VMD-L Mailing List

From: Woodson, Michael (miwoodso_at_UTMB.EDU)
Date: Thu Oct 23 2014 - 13:15:05 CDT

Hi Josh, I am not using a script to compile and install vmd. I was not using any options for configuring the plugins directory, or for make distrib. I tried mimicking the options in your script, but I still have the same problem.
In the past, I had strange problems when past versions hadn't been uninstalled completely, so I wonder if there might be a problem with previous installations, but I don't know what to do other than delete the /usr/local/lib/vmd directory and /usr/local/bin/vmd
________________________________
From: Josh Vermaas [vermaas2_at_illinois.edu]
Sent: Thursday, October 23, 2014 12:13 PM
To: Woodson, Michael; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Extensions menu empty

Hi Mike,

What were your configure options or the options for make distrib? My understanding is that the extensions menu items are a compile-time feature, and if they weren't in place properly during compilation, the VMD build will happily (try to) work without any extensions. Your .vmdrc lines may ameliorate the situation somewhat (possibly, I've never tested this) by providing the facilities so the commands in the terminal, but it won't change the extensions menu in my experience. This is not the optimal setup, and if I had to make an educated guess, make distrib didn't put the plugins where the main program expects them, but this normally causes the compilation to halt on missing molfiles, so I'm not sure what the issue is specifically. This is my compile and install makefile (adapted for not making debian packages) that is placed in the directory *above* the plugins and the source vmd directory during compilation. See if this helps at all to sort out what might be missing:

DESTDIR=$(shell pwd)
VMDVER="1.9.2beta1"
#These are the final install locations
PLUGINDIR=/usr/local/lib/vmd/plugins
PLUGINBINDIR=/usr/local/bin
export

all: compileplugins compilevmd

compileplugins:
    cd plugins; make LINUXAMD64 TCLINC=-I/usr/include/tcl8.6 TCLLIB=-L/usr/lib \
    NETCDFLIB=-L/usr/lib NETCDFINC=-I/usr/include/ -j 1 ; make distrib PLUGINDIR=$(DESTDIR)/vmd-$(VMDVER)/plugins

compilevmd:
    cd vmd-$(VMDVER); \
    ./configure LINUXAMD64 OPENGL FLTK TK ACTC XINERAMA LIBTACHYON NETCDF TCL PYTHON PTHREADS NUMPY COLVARS CUDA LIBOPTIX ; \
    cd src ; make

installplugins:
    cd plugins ; make distrib

installvmd:
    cd src; make install

install: installplugins installvmd

Now I also needed to make changes within the configure script so VMD would pick up my system python libraries (and CUDA, and Optix, and pretty much all of the other libraries), but I think you have already done this for your own system.

Good luck!
-Josh Vermaas

On 10/23/2014 10:27 AM, Woodson, Michael wrote:
Hi, I had written in a few days ago about compiling VMD against my native python build.
I thought I had gotten it to work, but I didn't check everything, and now notice that the "Extensions" drop-down menu in the "VMD Main" window isn't populated; clicking on it just brings down a small empty frame.
I have these lines:
set auto_path [linsert $auto_path 0 [file join $env(HOME) vmdplugins]]
and
vmd_plugin_scandirectory [file join $env(HOME) vmdplugins [vmdinfo arch] molfile] *.so
in my .vmdrc file, and it looks like it is, indeed, executing those commands. The ~/vmdplugins/LINUXAMD64/molfile directory has plenty of *plugin.so files. So does the directory in the vmd installation directory.
The other menus are fine, just Extensions.
Any help figuring this out would be greatly appreciated!
Mike W.