VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 14 2010 - 16:44:32 CST

Rich,
  My AIX builds are based on AIX 6.1 on the NCSA "BluePrint" Blue Waters
software testbed machine here at Illinois. I'm using Tcl 8.5.6 and I
compiled everything from source myself. When I compiled Tcl from
source, I had to workaround a bug in the Tcl stack space checking
that causes problems on AIX, documented here:
  http://old.nabble.com/--tcl-Bugs-1889719---Stack-space-check-fails-on-AIX-td18235084.html
 
For both VMD and NAMD, we compiled Tcl on this AIX 6.x box
using configure flags (approximately) like these:

define CFLAGS="-DTCL_NO_STACK_CHECK=1" at configure time, or edit the
makefile to add that definition.

env CC=xlc CFLAGS="-DTCL_NO_STACK_CHECK=1" --prefix=$HOME/tcl85
--disable-threads --disable-shared

I don't know if using xlc_r matters if you're just linking the library to
code that could use pthreadds.

More info on AIX stacks: https://computing.llnl.gov/mpi/aix_stack.html

You may want "-bmaxdata:0x80000000" at link time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 14, 2010 at 01:02:33PM -0800, Rich Cook wrote:
> We can also turn this around and let me ask you, what version of Tcl/
> Tk did you build against? I don't know what difference the AIX
> version would make.
>
> On Jan 11, 2010, at 5:24 PM, Rich Cook wrote:
>
> >Hello,
> >I have been on the injured list for a bit and am just getting back
> >to you. It would be cool to meet you sometime if you ever do drop by.
> >Here is I think the info you need. I have forgotton how to get the
> >AIX version information.
> >
> >rcook_at_up041 (src): uname -a
> >AIX up041 3 5 00C5D6DD4C00
> >It's AIX 5.something
> >
> >Tcl and Tk are both 8.5.8
> >
> >On Dec 30, 2009, at 11:03 AM, John Stone wrote:
> >
> >>
> >>Hi Rich,
> >>I just got back from your neck of the woods. I passed
> >>through Livermore twice last week while I was out in California
> >>visiting relatives. Someday I'll have to make a point to visit
> >>the lab and some of the people I know there when I'm out that way.
> >>
> >>Which version of AIX is your machine using? My builds on an AIX 6.x
> >>test machine at NCSA didn't have any of these problems. I compiled
> >>the Tcl/Tk libraries for myself, but I didn't use any particularly
> >>unusual build flags for those compiles. In the past with certain
> >>versions
> >>of AIX and xlc I have had to do things like override the
> >>compilation flags
> >>to reduce optimization in order to get a stable build, but in my
> >>recent
> >>builds on the AIX 6.x machine at NCSA I didn't need to do this.
> >>If you can tell me which exact Tcl/Tk minor version you're using,
> >>I can try doing a build of the same rev and see if this is a problem
> >>with Tcl itself or an interaction with VMD and Tcl.
> >>
> >>Cheers,
> >>John Stone
> >>vmd_at_ks.uiuc.edu
> >>
> >>On Thu, Dec 17, 2009 at 06:08:08PM -0800, Rich Cook wrote:
> >>>Yes, I have already done that and can give you any info you need.
> >>>
> >>>On Dec 17, 2009, at 5:52 PM, John Stone wrote:
> >>>
> >>>>
> >>>>Rich,
> >>>>I thought it was crashing in a Tk call, but I don't have your
> >>>>traceback in front of me, so that was my vague recollection. If it
> >>>>is dying in Tcl itself, then we're going to have to figure out what
> >>>>is actually going on there. Can you recompile your Tcl/Tk library
> >>>>with
> >>>>debugging symbols enabled (i.e. by adding -g to the compilation
> >>>>flags)?
> >>>>
> >>>>Cheers,
> >>>>John
> >>>>
> >>>>On Thu, Dec 17, 2009 at 05:35:12PM -0800, Rich Cook wrote:
> >>>>>It crashes when I disable Tk in the same place as before. I'm
> >>>>>confused, because you are telling me to disable Tk but it is
> >>>>>crashing
> >>>>>in a Tcl call. Is that intentional? I'm recompiling without Tcl
> >>>>>and
> >>>>>without Tk just to see what happens...
> >>>>>
> >>>>
> >>>>--
> >>>>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
> >
> >
> >
> >
>
>
> /* 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