VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Wed Dec 02 2009 - 13:26:42 CST

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