VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 03 2011 - 13:28:03 CST

Hi Susana,
  You would want to set the TCLINC and TCLLIB paths to the locations
of your locally installed Tcl library, e.g. the one in /usr/share or /usr/lib,
or wherever. You don't have to compile with NetCDF if you don't want to,
the Makefile will skip compiling the netcdfplugin if you don't define
the associated environment variables. At present I think the Makefile
assumes Tcl, so you should probably define that one. I will see about
changing that to make this kind of compilation of the plugin tree easier
for people in the future.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 03, 2011 at 11:15:58AM +0000, Susana Tomasio wrote:
> Thank you for your help.
>
> I think the problem is that I'm not setting the paths correctly.
>
> I am following these instructions:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html#compiling
>
> I am not sure what are these paths:
>
> ## MacOS X 10.2 framework paths used at UIUC
> setenv TCLINC -I/Projects/vmd/vmd/lib/tcl/include
> setenv TCLLIB -F/Projects/vmd/vmd/lib/tcl
>
> I have got several tcl directories but none
> in vmd/vmd/lib/tcl/include.
> I do have a tcl directoru which is in my vmd installation which is in
> /Applications/VMD 1.8.7.app/Contents/vmd/plugins/MACOSXX86/tcl
> but it doesn't include an include directory. I also have a tcl directory
> in
> /usr/share/1.3.31/tcl
>
> Do we need netcdf in a macosx?
>
> Thank you,
>
> Susana
>
> On Wed, Mar 2, 2011 at 6:46 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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 

-- 
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