From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 01 2011 - 12:33:03 CST

On Tue, Mar 1, 2011 at 12:50 PM, Susana Tomasio <susietomasio_at_gmail.com> wrote:
> Hi,
>
> How can I check that my plugin compilation was successful?

you should find the libmolfile_plugin.a and libmolfile_plugin.h
files in /usr/local/lib/vmd/plugins/MACOSXX86/molfile/

cheers,
    axel.

>
> 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
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.