Problem installing Neuron on 10.8.5 (with troubleshooting)
Posted: Sun Apr 06, 2014 11:06 am
I've had a few problems. I have been following the instructions on the following page because I want to install PyNN with Neuron, and the PyNN instructions say to follow these for installing Neuron first: http://www.neuron.yale.edu/neuron/downl ... x#ivandnrn
My OS is 10.8.5.
I had a problem running make for libtool (didn't record the error, it had something to do with gcc). So I downloaded the latest version of Xcode (5.1) instead of just having downloaded gcc. That seemed to fix the problem.
I initially skipped over MPI since I'm not planning on doing anything parallel, but then I had problems at the step for installing Interviews, so I went back and installed MPI. That did the trick.
Until I got to the stage of part II.D -- installing Neuron. I got the same problem as this thread: http://www.neuron.yale.edu/phpBB/viewto ... f=4&t=3049
I followed the solution, and it seemed to work… until I got to make install. Then I get the following error:
"
building 'neuron.hoc' extension
gcc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I../.././src/oc -I../oc -I../.././src/nrnmpi -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c inithoc.cpp -o build/temp.macosx-10.8-intel-2.7/inithoc.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'gcc' failed with exit status 1
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1
"
I googled the error and found this: http://kaspermunck.github.io/2014/03/fi ... ang-error/
It looks like it's a problem with Xcode 5.1
According to this page: http://stackoverflow.com/questions/2239 ... lang-error
I tried running make install -Wno-error=unused-command-line-argument-hard-error-in-future
but I don't know what I'm doing and that didn't work.
I also tried downloading the old 5.0.2 Xcode, but that didn't help.
I tried running the following command before make and make install, but I still get the same error:
./configure --prefix=/Application/NEURON/nrn --with-iv=/Application/NEURON/iv --with-pic --with-nrnpython --with-paranrn --with-x --with-readline=/usr/local/opt/readline --with-pic CC='clang' CXX='clang++' CFLAGS='-O3 -Wno-return-type -Wno-implicit-function-declaration -Wno-implicit-int -fPIC' CXXFLAGS='-O3 -Wno-return-type -Wno-implicit-function-declaration -Wno-implicit-int -fPIC'
Desperate, I saw this thread: http://www.neuron.yale.edu/phpBB/viewto ... f=4&t=2940
I tried both the following, although the error wasn't the same as I what I experienced:
1) if you are working from a mercurial repository update to version 3 using
hg update 'Release 7.3'
2) install cython. On my mac I have done this with macports using
sudo port install py27-cython
and then I configured with the extra option
CYTHON=cython-2.7
Still get the error.
one more bit of info, when I use make, I get a bunch of warnings: "
automake-1.14: warning: autoconf input should be named 'configure.ac', not 'configure.in'
src/e_editor/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/gnu/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/ivoc/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/ni_pci_6229/Makefile.am:18: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nmodl/Makefile.am:14: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrniv/Makefile.am:104: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnjava/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnmpi/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnoc/Makefile.am:56: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnpython/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/oc/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/cvodes/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/ida/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/shared/Makefile.am:17: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/uxnrnbbs/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/jolthoff/neuron/nrn/missing autoconf
configure.in:247: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
"
Any advice on how to fix this? Thanks!
My OS is 10.8.5.
I had a problem running make for libtool (didn't record the error, it had something to do with gcc). So I downloaded the latest version of Xcode (5.1) instead of just having downloaded gcc. That seemed to fix the problem.
I initially skipped over MPI since I'm not planning on doing anything parallel, but then I had problems at the step for installing Interviews, so I went back and installed MPI. That did the trick.
Until I got to the stage of part II.D -- installing Neuron. I got the same problem as this thread: http://www.neuron.yale.edu/phpBB/viewto ... f=4&t=3049
I followed the solution, and it seemed to work… until I got to make install. Then I get the following error:
"
building 'neuron.hoc' extension
gcc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I../.././src/oc -I../oc -I../.././src/nrnmpi -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c inithoc.cpp -o build/temp.macosx-10.8-intel-2.7/inithoc.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'gcc' failed with exit status 1
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1
"
I googled the error and found this: http://kaspermunck.github.io/2014/03/fi ... ang-error/
It looks like it's a problem with Xcode 5.1
According to this page: http://stackoverflow.com/questions/2239 ... lang-error
I tried running make install -Wno-error=unused-command-line-argument-hard-error-in-future
but I don't know what I'm doing and that didn't work.
I also tried downloading the old 5.0.2 Xcode, but that didn't help.
I tried running the following command before make and make install, but I still get the same error:
./configure --prefix=/Application/NEURON/nrn --with-iv=/Application/NEURON/iv --with-pic --with-nrnpython --with-paranrn --with-x --with-readline=/usr/local/opt/readline --with-pic CC='clang' CXX='clang++' CFLAGS='-O3 -Wno-return-type -Wno-implicit-function-declaration -Wno-implicit-int -fPIC' CXXFLAGS='-O3 -Wno-return-type -Wno-implicit-function-declaration -Wno-implicit-int -fPIC'
Desperate, I saw this thread: http://www.neuron.yale.edu/phpBB/viewto ... f=4&t=2940
I tried both the following, although the error wasn't the same as I what I experienced:
1) if you are working from a mercurial repository update to version 3 using
hg update 'Release 7.3'
2) install cython. On my mac I have done this with macports using
sudo port install py27-cython
and then I configured with the extra option
CYTHON=cython-2.7
Still get the error.
one more bit of info, when I use make, I get a bunch of warnings: "
automake-1.14: warning: autoconf input should be named 'configure.ac', not 'configure.in'
src/e_editor/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/gnu/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/ivoc/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/ni_pci_6229/Makefile.am:18: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nmodl/Makefile.am:14: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrniv/Makefile.am:104: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnjava/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnmpi/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnoc/Makefile.am:56: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/nrnpython/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/oc/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/cvodes/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/ida/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/sundials/shared/Makefile.am:17: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
src/uxnrnbbs/Makefile.am:6: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/jolthoff/neuron/nrn/missing autoconf
configure.in:247: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
"
Any advice on how to fix this? Thanks!