VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Tue Dec 01 2009 - 13:59:29 CST

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