VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 02 2011 - 12:46:57 CST

See if you got any errors during the plugin compilation before you
run the "make distrib" step. If you have questions, let me know.

Cheers,
  John

On Wed, Mar 02, 2011 at 04:14:31PM +0000, Susana Tomasio wrote:
> 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 

-- 
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