NEURON in Mac OsX 10.9.2

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luciana
Posts: 17
Joined: Sun Mar 09, 2014 2:29 pm

NEURON in Mac OsX 10.9.2

Post by luciana »

Hi!

I have Mac Os X 10.9.2 and I installed this version of NEURON:
http://www.neuron.yale.edu/ftp/neuron/v ... y1.1.0.dmg
but when I tried to run it, appears this:

Code: Select all

-e 
dyld: Library not loaded: /Applications/NEURON-7.3/nrn/x86_64/lib/libnrnoc.0.dylib
  Referenced from: /Volumes/NEURON-7.3/NEURON-7.3/nrn/x86_64/bin/nrniv
  Reason: image not found
./nrngui.sh: line 25:  1311 Trace/BPT trap: 5       ${NRNGUI}
nrngui exit status was 133
Press return key to exit
What should I do?
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

Sadly, my attempts to make NEURON position independent have not been completely successful (there is a catch 22 with the @executable_path solution when launching python and importing neuron).
You need to drag the contents of the dmg file to /Applications so that you have
/Applications/NEURON-7.3/nrn
luciana
Posts: 17
Joined: Sun Mar 09, 2014 2:29 pm

Re: NEURON in Mac OsX 10.9.2

Post by luciana »

hines wrote: You need to drag the contents of the dmg file to /Applications so that you have
/Applications/NEURON-7.3/nrn
But I did it when I installed it, I drag the NEURON Folder to Applications
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

Then the puzzle is why there is a mention of
/Volumes/NEURON-7.3/NEURON-7.3/nrn/x86_64/bin/nrniv
Can you tell me if the file
Library not loaded: /Applications/NEURON-7.3/nrn/x86_64/lib/libnrnoc.0.dylib
exists or not? Also does /Volumes/NEURON-7.3/NEURON-7.3/nrn/x86_64/bin/nrniv exist?
The former should exist and the latter should not.
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

Also , what is the url for the dmg file you used to install NEURON-7.3 . I need to verify that it installs correctly on my machine.
luciana
Posts: 17
Joined: Sun Mar 09, 2014 2:29 pm

Re: NEURON in Mac OsX 10.9.2

Post by luciana »

I have removed the NEURON application and installed it again (the same one).
And appears something new!:

Code: Select all

-e 
dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib
  Referenced from: /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv
  Reason: image not found
./nrngui.sh: line 25:  1312 Trace/BPT trap: 5       ${NRNGUI}
nrngui exit status was 133
Press return key to exit
What is happening now?

The url for the dog file that I used was:
http://www.neuron.yale.edu/ftp/neuron/v ... y1.1.0.dmg
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

It appears that X11 (XQuartz-2.7.4.dmg) is not installed. In my experience, when one launches NEURON and X11 does not exist, the system asks if you would like to download and install it.
Yet another puzzle regarding your machine. I see that https://www.macupdate.com/app/mac/26593/xquartz/
has a 2.7.5 version now which is
Updated for OS X 10.9 Mavericks support
luciana
Posts: 17
Joined: Sun Mar 09, 2014 2:29 pm

Re: NEURON in Mac OsX 10.9.2

Post by luciana »

It works!!! installing XQuartz 2.7.5 the message desappears and NEURON run perfectly.
Thank you very much I'm so happy
rkpowers
Posts: 2
Joined: Tue Jul 12, 2005 3:36 pm

Re: NEURON in Mac OsX 10.9.2

Post by rkpowers »

Recently 'upgraded' to Mavericks. I reinstalled the latest version of NEURON + Xcode + XQuartz 2.75. I am able to run nrngui and also compile new mod files, but when I attempt to open a file that uses these mod files they are not recognized and I get the following error message:

loading membrane mechanisms from /Applications/NEURON-7.3/Delta_F_sims/x86_64/.libs/libnrnmech.so
dlopen failed -
dlopen(/Applications/NEURON-7.3/Delta_F_sims/x86_64/.libs/libnrnmech.so, 2): Symbol not found: _getarg
Referenced from: /Applications/NEURON-7.3/Delta_F_sims/x86_64/.libs/libnrnmech.so
Expected in: flat namespace
in /Applications/NEURON-7.3/Delta_F_sims/x86_64/.libs/libnrnmech.so
Could not load /Applications/NEURON-7.3a/nrn/share/nrn/../../x86_64/lib/libnrnpython1013.dylib

Do I need to uninstall the old version of NEURON (7.3a)? And if so, how do I do it?
Thanks
Randy
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

Please try http://www.neuron.yale.edu/ftp/neuron/v ... 10.7.5.dmg
and we can work through any problems from that point. (First drag your existing /Applications/NEURON-7.3 to the trash.)
rkpowers
Posts: 2
Joined: Tue Jul 12, 2005 3:36 pm

Re: NEURON in Mac OsX 10.9.2

Post by rkpowers »

Great. That worked, eventually. I did have to set the path to NEURON as follows (you had given me this tip before):

export PATH=/Applications/NEURON-7.3/nrn/x86_64/bin:$PATH

Is there any way to set that permanently? As it is, I have to use this command each time I open a terminal window.
Thanks,
Randy
hines
Site Admin
Posts: 1603
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON in Mac OsX 10.9.2

Post by hines »

Your $HOME folder should have a file called .bash_profile
You can modify your PATH there.
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