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An error in 10.6 Snow Leopard
Posted: Tue Sep 08, 2009 12:15 am
by shhong
I got the following error in 10.6
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bash$ nrniv /Applications/NEURON/nrn/share/nrn/lib/hoc/stdrun.hoc
NEURON -- Release 7.0 (285:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html
nrniv(53939) malloc: *** error for object 0x100cabe58: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap
This is compiled with
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./configure --prefix=/Applications/NEURON/nrn --with-iv=/Applications/NEURON/iv/ --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib --with-pic --with-mpi --with-nrnpython CFLAGS='-O3 -arch x86_64 -m64 -fPIC -mfpmath=sse -msse3' CXXFLAGS='-O3 -arch x86_64 -m64 -fPIC -mfpmath=sse -msse3'
Re: An error in 10.6 Snow Leopard
Posted: Tue Sep 08, 2009 11:08 am
by hines
Please try the latest alpha version tar.gz found at
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/
or, if you have mercurial installed, even better to get the mercurial repository sources from:
http://www.neuron.yale.edu/hg/neuron/nrn/
Re: An error in 10.6 Snow Leopard
Posted: Tue Sep 08, 2009 10:58 pm
by shhong
I got the same error with the mercurial repository sources (344). nrniv seems to work, but also stops when nrngui.hoc is loaded.
Re: An error in 10.6 Snow Leopard
Posted: Wed Sep 09, 2009 12:09 am
by shhong
I also discovered that build.sh of iv cannot generate config.*, which makes configure fail.
Re: An error in 10.6 Snow Leopard
Posted: Sun Sep 13, 2009 9:05 pm
by wvangeit
I'm having exactly the same problem after installing (i.e. compiling from source) it on a new Snow Leopard.
Re: An error in 10.6 Snow Leopard
Posted: Wed Sep 16, 2009 7:56 am
by hines
Sorry I forgot to subscribe to this topic.
So far, compiling from the sources founders on a problem with --framework-carbon.
Just to see if there is a problem with the existing alpha distribution, someone please
install
http://www.neuron.yale.edu/ftp/neuron/v ... 0.4.11.dmg
and let us know if it works.
Re: An error in 10.6 Snow Leopard
Posted: Thu Sep 17, 2009 8:41 pm
by btorb
shhong and wvangeit came up with this solution which seems to work. (which works for the latest development code downloaded with mercurial)
at this point, automake fails to create the "config.sub" and "config.guess". copy these two files from either the downloadable tarball or from a previous installation (as I did). Then proceed with the following:
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./configure --prefix=$IDIR/nrn --build=i386 --with-iv=$IDIR/iv --with-nrnpython --with-paranrn CFLAGS="-O3 -arch i386" CXXFLAGS="-O3 -arch i386"
make sudo make install
in my case, IDIR=/Applications/NEURON-dev3, and i installed iv (with the nearly identical ./configure) to $IDIR/iv
All my code seems to run again although an error is given: special(83688) malloc: *** error for object 0x968e80: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Re: An error in 10.6 Snow Leopard
Posted: Fri Sep 18, 2009 7:26 am
by hines
Ok. Since there is no --enable-carbon configure arg, then that makes an x11 version.
Does x11 come along whenever the development environment is installed?
I'd still like to know if the
http://www.neuron.yale.edu/ftp/neuron/v ... 0.4.11.dmg
works. If not, I can make an OS X 10.5 version and that can be tried.
Re: An error in 10.6 Snow Leopard
Posted: Wed Sep 23, 2009 8:42 am
by hines
automake fails to create the "config.sub" and "config.guess"
Snow Leopard uses glibtool version 2.2.4 and that requires an extra argument to glibtoolize.
Edit build.sh and change
glibtoolize -c -f
to
glibtoolize -c -f -i
You should do that both in the iv and nrn build.sh files.
Sadly glibtool version 1 series does not allow this '-i' arg so to update the script I will eventually
have to switch to the version 2 series myself or put in a test. I'd switch to the new one but I cannot
get libtool version 2 series to work properly on my x86_64 centos5 machine.
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nrniv(53939) malloc: *** error for object 0x100cabe58: incorrect checksum for freed object...
Apparently snow leopard's posix_memalign does not work properly. Or perhaps it is a problem with gcc 4.2.1.
Anyway, a work around is to edit nrn/src/oc/symbol.c and change
#if HAVE_POSIX_MEMALIGN
to
#if 0 && HAVE_POSIX_MEMALIGN
I would expect this problem to go away when apple makes an update.
I see that the osx 10.4 built alpha version
http://www.neuron.yale.edu/ftp/neuron/v ... 0.4.11.dmg
works properly.