VMD-L Mailing List

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,
>> > > áAlthough VMD ships with the dynamically loadable plugins, those
>> > > would be difficult to use from Fortran. áI 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,
>> > > áJohn Stone
>> > > ávmd_at_ks.uiuc.edu
>> > >
>> > > On Tue, Mar 01, 2011 at 04:34:35PM +0000, Susana Tomasio wrote:
>> > >> á áHi John,
>> > >>
>> > >> á áThank you for your reply.
>> > >> á áI do have a directory with the molfile plugins which was created
>> > >> when I
>> > >> á áinstalled vmd.
>> > >> á áIt includes the .so files such as xyzplugin.so, moldenplugin.so
>> > >> etc. But
>> > >> á áthe files molfile_plugin.h and
>> > >> á ávmdplugin.h are in a different directory.
>> > >>
>> > >> á áThank you,
>> > >>
>> > >> á áSusana
>> > >>
>> > >> á áOn Tue, Mar 1, 2011 at 4:24 PM, John Stone <johns_at_ks.uiuc.edu>
>> > >> wrote:
>> > >>
>> > >> á á áHi Susana,
>> > >> á á á Before you compile the Fortran bindings, you'll have to have
>> > >> á á áalready compiled the plugins themselves. áDid you compile the
>> > >> plugins
>> > >> á á ábefore trying to compile the Fortran bindings? áIf so, there
>> > >> should be a
>> > >> á á á"compile" subdirectory in your plugin tree containing the plugin
>> > >> á á álibraries
>> > >> á á áand header files, which is the first step in the process to
>> > >> linking them
>> > >> á á áinto
>> > >> á á áyour Fortran code.
>> > >>
>> > >> á á áCheers,
>> > >> á á á John Stone
>> > >> á á á vmd_at_ks.uiuc.edu
>> > >>
>> > >> á á áOn Tue, Mar 01, 2011 at 04:16:18PM +0000, Susana Tomasio wrote:
>> > >> á á á> á áHi,
>> > >> á á á>
>> > >> á á á> á áI'm trying to compile the Fortran bindings for the VMD
>> > >> molfile
>> > >> á á áplugins of
>> > >> á á á> á áAxel Kohlmeyer on a MacOSX Snow Leopard.
>> > >> á á á> á áI have edited the Makefile to include the architecture and
>> > >> the c
>> > >> á á áand
>> > >> á á á> á áfortran compilers. I also edited NETCDFLIB to include the
>> > >> location
>> > >> á á á> á áof netcdf.
>> > >> á á á> á áThis is how the config section of my Makefile looks like:
>> > >> á á á>
>> > >> á á á>
>> > >> á á á
>> > >> ########################################################################
>> > >> á á á> á áARCH á á á á á = MACOSX86-64
>> > >> á á á> á áARCHDIR á á á á= /Applications/VMD\
>> > >> á á á> á á1.8.7.app/Contents/vmd/plugins/include/
>> > >> á á á> á áFC á á á á á á = g77
>> > >> á á á> á á#FC á á á á á á = g77
>> > >> á á á> á á#-fno-second-underscore
>> > >> á á á> á áCC á á á á á á = gcc
>> > >> á á á> á áLD á á á á á á = $(FC)
>> > >> á á á> á áOPT á á á á á á= -O2 -Wall
>> > >> á á á> á áCPPFLAGS á á á = -I../../include -I$(ARCHDIR) #
>> > >> á á á> á á-D_F77_F2C_UNDERSCORE
>> > >> á á á> á áCFLAGS á á á á = -c $(CPPFLAGS) $(OPT)
>> > >> á á á> á áFFLAGS á á á á = -c $(OPT)
>> > >> á á á> á áNETCDFLIB á á á= -L/opt/local/var/macports/software/netcdf/
>> > >> á á á> á á#/usr/lib64/netcdf-3
>> > >> á á á> á áNETCDFLDFLAGS á= -lnetcdf
>> > >> á á á> á áTCLLIB á á á á =
>> > >> á á á> á áTCLLDFLAGS á á = -ltcl8.4
>> > >> á á á> á áLDFLAGS á á á á= -L$(ARCHDIR) $(TCLLIB) $(NETCDFLIB)
>> > >> á á á> á áLDLIBS á á á á = -lmolfile_plugin $(NETCDFLDFLAGS)
>> > >> $(TCLLDFLAGS)
>> > >> á á á-lstdc++
>> > >> á á á> á á-ldl
>> > >> á á á>
>> > >> á á á
>> > >> ########################################################################
>> > >> á á á>
>> > >> á á á> á áI also copied the files molfile_plugin.h, vmdplugin.h and
>> > >> á á á> á álibmolfile_plugin.h to my working directory.
>> > >> á á á>
>> > >> á á á> á áWhen I typed "make" I got the following:
>> > >> á á á>
>> > >> á á á> á ág77 -c -O2 -Wall tester.f -o tester.o
>> > >> á á á> á ágcc -c -I../../include -I/Applications/VMD\
>> > >> á á á> á á1.8.7.app/Contents/vmd/plugins/include/ á-O2 -Wall
>> > >> f77_molfile.c -o
>> > >> á á á> á áf77_molfile.o
>> > >> á á á> á ág77 -o tester -L/Applications/VMD\
>> > >> á á á> á á1.8.7.app/Contents/vmd/plugins/include/
>> > >> á á á> á á-L/opt/local/var/macports/software/netcdf/ á átester.o
>> > >> á á áf77_molfile.o
>> > >> á á á> á á-lmolfile_plugin -lnetcdf -ltcl8.4 -lstdc++ -ldl
>> > >> á á á> á áld: library not found for -lmolfile_plugin
>> > >> á á á> á ácollect2: ld returned 1 exit status
>> > >> á á á> á ámake: *** [tester] Error 1
>> > >> á á á>
>> > >> á á á> á áI don't understand this error. It looks like it cannot find
>> > >> á á á> á á-lmolfile_plugin. But I don't think that there is such
>> > >> file.
>> > >> á á á>
>> > >> á á á> á áI would be grateful if anyone could help me with this.
>> > >> á á á>
>> > >> á á á> á áThank you.
>> > >> á á á>
>> > >> á á á> á áKind regards,
>> > >> á á á>
>> > >> á á á> á áSusana
>> > >> á á á--
>> > >> á á áNIH Resource for Macromolecular Modeling and Bioinformatics
>> > >> á á áBeckman Institute for Advanced Science and Technology
>> > >> á á áUniversity of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > >> á á áEmail: johns_at_ks.uiuc.edu á á á á á á á á Phone: 217-244-3349
>> > >> á á á WWW: http://www.ks.uiuc.edu/~johns/ á á áFax: 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 á á á á á á á á Phone: 217-244-3349
>> > > áWWW: http://www.ks.uiuc.edu/~johns/ á á áFax: 217-244-6078
>> > >
>> >
>> >
>> >
>> > --
>> > Dr. Axel Kohlmeyer
>> > akohlmey_at_gmail.com áhttp://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.