From: Susana Tomasio (susietomasio_at_gmail.com)
Date: Wed Mar 02 2011 - 09:40:13 CST

Hi,

Thank you for your help.
I'm still stuck in the plugins compilation step.
A directory called vmd was created in /usr/local/lib and includes a plugins
directory
which includes the directories LINUX, WIN32, include and noarch. But no
molfile directory with
libmolfile_plugin.a and libmolfile_plugin.h files was created.

Thank you,

Susana

On Tue, Mar 1, 2011 at 6:32 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>