HNN Install error: 'nrnivmodl: No such file or directory'

[Sliva, Danielle]

Hi Sam, 

I just tried following the Mac install instructions for HNN (https://github.com/jonescompneurolab/hnn/blob/master/installer/mac/mac-install-instructions.txt) and everything seemed to go well until I tried to "compile" HNN's biophysical model. I got the following error: 

make: nrnivmodl: No such file or directory

I tried installing the most recent NEURON package (nrn-7.6.master-1712.x86_64-osx.pkg), as well as an older one (7.5)- same thing.

Thanks, 

Danielle

--

Danielle D. Sliva

PhD Candidate, Jones Lab

Dept. of Neuroscience

Brown University

[sam n]

Hi Danielle,

Do you see anything (nrnivmodl, nrniv) in /Applications/NEURON-7.5/nrn/x86_64/bin

or /Applications/NEURON-7.6/nrn/x86_64/bin ?

Are you able to start NEURON from those directories

(with nrniv or nrniv -python from the commandline) ?

Sam

[Sliva, Danielle]

Hi Sam, 

Yes both are in the directory but when I try to run NEURON the command is not found: 

BML4C02VG0BVHTDH:bin dsliva$ ls -las

total 1008

  0 drwxr-xr-x  27 root  admin     864 May 15 10:52 .

  0 drwxr-xr-x   4 root  admin     128 May 15 10:52 ..

  8 -rwxr-xr-x   1 root  admin     383 May 15 10:51 bbswork.sh

  8 -rwxr-xr-x   1 root  admin     620 May 15 10:51 hel2mos1.sh

  8 -rwxr-xr-x   1 root  admin     155 May 15 10:50 idraw.sh

  8 -rwxr-xr-x   1 root  admin    2691 May 15 10:50 macnrn.term

 32 -rwxr-xr-x   1 root  admin   12848 May 15 10:52 memacs

  8 -rwxr-xr-x   1 root  admin     487 May 15 10:50 mknrndll.sh

  8 -rwxr-xr-x   1 root  admin    1886 May 15 10:51 mkthreadsafe

200 -rwxr-xr-x   1 root  admin  101132 May 15 10:52 modlunit

  8 -rwxr-xr-x   1 root  admin     470 May 15 10:50 modlunit.sh

  8 -rwxr-xr-x   1 root  admin     486 May 15 10:50 mos2nrn.sh

  8 -rwxr-xr-x   1 root  admin    2800 May 15 10:51 mos2nrn2.sh

  8 -rwxr-xr-x   1 root  admin     696 May 15 10:51 neurondemo

  8 -rwxr-xr-x   1 root  admin     504 May 15 10:50 neurondemo.sh

488 -rwxr-xr-x   1 root  admin  247420 May 15 10:52 nocmodl

  8 -rwxr-xr-x   1 root  admin     718 May 15 10:51 nrngui

  8 -rwxr-xr-x   1 root  admin     486 May 15 10:50 nrngui.sh

 96 -rwxr-xr-x   1 root  admin   47208 May 15 10:52 nrniv

  8 -rwxr-xr-x   1 root  admin    3962 May 15 10:51 nrniv_makefile

 16 -rwxr-xr-x   1 root  admin    4290 May 15 10:51 nrnivmodl

  8 -rwxr-xr-x   1 root  admin    2915 May 15 10:51 nrnmech_makefile

  8 -rwxr-xr-x   1 root  admin    2344 May 15 10:51 nrnoc_makefile

  8 -rwxr-xr-x   1 root  admin    1169 May 15 10:51 nrnocmodl

 24 -rwxr-xr-x   1 root  admin   10345 May 15 10:51 nrnpyenv.sh

  8 -rwxr-xr-x   1 root  admin     826 May 15 10:51 set_nrnpyenv.sh

  8 -rwxr-xr-x   1 root  admin      41 May 15 10:51 sortspike

BML4C02VG0BVHTDH:bin dsliva$ nrniv

-bash: nrniv: command not found

BML4C02VG0BVHTDH:bin dsliva$ nrniv -python

-bash: nrniv: command not found

I can run the NEURON demo and GUI- seems to open fine, but I'm also getting this when I open the GUI: 

Could not load either libnrnpython3 or libnrnpython2

pyver10=0 pylib=/usr/lib/libSystem.B.dylib

Thanks, 

Danielle

[sam n]

So that's all in /Applications/NEURON-7.5/nrn/x86_64/bin , which you also added to $PATH ?

Robert - any suggestion?

[McDougal, Robert]

What version is this?

There was a glitch in the mac 7.6 alpha that was out until this morning that could lead to a similar message. (If so, try with the latest.)

Also there's another glitch where if NEURON is installed on a Mac, the installer won't offer to update the path.... If so, check your ~/.bash_profile for any references to 7.5 and change them to 7.6.

---

From: hnns...@googlegroups.com <hnns...@googlegroups.com> on behalf of sam n <sam...@gmail.com>
Sent: Thursday, May 17, 2018 12:37:44 PM
To: Sliva, Danielle
Cc: HNNSolver; McDougal, Robert
Subject: Re: HNN Install error: 'nrnivmodl: No such file or directory'

 

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[Sliva, Danielle]

Ah i didn't notice that- changing 7.5 to 7.6 appeared to be the solution. The GUI is running now. Would you still recommend updating my NEURON version to the new 7.6?

Thanks for your help! 

Danielle

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[sam n]

You must have 7.6 installed if the simulation runs properly (should test it), since your paths are now set to point to the 7.6 location. If NEURON 7.6 not installed, should install it.

[Sliva, Danielle]

Yes I do have 7.6, but it was installed last night- so alpha version? Just wondering if there were any updates this morning that make it worthwhile to re-do the install. 

NEURON demo seems to work fine but command line does complain- 'Could not load either libnrnpython3 or libnrnpython2'

I'll try out the HNN tutorials. 

Thanks, 

Danielle

[sam n]

On Thu, May 17, 2018 at 1:30 PM, Sliva, Danielle <daniell...@brown.edu> wrote:

Yes I do have 7.6, but it was installed last night- so alpha version? Just wondering if there were any updates this morning that make it worthwhile to re-do the install. 

NEURON demo seems to work fine but command line does complain- 'Could not load either libnrnpython3 or libnrnpython2'

That looks like a problem - probably should reinstall NEURON 7.6. 

I'll try out the HNN tutorials. 

For later, can press the "Run simulation" button & make sure simulation produces an ERP output.