Neuron on OSX 10.5

Neuron on OSX 10.5

Postby jhp » Tue Oct 30, 2007 4:24 am

I was wondering if anyone has had any experiences with Leopard and Neuron. Is it save to update?
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Postby hines » Tue Oct 30, 2007 11:31 am

I'm curious as well. It is not necessary
to install NEURON to try it out. Just download the latest mac universal
binary from http://www.neuron.yale.edu/ftp/neuron/versions/alpha/
open the dmg and double click on the neurondemo. If it doesn't work, I'll have to build from the sources under 10.5
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->

Postby jhp » Wed Oct 31, 2007 5:02 pm

I tried it out myself:

The nrndemo seems to run fine although at startup it gives the following output.

oc: File exists
/Applications/NEURON-6.1/nrn/umac/bin/nrniv.app/Contents/MacOS/nrniv: errno set during call of xpanel
in /Applications/NEURON-6.1/nrn/share/nrn/demo/demo.hoc near line 72
^


However, I cannot compile my mods anymore. Here are the lines at which the compilation seems to go wrong. If you need the whole output, I can send you a file - just let me know.


...
/usr/bin/ld: for architecture i386
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libreadline.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libncurses.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libpython.dylib unknown flags (type) of section 6 (__TEXT,__dof_python) in load command 0
/usr/bin/ld: /System/Library/Frameworks/Carbon.framework/Carbon load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libSystem.dylib unknown flags (type) of section 6 (__TEXT,__dof_plockstat) in load command 0
/usr/bin/ld: /usr/lib/libSystem.B.dylib unknown flags (type) of section 6 (__TEXT,__dof_plockstat) in load command 0
/usr/bin/ld: /usr/lib/libncurses.5.4.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/libstdc++.6.dylib load command 8 unknown cmd field
/usr/bin/ld: /usr/lib/libgcc_s.1.dylib load command 8 unknown cmd field
/usr/bin/ld: /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon load command 7 unknown cmd field
collect2: ld returned 1 exit status
/usr/bin/ld: for architecture ppc
/usr/bin/ld: /usr/lib/gcc/powerpc-apple-darwin8/4.0.1/../../../libreadline.dylib load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/powerpc-apple-darwin8/4.0.1/../../../libncurses.dylib load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/powerpc-apple-darwin8/4.0.1/../../../libpython.dylib unknown flags (type) of section 7 (__TEXT,__dof_python) in load command 0
/usr/bin/ld: /System/Library/Frameworks/Carbon.framework/Carbon load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/gcc/powerpc-apple-darwin8/4.0.1/../../../libSystem.dylib unknown flags (type) of section 9 (__TEXT,__dof_plockstat) in load command 0
/usr/bin/ld: /usr/lib/libSystem.B.dylib unknown flags (type) of section 9 (__TEXT,__dof_plockstat) in load command 0
/usr/bin/ld: /usr/lib/libncurses.5.4.dylib load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/libstdc++.6.dylib load command 7 unknown cmd field
/usr/bin/ld: /usr/lib/libgcc_s.1.dylib load command 7 unknown cmd field
/usr/bin/ld: /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon load command 7 unknown cmd field
collect2: ld returned 1 exit status
lipo: can't open input file: /var/folders/Wv/WvY5WhenEs0rGRd-hIRCuk+++TI/-Tmp-//ccXMEi9b.out (No such file or directory)
make: *** [libnrnmech.la] Error 1



This is running NEURON-6.1 and OSX 10.5
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Postby DRA » Fri Nov 09, 2007 2:24 pm

I've been having problems running NEURON-6.0 since installing the new OSX 10.5 leopard. I was able to run the nrndemo in NEURON-6.1 from the dmg but got a different error than jhp:


oc: File exists
/Volumes/NEURON-6.1/NEURON-6.1/nrn/umac/bin/nrniv.app/Contents/MacOS/nrniv: errno set during call of xpanel
in /Volumes/NEURON-6.1/NEURON-6.1/nrn/share/nrn/lib/hoc/nrngui.hoc near line 2
nrnmainmenu()




I am also unable to compile mods and have similar errors occurring.
I have been trying to compile NEURON-6.1 from scratch on my machine but just haven't been able to get it right. The directions at http://www.neuron.yale.edu/neuron/insta ... d_osx.html definitely aren't working. If someone could help me out I'd be much obliged. Either a compiled version or better directions to compile the code on my native system would be great.

DA
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Location: University of Arizona

Postby ted » Mon Dec 31, 2007 12:21 pm

DRA wrote:I've been having problems running NEURON-6.0 since installing the new OSX 10.5 leopard.

Was this problem ever resolved?
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Leopard issue not resolved (?)

Postby dzw » Thu Jan 03, 2008 2:55 pm

I've recently installed Leopard and encountered similar problems as earlier posters. nrndemo runs OK, but I receive error messages when I try to compile mod files.
dzw
 

Postby BKnight430 » Mon Jan 28, 2008 1:48 pm

Any news on a fix for compiling in OSX Leopard?
BKnight430
 

Postby hines » Tue Jan 29, 2008 2:32 pm

/usr/bin/ld: /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libreadline.dylib load command 8 unknown cmd field

I'm guessing that the libtool I am using
is a bit out of date with respect to
os x 10.5. But to diagnose more thoroughly
i'll have to install that os on my mac and debug from there.
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Postby hines » Wed Feb 13, 2008 9:56 am

Try the relevant dmg file at
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/

Two problems were explicitly fixed for the Leapard version: Close the terminal window on exit. Avoid the error message on startup.

I am not certain that a distinct 10.5 version is really necessary since
I was able to run the 10.4 (Tiger) version under 10.5 (if the path to
the 10.4 version had no spaces, but that is another issue I'll deal with
since spaces are not supposed to matter). The point is that I did not
experience the "libreadline.dylib load" problem when dealing with
mod files.
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Postby hines » Thu Feb 14, 2008 7:53 am

Someone wrote to me that he continued to experience the
/usr/bin/ld: /Applications/NEURON-6.2/nrn/umac/lib/libnrnoc.
0.0.0.dylib load command 7 unknown cmd field
problem with the new 10.5 dmg of NEURON. It turns out that after you upgrade from 10.4 to 10.5 you also need to re-install the 10.5 developer tools that come with the installation dvd. Then everything works.
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Postby sdhawan » Fri May 30, 2008 8:08 am

Just a confirmation:
What didn't work for me: Mac OS 10.5.3 with Xcode 2.5 and Neuron 6.1/6.2
What worked: Mac OS 10.5.3 with Xcode 3.0 and Neuron 6.2.alpha-1010


[quote="hines"...It turns out that after you upgrade from 10.4 to 10.5 you also need to re-install the 10.5 developer tools that come with the installation dvd. Then everything works.[/quote]
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