From: Albert (mailmd2011_at_gmail.com)
Date: Wed Jan 23 2013 - 12:17:49 CST

On 01/23/2013 07:12 PM, John Stone wrote:
> You need to compile the VMD plugins before compiling VMD itself.
> The missing "libmolfile_plugin.a" is the reason for the linker error
> below. Please follow the steps described in the VMD developer
> documentation, the first step listed there is compilation of the plugins,
> and doing a "make distrib" to copy them into the target directory that
> you've told VMD to look at when linking against the plugins...
> (controlled by the PLUGINDIR environment variable)
>
> Cheers,
> John Stone

thank you for kind comments.

I first put the plugin directory into vmd source code: /soft/vmd-1.91/plugin

then I do:

make LINUXAMD64

after that I configure VMD by command:

./configure LINUXAMD64 OPENGL FLTK TK CUDA IMD LIBSBALL XINERAMA XINPUT
LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT

cd src

make

Then, the make steps goes for a while until it stopped with new errors:

Linking vmd_LINUXAMD64 ...
ln: failed to create symbolic link `./foobar': File exists
/soft/python2.7/lib/python2.7/config/libpython2.7.a(posixmodule.o): In
function `posix_tmpnam':
/home/albert/Desktop/desmond/Python-2.7.3/./Modules/posixmodule.c:7432:
warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
Stride.o: In function `ss_from_stride(DrawMolecule*)':
Stride.C:(.text+0x41): warning: the use of `tempnam' is dangerous,
better use `mkstemp'
LibTachyonDisplayDevice.o: In function
`LibTachyonDisplayDevice::tex_colormaterial(float*, int)':
LibTachyonDisplayDevice.C:(.text+0x13b): undefined reference to
`rt_tex_transmode'
LibTachyonDisplayDevice.o: In function
`LibTachyonDisplayDevice::write_materials()':
LibTachyonDisplayDevice.C:(.text+0x825): undefined reference to
`rt_background_gradient'
LibTachyonDisplayDevice.o: In function
`LibTachyonDisplayDevice::define_volume_texture(int, int, int, int,
float const*, float const*, float const*, unsigned char*)':
LibTachyonDisplayDevice.C:(.text+0x1851): undefined reference to
`rt_define_teximage_rgb24'
/usr/local/cuda/lib64/libcudart.so: undefined reference to
`memcpy_at_GLIBC_2.14'
collect2: ld returned 1 exit status
make: *** [vmd_LINUXAMD64] Error 1