VMD-L Mailing List
From: Pieter van 't Hof (pieter.van.t.hof_at_logica.com)
Date: Tue Dec 01 2009 - 03:40:05 CST
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Hi Rich,
When I had to build VMD I ran into quite some errors myself. I found a
pretty good step-by-step guide here:
http://debianclusters.cs.uni.edu/index.php/NAMD:_Building_vmd
Using this guide I managed to compile VMD :) Maybe it can help you to.
Good luck,
Pieter
-----Original Message-----
From: Dipesh Bhattarai <dipesh.bhattarai_at_gmail.com>
To: Rich Cook <rcook_at_llnl.gov>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: building VMD is tricky -please help
Date: Mon, 30 Nov 2009 19:32:09 -0600
Hi Rich,
I faced similar problem when I tried building VMD from the source code.
>From your description, it seem, VMD is unable to find Python library in
the 'lib' directory. To take care of that problem, you will either have
to compile Python in the directory or modify the makefile so that it
points to correct python header and library files. Usually python comes
preinstalled in Linux box, so I recommend you modify the makefile
itself.
Dipesh
On Mon, Nov 30, 2009 at 5:49 PM, Rich Cook <rcook_at_llnl.gov> 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
-- Dipesh Bhattarai, PhD Please help Logica to respect the environment by not printing this email / Pour contribuer comme Logica au respect de l'environnement, merci de ne pas imprimer ce mail / Bitte drucken Sie diese Nachricht nicht aus und helfen Sie so Logica dabei, die Umwelt zu sch|tzen. / Por favor ajude a Logica a respeitar o ambiente nao imprimindo este correio electronico. This e-mail and any attachment is for authorised use by the intended recipient(s) only. It may contain proprietary material, confidential information and/or be subject to legal privilege. It should not be copied, disclosed to, retained or used by, any other party. If you are not an intended recipient then please promptly delete this e-mail and any attachment and all copies and inform the sender. Thank you.
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