Page 1 of 1
Compiling Mod Files on Catalina
Posted: Mon Oct 19, 2020 8:18 am
by landoskape
Hi. I just downloaded NEURON on Mac Catalina (10.15.7) and am trying to compile mod files from modeldb.
I have tried two ways, dragging a mod folder (with a list of .mod files in it) to the mknrndll application. I have also tried navigating to the mod folder in a terminal and running mknrndll directly.
Afterwards, an x86_64 folder is successfully created that contains .mod files, .c files, .o files, and an empty x86_64 folder. There are no hidden files present. Both methods throw the following error:
Code: Select all
clang-4.0: error: no such file or directory: '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/libreadline.tbd'
make: *** [x86_64/libnrnmech.dylib] Error 1
I've tried reinstalling command line tools (I had to download it from a dmg file on developer.apple.com, I downloaded "Command Line Tools for XCode 12".
Seems like I'm missing a file that is needed to make some of the mod files. Any thoughts?
Re: Compiling Mod Files on Catalina
Posted: Sat Oct 24, 2020 1:08 pm
by landoskape
Problem solved. Running mknrndll called the libreadline function from the Xcode.app directory in applications. That folder doesn't exist without downloading Xcode, which I did from the app store. After downloading XCode (12.1), I compiled the mod directory again and it was successful.
Re: Compiling Mod Files on Catalina
Posted: Wed Oct 28, 2020 12:44 pm
by ted
Thank you for reporting how you fixed the problem.
So "Command Line Tools for XCode 12", which you installed first, isn't the same as "Xcode 12.1", which fixed the problem?
Re: Compiling Mod Files on Catalina
Posted: Tue Nov 17, 2020 8:50 pm
by aplainbee
Hi! I ran into the exact same problem as landoskape when I was attempting to run the 2002 MRG axon model(Accessible at
https://senselab.med.yale.edu/ModelDB/s ... 810#tabs-1). I was wondering if anyone could suggest any other tips on how to configure my computer to successfully compile the mod file. I've made sure that I've downloaded XQuartz, Xcode 12.2, and the Command Line Tools for 12.2. Additionally, I can run NEURON fine by itself, but running the model is proving to be a challenge. I'd appreciate any insight, thank you in advance!
Here is the error I get when I try compiling AXNODE.mod.
Code: Select all
[-e
/usr/bin/xcrun
Creating x86_64 directory for .o files.
/Users/p.bhat/Desktop/MRGaxon
AXNODE.mod
AXNODE.mod
mkdir -p x86_64
-> Compiling mod_func.c
cc -g -O2 -I. -I.. -I/Applications/NEURON-7.8//include -I/usr/local/Cellar/open-mpi/4.0.1_1/include -fPIC -c mod_func.c -o mod_func.o
-> NMODL AXNODE.mod
MODLUNIT=/Applications/NEURON-7.8//share/nrn/lib/nrnunits.lib \
/Applications/NEURON-7.8//bin/nocmodl AXNODE.mod
Translating AXNODE.mod into AXNODE.c
Thread Safe
-> Compiling x86_64/AXNODE.c
(cd .. ; cc -g -O2 -I. -I.. -I/Applications/NEURON-7.8//include -I/usr/local/Cellar/open-mpi/4.0.1_1/include -fPIC -c x86_64/AXNODE.c -o x86_64/AXNODE.o)
=> LINKING library x86_64/libnrnmech.dylib Mod files: AXNODE.mod
(cd .. ; c++ -g -O2 -std=c++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -fPIC -I /Applications/NEURON-7.8//include -o x86_64/libnrnmech.dylib -Wl,-install_name,@rpath/libnrnmech.dylib \
x86_64/mod_func.o x86_64/AXNODE.o -L/Applications/NEURON-7.8//lib -lnrniv -Wl,-rpath,/Applications/NEURON-7.8//lib /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/libreadline.tbd -lcurses -lform)
clang: [color=#FF0000]error[/color]: no such file or directory: '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/libreadline.tbd'
make: *** [x86_64/libnrnmech.dylib] Error 1
Press 'return' key to close]
Re: Compiling Mod Files on Catalina
Posted: Wed Nov 18, 2020 2:51 pm
by cbutson
I am having the same problem: compiling mod files using mknrndll fails because of a missing file in Xcode:
clang: error: no such file or directory: '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/libreadline.tbd'
I am running OSX 10.15.7 and the latest versions of Xcode (12.2) and NEURON (7.8.1). Both were installed today, and I confirmed that Command Line Tools are installed in Xcode (I checked in Preferences->Locations).
I noticed that the directory /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
doesn't exist, so I created an alias for this directory that points to the directory that does exist:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
Addendum and possible solution (added later): I solved this problem by installing NEURON 7.7.
Thanks for any ideas about how to get this working with NEURON 7.8,
Chris
Re: Compiling Mod Files on Catalina
Posted: Thu Nov 19, 2020 8:51 am
by aplainbee
Hi Chris,
I'm glad installing the older version worked for you :)
I will give that a try. Can you please share how to created an alias to change the directory NEURON was looking at? Thank you!
Re: Compiling Mod Files on Catalina
Posted: Sat Nov 21, 2020 11:52 am
by hines
Because of these perennial problems with readline when binary distributions are installed, we will be taking the tack during build of compiling a recent version of readline ourselves as a libreadline.a file along with ncurses and incorporating that into the libnrniv.dylib. I hope after that I'll never see another issue about readline again. This strategy has already been taken with the neuron wheel installation files and now needs to be applied to the pkg files that I publish.
Re: Compiling Mod Files on Catalina
Posted: Mon Nov 23, 2020 6:50 am
by hines
A work around for now for readline problems is to try
nrn-7.8.1-2-gdfe33e60-osx-27-36-37-38-39.pkg
or
nrn-8.0.dev-239-g8f2aaaa9.w64-mingw-py-27-36-37-38-39-setup.exe
at
https://neuron.yale.edu/ftp/neuron/versions/alpha/
These use NEURON's internal readline sources.
Re: Compiling Mod Files on Catalina
Posted: Tue Jan 05, 2021 3:17 pm
by landoskape
ted wrote: ↑Wed Oct 28, 2020 12:44 pm
Thank you for reporting how you fixed the problem.
So "Command Line Tools for XCode 12", which you installed first, isn't the same as "Xcode 12.1", which fixed the problem?
Sorry for the delayed reply, glad to see that this conversation was useful.
That's right -Command Line Tools is a subset of Xcode 12.1, and although only a few lines of code from Xcode 12.1 were needed, I had to download the whole package to access them.