VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Mon Nov 30 2009 - 17:49:23 CST

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