VMD-L Mailing List

From: Susana Tomasio (susietomasio_at_gmail.com)
Date: Wed Mar 02 2011 - 10:14:31 CST

Hi John,

No, there isn't. There is a LINUX/tcl subdirectory which includes an
intersurf1.1 directory.

I guess the plugin tree wasn't sucessfully build.

Cheers,

Susana

On Wed, Mar 2, 2011 at 4:07 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Susana,
> There isn't a LINUX/molfile subdirectory? When I build the plugin
> tree successfully and run the "make distrib" step, I get the library
> file within a molfile subdirectory contained by the target architecture
> directory:
> LINUX/molfile/libmolfile_plugin.a
>
> Cheers,
> John
>
> On Wed, Mar 02, 2011 at 03:40:13PM +0000, Susana Tomasio wrote:
> > 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
>
> --
> 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
>