VMD-L Mailing List

From: Susana Tomasio (susietomasio_at_gmail.com)
Date: Tue Mar 01 2011 - 10:53:49 CST

Thank you for your message.

I don't have much experience compiling VMD plugins from source codes.

Are these instructions okay:

http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

Thank you,

Susana

On Tue, Mar 1, 2011 at 4:38 PM, 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
> 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
>