About that "illegal instruction" error you see on SOME linux systems. (was Re: Swarm RH 8.0

[Paul E Johnson]

I've traced this problem back to some incredibly "fine grained" 
difference between CPUs and the compilation of the HDF5 library.  I 
shipped a description to the hdf5 team, and they could not explain it 
either. They said hdf5's configure assumes you are on an i686 platform, 
but that could not explain the problem very well in my opinion, since 
most people who see this problem tell me they have Pentium III.  It is 
easy to see that my precompiled hdf5 just won't work on a Pentium I or 
II machine, but PIII and IV should be OK.  One might be concerned about 
some athlons.  I'm beginning to suspect that this hdf5 problem is 
revealing some kind of "pentium bug".  (Once I bought a Gateway pc and 
after a couple of years I learnt that MS Excel gave bad random numbers 
because of a flaw in the CPU that Intel acknowledged but did not fix).

Here is something you could try. Download the SRPM file for hdf5

http://lark.cc.ku.edu/~pauljohn/software/hdf5-1.4.4-1RH80.src.rpm

and see if you can rebuild it on your system. If you have the settings 
so that non-root people can build RPMS, then it should be as easy as 
"rpmbuild --rebuild blah.blah.src.rpm".  It might be informative to 
install the SRPM, then try a build "rpmbuild -ba hdf5.spec" in the SPEC 
dir and, even if it fails, you will end up with the hdf5 build tree in 
your BUILD dir and you can do some experiments.  If your system is like 
the other ones I've seen, the rebuild will fail and you will get some 
error messages we (me or you) could send to the hdf5 team.

If the build fails, you could look at the spec file in the SRPM and I 
think you could add a configure flag to force it to assume you are on i386.

I just learned of this problem after I built the hdf5 rpm, and I realize 
I'm lying when my rpm is packaged with the "i386" in the title when it 
ought to be i686.

If you want to create for me an account on your system and privately 
email me the name/password, I could dig around, but I'm almost certain 
(on the basis of experience with a few other users) that the problem 
will trace back to hdf5.

On the one other machine were I have been able to test this problem 
through, I was able to successfully build Swarm without the hdf5 support 
and that user was happy enough with that build.


Triola, Marc wrote:
> Paul,
>   I am a Medical Informatics fellow at New York University School of
> Medicine.  One of my research projects involves simulating the
> transmission of organisms in our Intensive Care Unit.  I have been using
> the Easel programming language (www.cert.org/easel) with some success.
> Because of the long time it takes to complete my sims, I am strongly
> considering switching to swarm.  I am new to Linux and am running RH
> 8.0.  I downloaded your awesome rpm for 8.0 and installed it by double
> clicking (seemed almost too easy).  When I try to make the heatbugs
> files, I get the following output (below).  The subsequent executable
> that is created just gives me an 'illegal instruction' error.  Any ideas
> on what I've done wrong?
>   Thanks,
>       Marc
>
> /bin/sh /usr/bin/libtool-swarm --mode link gcc -g -O2 -march=i386
> -mcpu=i686 -L/usr/lib/swarm -rpath /usr/lib/swarm  -o heatbugs Heatbug.o
> HeatSpace.o main.o HeatbugModelSwarm.o HeatbugObserverSwarm.o
> HeatbugBatchSwarm.o  -lswarm -lobjc gcc -g -O2 -march=i386 -mcpu=i686 -o
> heatbugs Heatbug.o HeatSpace.o main.o HeatbugModelSwarm.o
> HeatbugObserverSwarm.o HeatbugBatchSwarm.o  -L/usr/lib/swarm
> /usr/lib/swarm/libswarm.so
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/space
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/analysis
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/simtoolsgui
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/simtools
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/random
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/tkobjc
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/tclobjc
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/objectbase
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/activity
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/defobj
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/collections
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/src/misc
> -L/home/pauljohn/LinuxDownloads/redhat/BUILD/swarm-2.1.141.20021019/=wit
> h-hdf/libobjc -L/usr/lib -L/usr/X11R6/lib /usr/lib/swarm/libspace.so
> /usr/lib/swarm/libanalysis.so /usr/lib/swarm/libsimtoolsgui.so
> /usr/lib/swarm/libsimtools.so /usr/lib/swarm/librandom.so
> /usr/lib/swarm/libtkobjc.so /usr/lib/swarm/libtclobjc.so
> /usr/lib/swarm/libobjectbase.so /usr/lib/swarm/libactivity.so
> /usr/lib/swarm/libdefobj.so /usr/lib/swarm/libcollections.so
> /usr/lib/swarm/libmisc.so -lBLT24 -ltk8.3 -ltcl8.3 -lXpm -lpng
> /usr/lib/libhdf5.so -lz -lX11 -lm -ldl /usr/lib/swarm/libobjc.so -lgcc
> -Wl,--rpath -Wl,/usr/lib/swarm -Wl,--rpath -Wl,/usr/lib/swarm
> -Wl,--rpath -Wl,/usr/lib -Wl,--rpath -Wl,/usr/X11R6/lib
> _________________________________________ 
> Marc M. Triola, M.D.
> New York University School of Medicine
> (212) 263-3978 
>  



--
Paul E. Johnson                       email: address@hidden
Dept. of Political Science            http://lark.cc.ku.edu/~pauljohn
1541 Lilac Lane, Rm 504
University of Kansas                  Office: (785) 864-9086
Lawrence, Kansas 66044-3177           FAX: (785) 864-5700


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