From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 01 2011 - 12:32:51 CST

Hi,
  If you got no compilation errors, then the static and dynamics libraries
and header files will be found in the subdirectory you targeted with
the "make distrib" step, under "MACOSXX86".

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 01, 2011 at 05:50:03PM +0000, Susana Tomasio wrote:
> 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,
> > > aAlthough VMD ships with the dynamically loadable plugins, those
> > > would be difficult to use from Fortran. aI 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,
> > > aJohn Stone
> > > avmd_at_ks.uiuc.edu
> > >
> > > On Tue, Mar 01, 2011 at 04:34:35PM +0000, Susana Tomasio wrote:
> > >> a aHi John,
> > >>
> > >> a aThank you for your reply.
> > >> a aI do have a directory with the molfile plugins which was created
> when I
> > >> a ainstalled vmd.
> > >> a aIt includes the .so files such as xyzplugin.so, moldenplugin.so
> etc. But
> > >> a athe files molfile_plugin.h and
> > >> a avmdplugin.h are in a different directory.
> > >>
> > >> a aThank you,
> > >>
> > >> a aSusana
> > >>
> > >> a aOn Tue, Mar 1, 2011 at 4:24 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> > >>
> > >> a a aHi Susana,
> > >> a a a Before you compile the Fortran bindings, you'll have to have
> > >> a a aalready compiled the plugins themselves. aDid you compile the
> plugins
> > >> a a abefore trying to compile the Fortran bindings? aIf so, there
> should be a
> > >> a a a"compile" subdirectory in your plugin tree containing the
> plugin
> > >> a a alibraries
> > >> a a aand header files, which is the first step in the process to
> linking them
> > >> a a ainto
> > >> a a ayour Fortran code.
> > >>
> > >> a a aCheers,
> > >> a a a John Stone
> > >> a a a vmd_at_ks.uiuc.edu
> > >>
> > >> a a aOn Tue, Mar 01, 2011 at 04:16:18PM +0000, Susana Tomasio
> wrote:
> > >> a a a> a aHi,
> > >> a a a>
> > >> a a a> a aI'm trying to compile the Fortran bindings for the VMD
> molfile
> > >> a a aplugins of
> > >> a a a> a aAxel Kohlmeyer on a MacOSX Snow Leopard.
> > >> a a a> a aI have edited the Makefile to include the architecture
> and the c
> > >> a a aand
> > >> a a a> a afortran compilers. I also edited NETCDFLIB to include the
> location
> > >> a a a> a aof netcdf.
> > >> a a a> a aThis is how the config section of my Makefile looks like:
> > >> a a a>
> > >> a a a>
> > >> a a a
> ########################################################################
> > >> a a a> a aARCH a a a a a = MACOSX86-64
> > >> a a a> a aARCHDIR a a a a= /Applications/VMD\
> > >> a a a> a a1.8.7.app/Contents/vmd/plugins/include/
> > >> a a a> a aFC a a a a a a = g77
> > >> a a a> a a#FC a a a a a a = g77
> > >> a a a> a a#-fno-second-underscore
> > >> a a a> a aCC a a a a a a = gcc
> > >> a a a> a aLD a a a a a a = $(FC)
> > >> a a a> a aOPT a a a a a a= -O2 -Wall
> > >> a a a> a aCPPFLAGS a a a = -I../../include -I$(ARCHDIR) #
> > >> a a a> a a-D_F77_F2C_UNDERSCORE
> > >> a a a> a aCFLAGS a a a a = -c $(CPPFLAGS) $(OPT)
> > >> a a a> a aFFLAGS a a a a = -c $(OPT)
> > >> a a a> a aNETCDFLIB a a a=
> -L/opt/local/var/macports/software/netcdf/
> > >> a a a> a a#/usr/lib64/netcdf-3
> > >> a a a> a aNETCDFLDFLAGS a= -lnetcdf
> > >> a a a> a aTCLLIB a a a a =
> > >> a a a> a aTCLLDFLAGS a a = -ltcl8.4
> > >> a a a> a aLDFLAGS a a a a= -L$(ARCHDIR) $(TCLLIB) $(NETCDFLIB)
> > >> a a a> a aLDLIBS a a a a = -lmolfile_plugin $(NETCDFLDFLAGS)
> $(TCLLDFLAGS)
> > >> a a a-lstdc++
> > >> a a a> a a-ldl
> > >> a a a>
> > >> a a a
> ########################################################################
> > >> a a a>
> > >> a a a> a aI also copied the files molfile_plugin.h, vmdplugin.h and
> > >> a a a> a alibmolfile_plugin.h to my working directory.
> > >> a a a>
> > >> a a a> a aWhen I typed "make" I got the following:
> > >> a a a>
> > >> a a a> a ag77 -c -O2 -Wall tester.f -o tester.o
> > >> a a a> a agcc -c -I../../include -I/Applications/VMD\
> > >> a a a> a a1.8.7.app/Contents/vmd/plugins/include/ a-O2 -Wall
> f77_molfile.c -o
> > >> a a a> a af77_molfile.o
> > >> a a a> a ag77 -o tester -L/Applications/VMD\
> > >> a a a> a a1.8.7.app/Contents/vmd/plugins/include/
> > >> a a a> a a-L/opt/local/var/macports/software/netcdf/ a atester.o
> > >> a a af77_molfile.o
> > >> a a a> a a-lmolfile_plugin -lnetcdf -ltcl8.4 -lstdc++ -ldl
> > >> a a a> a ald: library not found for -lmolfile_plugin
> > >> a a a> a acollect2: ld returned 1 exit status
> > >> a a a> a amake: *** [tester] Error 1
> > >> a a a>
> > >> a a a> a aI don't understand this error. It looks like it cannot
> find
> > >> a a a> a a-lmolfile_plugin. But I don't think that there is such
> file.
> > >> a a a>
> > >> a a a> a aI would be grateful if anyone could help me with this.
> > >> a a a>
> > >> a a a> a aThank you.
> > >> a a a>
> > >> a a a> a aKind regards,
> > >> a a a>
> > >> a a a> a aSusana
> > >> a a a--
> > >> a a aNIH Resource for Macromolecular Modeling and Bioinformatics
> > >> a a aBeckman Institute for Advanced Science and Technology
> > >> a a aUniversity of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > >> a a aEmail: johns_at_ks.uiuc.edu a a a a a a a a Phone: 217-244-3349
> > >> a a a WWW: http://www.ks.uiuc.edu/~johns/ a a aFax: 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 a a a a a a a a Phone: 217-244-3349
> > > aWWW: http://www.ks.uiuc.edu/~johns/ a a aFax: 217-244-6078
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com ahttp://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

-- 
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