VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 02 2009 - 13:39:53 CST

Rich,
  What version of MacOS X are you guys running? I know remote
X11/GLX display has been both broken and fixed over the years in
various revs of MacOS X. One thing I was just thinking about that
you might try checking: Are you running a 64-bit VMD and attempting
to display to a 32-bit Mac (or a 32-bit MacOS X)? It would be good to
narrow down the range of possible causes. What happens if you try a
32-bit VMD remote displaying to the Mac (if that's not already what
you're trying)? I assume both the Mac and Linux machines are x86 based?
(e.g. both ends of the connection are little-endian byte order)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 02, 2009 at 11:26:42AM -0800, Rich Cook wrote:
> Yes, clearly there is a flaw in Apple's X11, no doubt. Furthermore,
> it's a flaw in the video driver -- I had to do a "sudo reboot now". I
> tried displaying to my linux desktop and there was no problem. I'll
> see if upgrading the X11 fixes things.
> At the same time, VMD is the only app that causes this, so I suspect
> there is an error code being ignored or an assumption being made,
> followed by an ill-fated call to a non-existent routine. Naturally
> this should never crash an X11 server. But we all know X11 is not a
> pristine piece of engineering -- hell, neither is the code I write.
> Anyhow, I guess I have the source code, so I could compile in debug
> and see if I can find the instruction that causes things to go bonkers
> -- of course, the trouble is that X11 is asynchronous. Sigh.
> We have a lot of Mac users here, so this is actually relevant and not
> just a personal peeve of mine. I'll keep looking --
>
> On Dec 1, 2009, at 5:51 PM, John Stone wrote:
>
> >
> >Rich,
> > If your Mac is crashing that would indicate that you have a
> >broken video driver or that the X11 implementation on your version
> >of MacOS has a serious flaw. It should not be possible for any
> >OpenGL or X11 application to crash the windowing system, as the X11
> >server and GLX implementation are supposed to check the parameters
> >passed in through the API routines. Building VMD from source won't
> >change anything of substance unless you encountered a rare case where
> >the local host (where VMD was running) was sending garbage to the
> >remote Mac, but even this should not be capable of crashing the remote
> >system, so it would really require flaws on both ends. I can tell you
> >that remote display of VMD works fine for me on machines that have
> >functional X11 and GLX implementations. We do have a few Linux
> >machines
> >in our lab that have an X11 with broken GLX functionality,
> >but this is cured in the recent linux distros in our lab, and
> >I've never had problems on commercial Unix OSes like AIX, IRIX,
> >Solaris, though I realize these are likely not of interest to you.
> >I'm in a rush to head off for the time being, I'll reply to your
> >other emails later tonight when I get a chance.
> >
> >Cheers,
> > John
> >
> >
> >On Tue, Dec 01, 2009 at 03:50:48PM -0800, Rich Cook wrote:
> >>I guess I should share that I'm building from source because the
> >>binary installation did not work for me. We install on our clusters,
> >>and when I display back to my Mac workstation, it crashed my entire
> >>machine, quite an impressive feat! I'm hoping a source build changes
> >>things, as I can then pick and choose which modules to include.
> >>
> >>On Dec 1, 2009, at 12:03 PM, John Stone wrote:
> >>
> >>>
> >>>Rich,
> >>>I'll go ahead and add new environment variables for the Python stuff
> >>>since a lot of people end up building from source in order to
> >>>integrate
> >>>VMD with their favorite Python version and Python library
> >>>installation.
> >>>
> >>>Are you doing your builds from CVS, or from the source tarballs for
> >>>the
> >>>official release? I can send you a note when I've modified the
> >>>configure
> >>>script to enable the environment variable overrides and committed it
> >>>to CVS.
> >>>
> >>>Cheers,
> >>>John Stone
> >>>vmd_at_ks.uiuc.edu
> >>>
> >>>On Tue, Dec 01, 2009 at 11:59:29AM -0800, Rich Cook wrote:
> >>>>Thanks, that's helpful. It would be great if this stuff could be
> >>>>done
> >>>>from the command line, as you can see I automate things to deploy
> >>>>on
> >>>>more than one machine, and hand-editing files is a non-starter in
> >>>>this
> >>>>environment -- I end up writing sed scripts to take care of it.
> >>>>
> >>>>But thanks again for the information.
> >>>>
> >>>>On Dec 1, 2009, at 8:05 AM, John Stone wrote:
> >>>>
> >>>>>
> >>>>>Hi,
> >>>>>The standard VMD 'configure' script expects all of the libraries
> >>>>>to be found in vmd/lib rather than in /usr/local or other
> >>>>>locations.
> >>>>>We do this because when we build VMD here we have to have strict
> >>>>>control
> >>>>>over which versions of the various libraries we are linking
> >>>>>against,
> >>>>>and
> >>>>>this prevents us from accidentally picking up a bad version of
> >>>>>Tcl,
> >>>>>Python,
> >>>>>or FLTK from the /usr/local tree on system we're compiling on.
> >>>>>
> >>>>>You can redirect the VMD compilation to use whatever directory
> >>>>>structure
> >>>>>you like by editing the appropriate lines in the 'configure'
> >>>>>script
> >>>>>prior to generating the makefiles etc. Look in the 'configure'
> >>>>>script
> >>>>>starting on line 1027 and you'll see where the default Python
> >>>>>include
> >>>>>and linkage paths are set. You can simply edit those directory
> >>>>>paths
> >>>>>and you should be in business. This is often simpler than
> >>>>>manually
> >>>>>editing
> >>>>>the makefile that the configure script generates, although that
> >>>>>approach
> >>>>>would work equally well if you're more comfortable with it.
> >>>>>
> >>>>>For Tcl/Tk we allow overriding default paths with the use of a few
> >>>>>environment variables (see line 22-31 in the 'configure' script).
> >>>>>If people would find it helpful, I could add logic to allow the
> >>>>>same
> >>>>>kinds of overrides for Python and other libraries that are often
> >>>>>part
> >>>>>of the default OS install.
> >>>>>
> >>>>>Let me know if you have more questions.
> >>>>>
> >>>>>Cheers,
> >>>>>John Stone
> >>>>>vmd_at_ks.uiuc.edu
> >>>>>
> >>>>>
> >>>>>On Mon, Nov 30, 2009 at 03:49:23PM -0800, Rich Cook wrote:
> >>>>>>Hello,
> >>>>>>
> >>>>>>I am using the below script to install VMD 1.8.7. I'm almost
> >>>>>>there,
> >>>>>>but the build seems to be unable to find the python library. Can
> >>>>>>some
> >>>>>>wise person here help me? I find the build instructions to be
> >>>>>>confusing and incomplete. Thanks for any help or pointers to
> >>>>>>additional info.
> >>>>>>
> >>>>>>Here is my machine info:
> >>>>>>rcook_at_zeus287 (src): uname -a
> >>>>>>Linux zeus287 2.6.18-76chaos #1 SMP Fri Aug 14 13:22:06 EDT 2009
> >>>>>>x86_64 x86_64 x86_64 GNU/Linux
> >>>>>>
> >>>>>>Do I need to download and install Python 2.5 in the vmd-1.8.7
> >>>>>>directory to get it in there?
> >>>>>>Here is the installation script:
> >>>>>>#
> >>>>>>=
> >>>>>>=
> >>>>>>=
> >>>>>>=
> >>>>>>=================================================================
> >>>>>># begin installation script for vmd
> >>>>>>#!/usr/bin/env bash
> >>>>>>if ! . $HOME/RC_bash_lib/shellfuncs.sh; then
> >>>>>>echo "need shellfuncs, time to exit, bye bye"
> >>>>>>exit 1
> >>>>>>fi
> >>>>>>
> >>>>>>set -x
> >>>>>>cd /usr/global/tools/vmd/1.8.7
> >>>>>>
> >>>>>>rm -rf $SYS_TYPE/{src,bin,lib}
> >>>>>>mkdir -p $SYS_TYPE/src
> >>>>>>cd $SYS_TYPE
> >>>>>>[ -d Tcl ] || errexit "You must have Tcl installed in $(pwd)/Tcl"
> >>>>>>
> >>>>>>cd src
> >>>>>>tar -xvzf /usr/global/tools/vmd/1.8.7/tarballs/
> >>>>>>vmd-1.8.7.src.tar.gz
> >>>>>>
> >>>>>>echo
> >>>>>>"============================================================"
> >>>>>>echo "First the plugins have to be built"
> >>>>>>cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/plugins
> >>>>>>gmake LINUXAMD64 TCLINC=-I/usr/global/tools/vmd/1.8.7/$SYS_TYPE/
> >>>>>>Tcl/
> >>>>>>include TCLLIB=-L/usr/global/tools/vmd/1.8.7/$SYS_TYPE/Tcl/lib/
> >>>>>>export PLUGINDIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/
> >>>>>>vmd-1.8.7/
> >>>>>>plugins
> >>>>>>gmake distrib
> >>>>>>
> >>>>>>echo
> >>>>>>"============================================================"
> >>>>>>echo "Now build SURF"
> >>>>>>cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/vmd-1.8.7/lib/surf
> >>>>>>uncompress surf.tar.Z -c | tar -xv || errexit "could not untar
> >>>>>>surf
> >>>>>>library"
> >>>>>>gmake depend
> >>>>>>gmake
> >>>>>>mv surf surf_LINUXAMD64
> >>>>>>
> >>>>>>echo
> >>>>>>"============================================================"
> >>>>>>echo "Now make Fltk"
> >>>>>>cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/
> >>>>>>tar -xvzf /usr/global/tools/vmd/1.8.7/tarballs/fltk-1.1.10rc3-
> >>>>>>source.tar.gz
> >>>>>>cd fltk-1.1.10rc3 || errexit "cannot cd to fltk directory"
> >>>>>>./configure --prefix=/usr/global/tools/vmd/1.8.7/$SYS_TYPE
> >>>>>>gmake
> >>>>>>gmake install || errexit "Cannot build Fltk library"
> >>>>>>
> >>>>>>echo
> >>>>>>"============================================================"
> >>>>>>echo "Now the main thing can be built"
> >>>>>>cd /usr/global/tools/vmd/1.8.7/$SYS_TYPE/src/vmd-1.8.7
> >>>>>>sedfiles -e "s:install_bin_dir=\"/usr/local/bin
> >>>>>>\":install_bin_dir=
> >>>>>>\"/
> >>>>>>usr/global/tools/vmd/1.8.7/$SYS_TYPE/bin\":" -e
> >>>>>>"s:install_library_dir=
> >>>>>>\"/usr/local/lib:install_library_dir=\"/usr/global/tools/vmd/
> >>>>>>1.8.7/$SYS_TYPE/lib:" configure
> >>>>>>chmod 775 configure
> >>>>>>export TCL_INCLUDE_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//
> >>>>>>include
> >>>>>>export TCL_LIBRARY_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//lib
> >>>>>>export TK_INCLUDE_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//
> >>>>>>include
> >>>>>>export TK_LIBRARY_DIR=/usr/global/tools/vmd/1.8.7/$SYS_TYPE//lib
> >>>>>>
> >>>>>>./configure LINUXAMD64 OPENGL FLTK ACTC NETCDF TK TCL PYTHON
> >>>>>>NUMPY
> >>>>>>PTHREADS LP64 PTHREADS NOSILENT
> >>>>>>cd src
> >>>>>>gmake # <--------- this fails
> >>>>>>gmake install
> >>>>>>
> >>>>>># end vmd installation script
> >>>>>>#=============================================================
> >>>>>>Here is the error:
> >>>>>>
> >>>>>> g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-
> >>>>>>math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDGRAPHICS -DVMDACTC -
> >>>>>>DVMDPYTHON -DVMDTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -
> >>>>>>DVMDNUMPY -
> >>>>>>DVMDORBITALS -DVMDWITHORBITALS -DVMDWITHCARBS -DVMDPOLYHEDRA -
> >>>>>>DVMDSURF
> >>>>>>-DVMDMSMS -DVMDFIELDLINES -DVMDPBCSMOOTH -DVMDTCL -DVMDTK -
> >>>>>>DVMDSTATICPLUGINS -DVMDGUI -DVMDFLTK -I../lib/actc/include -
> >>>>>>I../
> >>>>>>lib/
> >>>>>>python/lib_LINUXAMD64/include/python2.5 -I../lib/numpy/
> >>>>>>lib_LINUXAMD64/
> >>>>>>include -I../lib/python/lib_LINUXAMD64/lib/python2.5/site-
> >>>>>>packages/
> >>>>>>numpy/core/include -I/usr/global/tools/vmd/1.8.7/
> >>>>>>chaos_4_x86_64_ib//
> >>>>>>include -I/usr/global/tools/vmd/1.8.7/chaos_4_x86_64_ib//
> >>>>>>include -
> >>>>>>I../
> >>>>>>plugins/include -I../plugins/LINUXAMD64/molfile -I../lib/netcdf/
> >>>>>>include -I../lib/fltk/include -I. -c PythonTextInterp.C -o ../
> >>>>>>LINUXAMD64/PythonTextInterp.o
> >>>>>>Compiling PythonTextInterp.C --> PythonTextInterp.o ...
> >>>>>>In file included from PythonTextInterp.C:21:
> >>>>>>py_commands.h:28:20: error: Python.h: No such file or directory
> >>>>>>PythonTextInterp.C:32:21: error: errcode.h: No such file or
> >>>>>>directory
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>/* A function that takes a single integer argument and returns
> >>>>>>a pointer to a function that takes two integer arguments and
> >>>>>>returns a floating-point number. */
> >>>>>>float (*func2(int a))(int, int);
> >>>>>>Rich Cook
> >>>>>>rcook_at_llnl.gov
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>--
> >>>>>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
> >>>>>
> >>>>
> >>>>
> >>>>/* A function that takes a single integer argument and returns
> >>>>a pointer to a function that takes two integer arguments and
> >>>>returns a floating-point number. */
> >>>>float (*func2(int a))(int, int);
> >>>>Rich Cook
> >>>>rcook_at_llnl.gov
> >>>>
> >>>>
> >>>>
> >>>
> >>>--
> >>>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
> >>>
> >>
> >>
> >>/* A function that takes a single integer argument and returns
> >> a pointer to a function that takes two integer arguments and
> >> returns a floating-point number. */
> >>float (*func2(int a))(int, int);
> >>Rich Cook
> >>rcook_at_llnl.gov
> >>
> >>
> >>
> >
> >--
> >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
> >
>
>
> /* A function that takes a single integer argument and returns
> a pointer to a function that takes two integer arguments and
> returns a floating-point number. */
> float (*func2(int a))(int, int);
> Rich Cook
> rcook_at_llnl.gov
>
>
> 

-- 
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