I am new to NEURON, and recently, I've run into some problems when trying to execute a HOC file. For some context, I am running NEURON 8.0.0 on macOS BigSur 11.6 on Intel MacBook Pro.
When I tried to execute the following code:
load_file("nrngui.hoc")
// Loads all celltypes from celltypes.txt, etc.
load_file("makecells_Axons.hoc")
// Plot output of CBCs, Aiis, and GCs separately
load_file("plot_Axons_IClamp_Axon.ses")
// Apply stimulation
load_file("Stim_Axon_TimeCourse.hoc")// Loads voltages for each compartment (from running 'interp3') and applies using 'extracellular'
//load_file("Stim_Axon_Auto_Asym.hoc")
I get the following output with an error:
It returns "Intel MKL FATAL Error." I looked into this and found a stack overflow thread that addresses the same type of error: https://stackoverflow.com/questions/366 ... mkl-def-so-e
NEURON -- VERSION 8.0.0 release/8.0 (429d11ef3) 2021-04-30
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2021
See http://neuron.yale.edu/neuron/credits
loading membrane mechanisms from /Users/sangwoncha/Downloads/Nrn-3/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
"INaP.mod" "IT.mod" "I_Leak.mod" "Ih.mod" "capump.mod" "spike.mod"
INTEL MKL ERROR: dlopen(/Users/sangwoncha/opt/anaconda3/lib/libmkl_intel_thread.1.dylib, 9): Library not loaded: @rpath/libiomp5.dylib
Referenced from: /Users/sangwoncha/opt/anaconda3/lib/libmkl_intel_thread.1.dylib
Reason: image not found.
Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.1.dylib.
nrngui exit status was 2
Press return key to exit
One of the answers suggested to execute the following lines:
However, my MacBook could not execute the first line and spat out the following error message:conda install nomkl numpy scipy scikit-learn numexpr
conda remove mkl mkl-service
and goes on to list various elements of my environment that is incompatible with 'nomkl.' One of the answers to the stack overflow thread linked above suggest that the problem lies with Anaconda. None of my lab members encountered this problem before and therefore was not able to help. At this point, being completely new to this kind of stuff, I feel very lost and have no idea what I am doing. Any input/help in troubleshooting this would be appreciated.UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- alabaster -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- anaconda==2021.05 -> python[version='3.7.10|3.9.4|3.8.8',build='h88f2d9e_5|h88f2d9e_0']
- appdirs -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- argon2-cffi -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- astroid -> python[version='>=3.10,<3.11.0a0']
- atomicwrites -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- attrs -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- autopep8 -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- backports -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']
- backports.functools_lru_cache -> python[version='>=2.7,<2.8.0a0']
- bkcharts -> python[version='>=3.7.1,<3.8.0a0']
- brotlipy -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- clyent -> python[version='>=3.10,<3.11.0a0']
- colorama -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- conda-verify -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- contextlib2 -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- cython -> python[version='>=3.10,<3.11.0a0']
- defusedxml -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- flake8 -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
- gevent -> python[version='>=3.10,<3.11.0a0']
- glob2 -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- h5py -> python[version='<3']
- html5lib -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']
- imageio -> python[version='>=3.9,<3.10.0a0']
- imagesize -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- ipywidgets -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- isort -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
- jdcal -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']
- jsonschema -> python[version='>=3.10,<3.11.0a0']
- mock -> python[version='>=3.9,<3.10.0a0']
- more-itertools -> python[version='>=3.9,<3.10.0a0']
- nose -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
- numba -> python[version='3.4.*|>=3.10,<3.11.0a0']
- olefile -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- path -> python[version='>=2.7,<2.8.0a0']
- pickleshare -> python[version='>=3.9,<3.10.0a0']
- prometheus_client -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- pycparser -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0']
- pyflakes -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
- pyopenssl -> python[version='>=3.9,<3.10.0a0']
- pyrsistent -> python[version='>=3.5,<3.6.0a0']
- python-dateutil -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- pytz -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- qtpy -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- rope -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- singledispatch -> python[version='>=3.9,<3.10.0a0']
- sniffio -> python[version='>=3,<3.7']
- snowballstemmer -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- sortedcollections -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- sphinxcontrib-websupport -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- statsmodels -> python[version='>=3.7.1,<3.8.0a0']
- sympy -> python[version='>=3.10,<3.11.0a0']
- tblib -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- tifffile -> python[version='>=2.7,<2.8.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0']
- tornado -> python[version='>=3.10,<3.11.0a0']
- typing_extensions -> python[version='>=3.9,<3.10.0a0']
- watchdog -> python[version='>=3.5,<3.6.0a0']
- wheel -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0']
- wurlitzer -> python[version='<3.4']
- xlrd -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- xlsxwriter -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- xmltodict -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
- yapf -> python[version='>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- zict -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- zope.event -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0']
- zope.interface -> python[version='>=3.10,<3.11.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package openssl conflicts for:
sphinxcontrib-qthelp -> python[version='>=3.5'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.0.2p,<1.0.3a']
iniconfig -> python -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.0.2p,<1.0.3a']
flask -> python[version='>=3.6'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.0.2p,<1.0.3a']
backports.weakref -> python -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.0.2p,<1.0.3a']
testpath -> python[version='>=3.6'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|
P.S. Since I am new to using command-line interface and NEURON, I hope that you understand that I may get some of the terminology mixed up here and there. I will try my best to follow along and provide any information on my end that may be helpful in addressing this issue.