From: Susana Tomasio (susietomasio_at_gmail.com)
Date: Tue Mar 01 2011 - 11:50:03 CST

Hi,

How can I check that my plugin compilation was successful?

This is what I did:

I downloaded vmd soure code (vmd-1.8.7-src.tar.gz)

tar -zxvf vmd-1.8.7.src.tar.gz
cd plugins
tcsh
setenv TCLINC -I/usr/include/tcl
setenv TCLLIB -F/usr/lib/
setenv OSARCH MACOSXX86
make clean
make $OSARCH TCLINC=-I/usr/include/tcl TCLLIB=-F/usr/lib/
sudo make distrib PLUGINDIR=/usr/local/lib/vmd/plugins

Cheers,

Susana

On Tue, Mar 1, 2011 at 5:28 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Axel,
> Yes, in principle one could use the dynamic plugins, but without
> the necessary loading infrastructure implemented, it's not what I'd suggest
> for someone just getting started. This is exactly why I said "it would be
> difficult", since one would first have to write the loading code. ;-)
>
> This will likely be solved in an upcoming version of the plugin tree
> later this summer, as I need the dynamic loading mechanism to be easy
> to incorporate into other plugins (like psfgen). When implemented,
> it also take care of the Fortran case too.
>
> Cheers,
> John
>
> On Tue, Mar 01, 2011 at 12:23:36PM -0500, Axel Kohlmeyer wrote:
> > On Tue, Mar 1, 2011 at 11:38 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > >
> > > Susana,
> > > Although VMD ships with the dynamically loadable plugins, those
> > > would be difficult to use from Fortran. I think you will find it
> >
> > john,
> >
> > since the fortran warppers are written in C, there is no principal
> difference
> > to load shared objects instead of the static plugins between the fortran
> > wrappers and VMD itself. it is only that i didn't write code for
> registering
> > them in addition to the static ones. lazyness, i guess.
> >
> > cheers,
> > axel.
> >
> > > much easier to compile the VMD plugins from source code and use the
> > > statically linkable version, "libmolfile_plugin.a", that is built
> > > when you compile the plugins yourself.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Tue, Mar 01, 2011 at 04:34:35PM +0000, Susana Tomasio wrote:
> > >> Hi John,
> > >>
> > >> Thank you for your reply.
> > >> I do have a directory with the molfile plugins which was created
> when I
> > >> installed vmd.
> > >> It includes the .so files such as xyzplugin.so, moldenplugin.so
> etc. But
> > >> the files molfile_plugin.h and
> > >> vmdplugin.h are in a different directory.
> > >>
> > >> Thank you,
> > >>
> > >> Susana
> > >>
> > >> On Tue, Mar 1, 2011 at 4:24 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > >>
> > >> Hi Susana,
> > >> Before you compile the Fortran bindings, you'll have to have
> > >> already compiled the plugins themselves. Did you compile the
> plugins
> > >> before trying to compile the Fortran bindings? If so, there
> should be a
> > >> "compile" subdirectory in your plugin tree containing the plugin
> > >> libraries
> > >> and header files, which is the first step in the process to
> linking them
> > >> into
> > >> your Fortran code.
> > >>
> > >> Cheers,
> > >> John Stone
> > >> vmd_at_ks.uiuc.edu
> > >>
> > >> On Tue, Mar 01, 2011 at 04:16:18PM +0000, Susana Tomasio wrote:
> > >> > Hi,
> > >> >
> > >> > I'm trying to compile the Fortran bindings for the VMD
> molfile
> > >> plugins of
> > >> > Axel Kohlmeyer on a MacOSX Snow Leopard.
> > >> > I have edited the Makefile to include the architecture and
> the c
> > >> and
> > >> > fortran compilers. I also edited NETCDFLIB to include the
> location
> > >> > of netcdf.
> > >> > This is how the config section of my Makefile looks like:
> > >> >
> > >> >
> > >>
> ########################################################################
> > >> > ARCH = MACOSX86-64
> > >> > ARCHDIR = /Applications/VMD\
> > >> > 1.8.7.app/Contents/vmd/plugins/include/
> > >> > FC = g77
> > >> > #FC = g77
> > >> > #-fno-second-underscore
> > >> > CC = gcc
> > >> > LD = $(FC)
> > >> > OPT = -O2 -Wall
> > >> > CPPFLAGS = -I../../include -I$(ARCHDIR) #
> > >> > -D_F77_F2C_UNDERSCORE
> > >> > CFLAGS = -c $(CPPFLAGS) $(OPT)
> > >> > FFLAGS = -c $(OPT)
> > >> > NETCDFLIB = -L/opt/local/var/macports/software/netcdf/
> > >> > #/usr/lib64/netcdf-3
> > >> > NETCDFLDFLAGS = -lnetcdf
> > >> > TCLLIB =
> > >> > TCLLDFLAGS = -ltcl8.4
> > >> > LDFLAGS = -L$(ARCHDIR) $(TCLLIB) $(NETCDFLIB)
> > >> > LDLIBS = -lmolfile_plugin $(NETCDFLDFLAGS)
> $(TCLLDFLAGS)
> > >> -lstdc++
> > >> > -ldl
> > >> >
> > >>
> ########################################################################
> > >> >
> > >> > I also copied the files molfile_plugin.h, vmdplugin.h and
> > >> > libmolfile_plugin.h to my working directory.
> > >> >
> > >> > When I typed "make" I got the following:
> > >> >
> > >> > g77 -c -O2 -Wall tester.f -o tester.o
> > >> > gcc -c -I../../include -I/Applications/VMD\
> > >> > 1.8.7.app/Contents/vmd/plugins/include/ -O2 -Wall
> f77_molfile.c -o
> > >> > f77_molfile.o
> > >> > g77 -o tester -L/Applications/VMD\
> > >> > 1.8.7.app/Contents/vmd/plugins/include/
> > >> > -L/opt/local/var/macports/software/netcdf/ tester.o
> > >> f77_molfile.o
> > >> > -lmolfile_plugin -lnetcdf -ltcl8.4 -lstdc++ -ldl
> > >> > ld: library not found for -lmolfile_plugin
> > >> > collect2: ld returned 1 exit status
> > >> > make: *** [tester] Error 1
> > >> >
> > >> > I don't understand this error. It looks like it cannot find
> > >> > -lmolfile_plugin. But I don't think that there is such file.
> > >> >
> > >> > I would be grateful if anyone could help me with this.
> > >> >
> > >> > Thank you.
> > >> >
> > >> > Kind regards,
> > >> >
> > >> > Susana
> > >> --
> > >> 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
> > >
> > > --
> > > 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
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
>
> --
> 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
>