVMDPOLYHEDRA -
> >>>> DVMDSURF
> >>>> -DVMDMSMS -DVMDFIELDLINES -DVMDPBCSMOOTH -DVMDTCL -DVMDTK -
> >>>> DVMDSTATICPLUGINS -DVMDGUI -DVMDFLTK -I../lib/actc/include -I../
> >>>> lib/
> >>>> python/lib_LINUXAMD64/include/python2.5 -I../lib/numpy/
> >>>> lib_LINUXAMD64/
> >>>> include -I../lib/python/lib_LINUXAMD64/lib/python2.5/site-packages/
> >>>> numpy/core/include -I/usr/global/tools/vmd/1.8.7/
> >>>> chaos_4_x86_64_ib//
> >>>> include -I/usr/global/tools/vmd/1.8.7/chaos_4_x86_64_ib//include -
> >>>> I../
> >>>> plugins/include -I../plugins/LINUXAMD64/molfile -I../lib/netcdf/
> >>>> include -I../lib/fltk/include -I. -c PythonTextInterp.C -o ../
> >>>> LINUXAMD64/PythonTextInterp.o
> >>>> Compiling PythonTextInterp.C --> PythonTextInterp.o ...
> >>>> In file included from PythonTextInterp.C:21:
> >>>> py_commands.h:28:20: error: Python.h: No such file or directory
> >>>> PythonTextInterp.C:32:21: error: errcode.h: No such file or
> >>>> directory
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> /* A function that takes a single integer argument and returns
> >>>> a pointer to a function that takes two integer arguments and
> >>>> returns a floating-point number. */
> >>>> float (*func2(int a))(int, int);
> >>>> Rich Cook
> >>>> rcook_at_llnl.gov
> >>>>
> >>>>
> >>>>
> >>>
> >>> --
> >>> NIH Resource for Macromolecular Modeling and Bioinformatics
> >>> Beckman Institute for Advanced Science and Technology
> >>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >>> WWW: http://**www.**ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >>>
> >>
> >>
> >> /* A function that takes a single integer argument and returns
> >> a pointer to a function that takes two integer arguments and
> >> returns a floating-point number. */
> >> float (*func2(int a))(int, int);
> >> Rich Cook
> >> rcook_at_llnl.gov
> >>
> >>
> >>
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://*www.*ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> /* A function that takes a single integer argument and returns
> a pointer to a function that takes two integer arguments and
> returns a floating-point number. */
> float (*func2(int a))(int, int);
> Rich Cook
> rcook_at_llnl.gov
>
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.