Hi,
I have compiled NEURON-7.3 from source on OSX mavericks (with--nrnpython and with--paranrn).
First I installed the appropriate version of Xcode, and then after the first incidence of the problem reported below, I removed it and reinstalled it. Also I have done the same with 'command line tools'. I am unsure if command line tools is redundant and included in Xcode, but I have done it anyway.
I still get the same problem. I can't compile *.mod files using nrnivmodl. This compilation still works on my Linux system. I think I have read all of the applicable trouble shooting, but I don't think it helps with this particular problem. Ie I have read:
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http://www.neuron.yale.edu/neuron/downl ... ac_install
Problem: Mknrndll does not work.
Solution: Install the Development environment that came with your system. The installer may be on your hard drive or on a separate system CD. Check the current OS X page to see if Apple mentions whether using the installer's default choices actually installs enough of the development environment. It is the "XCode" package that you need to install.
If you can't find your system CD, you can download XCode from the Apple web site. Be sure to get the version of XCode that matches your OS version, e.g. 10.4, and processor, e.g. Intel.
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and
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http://www.neuron.yale.edu/neuron/downl ... ac_install
Problem: Can't compile mod files.
Lion and Mountain Lion both need the latest version of the command line developer tools to compile mod files. Go to
http://developer.apple.com/opensource and click on the "Download command line developer tools . . . " link. You'll have to sign in with your Apple ID and password.
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I compile a whole bunch of mechanisms, actually the list of mechanisms is repeated twice so its not really as big as it looks (output below)
Below is an example of the output.
MacBook-Pro:expericomp20140421 kappa$ nrnivmodl
/Users/kappa/project/expericomp20140421
AMPA.mod AMPAr.mod ANsyn.mod CA1ih.mod CA1ika.mod CA1ikdr.mod CA1ina.mod CaDynamics_E2.mod Ca_HVA.mod Ca_LVAst.mod GABAa.mod GABAar.mod GABAb.mod GABAbr.mod Gfluct.mod H.mod IA.mod IL.mod IL3.mod Iahp.mod Ican.mod Ih.mod Im.mod K_Pst.mod K_Tst.mod Kaxon.mod Kdend.mod Ksoma.mod LcaMig.mod NMDA.mod NMDAr.mod NaTa_t.mod NaTs2_t.mod Naaxon.mod Nadend.mod Nap_Et2.mod Nasoma.mod SK_E2.mod SKv3_1.mod STDPE2Syn.mod ampa_syn.mod ampanmda.mod bgka.mod burststim2.mod ca.mod cagk.mod cal.mod calH.mod caolmw.mod capr.mod car.mod cat.mod ccanl.mod cp.mod cp2.mod epsp.mod expsid.mod fi.mod field.mod gammastim.mod gap.mod gskch.mod hNa.mod hha2.mod hha_old.mod icaolmw.mod icapr.mod ichan2.mod iholmkop.mod iholmw.mod ihpyrkop.mod infot.mod intf_.mod intfsw.mod kad.mod kahppr.mod kaolmkop.mod kap.mod kapyrkop.mod kca.mod kcaolmw.mod kcpr.mod kdr2.mod kdrbwb.mod kdrolmkop.mod kdrpr.mod kdrpyrkop.mod km.mod kmbg.mod kv.mod misc.mod my_c_code_compiled_as.mod my_exp2syn.mod naf2.mod nafbwb.mod nafolmkop.mod nafpr.mod nafpyrkop.mod nap.mod nca.mod ntIh.mod nthh.mod ntt.mod pregencv.mod regn_stim.mod somacar.mod staley.mod stats.mod updown.mod vecevent.mod vecst.mod xtra2.mod
AMPA.mod AMPAr.mod ANsyn.mod CA1ih.mod CA1ika.mod CA1ikdr.mod CA1ina.mod CaDynamics_E2.mod Ca_HVA.mod Ca_LVAst.mod GABAa.mod GABAar.mod GABAb.mod GABAbr.mod Gfluct.mod H.mod IA.mod IL.mod IL3.mod Iahp.mod Ican.mod Ih.mod Im.mod K_Pst.mod K_Tst.mod Kaxon.mod Kdend.mod Ksoma.mod LcaMig.mod NMDA.mod NMDAr.mod NaTa_t.mod NaTs2_t.mod Naaxon.mod Nadend.mod Nap_Et2.mod Nasoma.mod SK_E2.mod SKv3_1.mod STDPE2Syn.mod ampa_syn.mod ampanmda.mod bgka.mod burststim2.mod ca.mod cagk.mod cal.mod calH.mod caolmw.mod capr.mod car.mod cat.mod ccanl.mod cp.mod cp2.mod epsp.mod expsid.mod fi.mod field.mod gammastim.mod gap.mod gskch.mod hNa.mod hha2.mod hha_old.mod icaolmw.mod icapr.mod ichan2.mod iholmkop.mod iholmw.mod ihpyrkop.mod infot.mod intf_.mod intfsw.mod kad.mod kahppr.mod kaolmkop.mod kap.mod kapyrkop.mod kca.mod kcaolmw.mod kcpr.mod kdr2.mod kdrbwb.mod kdrolmkop.mod kdrpr.mod kdrpyrkop.mod km.mod kmbg.mod kv.mod misc.mod my_c_code_compiled_as.mod my_exp2syn.mod naf2.mod nafbwb.mod nafolmkop.mod nafpr.mod nafpyrkop.mod nap.mod nca.mod ntIh.mod nthh.mod ntt.mod pregencv.mod regn_stim.mod somacar.mod staley.mod stats.mod updown.mod vecevent.mod vecst.mod xtra2.mod
"/Applications/NEURON-7.3/nrn/share/nrn/libtool" --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I"/Applications/NEURON-7.3/nrn/include/nrn" -I"/Applications/NEURON-7.3/nrn/x86_64/lib" -g -O2 -c -o AMPAr.lo `test -f 'AMPAr.c' || echo '/'`AMPAr.c
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/Applications/NEURON-7.3/nrn/include/nrn -I/Applications/NEURON-7.3/nrn/x86_64/lib -g -O2 -c AMPAr.c -fno-common -DPIC -o .libs/AMPAr.o
In file included from AMPAr.c:265:
../misc.h:8:10: fatal error: 'values.h' file not found
#include <values.h>
^
1 error generated.
make: *** [AMPAr.lo] Error 1
MacBook-Pro:expericomp20140421 kappa$
The problem is here.
In file included from AMPAr.c:265:
../misc.h:8:10: fatal error: 'values.h' file not found
#include <values.h>
but if I deleted AMPAr.mod a similar problem would emerge somewhere else. Other similar errors which would also emerge are related to features.h. I get the sense that nrnivmodl is not properly linked up to some library or something, but since I have done all of the recommended troubleshooting steps I don't know how to remediate this.
The following works however. So I think that my system could compile mod files at some point. Although I get the sense that there might be a difference in creating NEURONs in built mechanisms when building NEURON initially, and compiling mechanisms after NEURON is built.
MacBook-Pro:bin kappa$ ./neurondemo
NEURON -- VERSION 7.3 ansi (1078:2b0c984183df) 2014-04-04
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See
http://www.neuron.yale.edu/neuron/credits
loading membrane mechanisms from /Applications/NEURON-7.3/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
oc>
Any help would be greatly appreciated.
Thanks.
Russell.