NEURON with Python 3.1 installation

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

Post Reply
kadir

NEURON with Python 3.1 installation

Post by kadir » Fri Feb 18, 2011 1:23 pm

I am trying to install NEURON as a Python 3.1 module.

First, I tried to do it with Python 2.6. I followed the instruction at http://www.davison.webfactional.com/not ... on-python/ and the installation was successful.

Then, I changed the "python link" to python3 and got:

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$ ls -al python
lrwxrwxrwx 1 root root 7 2011-02-18 17:27 python -> python3
I removed NEURON and tried to reinstall for Python 3. When I entered

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$ sudo ./configure --prefix=/opt/nrn-7.1 --with-iv=/opt/iv-17 --with-nrnpython
it gave me the following error:

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Python binary found (/usr/bin/python)
checking nrnpython configuration...   File "<string>", line 2
    print distutils.sysconfig.get_python_version()
                  ^
SyntaxError: invalid syntax
get_python_version()  '' returning '2.4'
  File "<string>", line 2
    print distutils.sysconfig.get_python_inc(1)
                  ^
SyntaxError: invalid syntax
get_python_inc(1)  '' returning ''
configure: error: cannot determine python include directory. Need to
explicitly specify PYINCDIR
Does anyone know how to cope with this or another way to install NEURON as a Python 3.1 module?

Thanks in advance

ted
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Posts: 5632
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: NEURON with Python 3.1 installation

Post by ted » Fri Feb 18, 2011 8:30 pm

Suggest you try this with NEURON v. 7.2, either from a recent alpha package or the latest development code from the mercurial repository.

kadir

Re: NEURON with Python 3.1 installation

Post by kadir » Sat Feb 26, 2011 12:05 pm

i think the configuration was successful with NEURON 7.2. here's what i got:

Code: Select all

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
abort: couldn't find mercurial libraries in [/usr/local/lib/python2.6/dist-packages /usr/local/bin /usr/lib/python3.1 /usr/lib/python3.1/plat-linux2 /usr/lib/python3.1/lib-dynload /usr/local/lib/python3.1/dist-packages /usr/lib/python3/dist-packages]
(check your install and PYTHONPATH)
Not trying to build rpms for your system (use --enable-rpm-rules to override) 
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) mawk
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) none
checking how to run the C++ preprocessor... g++ -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
Python binary found (/usr/bin/python)
checking nrnpython configuration... get_python_version()  '3.1'
sys.version_info[0]  '3'
get_python_inc(1)  '/usr/include/python3.1'
get_config_var('LIBS')  '-lpthread -ldl  -lutil'
get_config_var('LINKFORSHARED')  '-Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions'
get_config_var('LIBDIR')  '/usr/lib'
checking if python include files and libraries work... yes
configure: Use the NRNMECH_DLL_STYLE for "special"
checking for tgetent in -lncurses... yes
checking which library has the termcap functions... using libncurses
checking checking compilation with -lreadline... ok
Do not compile neosim specific code.
Not building the nrnjava interface
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... no
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking sgtty.h usability... yes
checking sgtty.h presence... yes
checking for sgtty.h... yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking termio.h usability... yes
checking termio.h presence... yes
checking for termio.h... yes
checking for unistd.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking varargs.h usability... no
checking varargs.h presence... no
checking for varargs.h... no
checking stropts.h usability... yes
checking stropts.h presence... yes
checking for stropts.h... yes
checking sys/conf.h usability... no
checking sys/conf.h presence... no
checking for sys/conf.h... no
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
configure: Using pthreads.
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
configure: successful.
PTHREAD_LIBS=
PTHREAD_CFLAGS=-pthread
PTHREAD_CC=gcc
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking stream.h usability... no
checking stream.h presence... no
checking for stream.h... no
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for int32_t... yes
checking for u_int32_t... yes
checking for u_int... yes
checking whether byte ordering is bigendian... no
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for working alloca.h... yes
checking for alloca... yes
checking for working memcmp... yes
checking return type of signal handlers... void
checking for vprintf... yes
checking for _doprnt... no
checking for ftime... yes
checking for getcwd... yes
checking for getpw... yes
checking for gethostname... yes
checking for gettimeofday... yes
checking for mkdir... yes
checking for putenv... yes
checking for setenv... yes
checking for select... yes
checking for strdup... yes
checking for strstr... yes
checking for index... yes
checking for bzero... yes
checking for bcopy... yes
checking for stty... no
checking for lockf... yes
checking for isatty... yes
checking for mkstemp... yes
checking for setitimer... yes
checking for sigaction... yes
checking for fesetround... yes
checking for posix_memalign... yes
checking if SIGBUS defined in signal.h... yes
checking if SIGSEGV defined in signal.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) none
checking _G_config.h usability... yes
checking _G_config.h presence... yes
checking for _G_config.h... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler has stringstream... yes
checking compilation with interviews... ok
checking if InterViews is up to date with respect to nrn-5.6 and later... ok
The signal function does not need a cast for the handler
checking /include/pvm3.h usability... no
checking /include/pvm3.h presence... no
checking for /include/pvm3.h... no

do SIGPOLL and I_GETSIG work: no
 But see config.log to see why it failed.
checking whether the compiler supports Standard Template Library... yes
NRNOC_X11 = 1
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/e_editor/Makefile
config.status: creating src/modlunit/Makefile
config.status: creating src/nmodl/Makefile
config.status: creating nrnrpm.spec
config.status: creating src/sundials/Makefile
config.status: creating src/sundials/shared/Makefile
config.status: creating src/sundials/cvodes/Makefile
config.status: creating src/sundials/ida/Makefile
config.status: creating src/sparse/Makefile
config.status: creating src/memacs/Makefile
config.status: creating src/readline/Makefile
config.status: creating src/sparse13/Makefile
config.status: creating src/oc/Makefile
config.status: creating src/scopmath/Makefile
config.status: creating src/nrnoc/Makefile
config.status: creating src/gnu/Makefile
config.status: creating src/uxnrnbbs/Makefile
config.status: creating src/mesch/Makefile
config.status: creating src/uxnrnbbs/mos2nrn.h
config.status: creating src/nrnmpi/Makefile
config.status: creating src/ivoc/Makefile
config.status: creating src/nrncvode/Makefile
config.status: creating src/parallel/Makefile
config.status: creating src/nrniv/Makefile
config.status: creating src/ivos/Makefile
config.status: creating src/ivos/InterViews/Makefile
config.status: creating src/ivos/OS/Makefile
config.status: creating src/nrnjava/Makefile
config.status: creating src/nrnjava/nrnccmb/Makefile
config.status: creating src/nrnjava/neuron/Makefile
config.status: creating src/nrnpython/Makefile
config.status: creating src/ni_pci_6229/Makefile
config.status: creating src/mac/Makefile
config.status: creating src/mswin/Makefile
config.status: creating src/mswin/batch/Makefile
config.status: creating src/mswin/nrnsetup.nsi
config.status: creating src/mswin/nrncygso.sh
config.status: creating src/mswin/lib/mknrndll.mak
config.status: creating src/mswin/extra/Makefile
config.status: creating src/mswin/rdln/Makefile
config.status: creating src/mswin/windll/Makefile
config.status: creating src/mswin/winio/Makefile
config.status: creating src/mswin/wnrnbbs/Makefile
config.status: creating src/mswin/lib/Makefile
config.status: creating src/mswin/bin/Makefile
config.status: creating src/neuronmusic/Makefile
config.status: creating src/neuronmusic/setup.py
config.status: creating share/Makefile
config.status: creating bin/nrnoc_makefile
config.status: WARNING:  'bin/nrnoc_makefile.in' seems to ignore the --datarootdir setting
config.status: creating bin/nrniv_makefile
config.status: WARNING:  'bin/nrniv_makefile.in' seems to ignore the --datarootdir setting
config.status: creating bin/nrnmech_makefile
config.status: creating share/lib/Makefile
config.status: creating share/lib/hoc/Makefile
config.status: creating share/lib/python/Makefile
config.status: creating share/lib/hoc/celbild/Makefile
config.status: creating share/lib/hoc/mulfit/Makefile
config.status: creating share/lib/hoc/netbild/Makefile
config.status: creating share/lib/hoc/lincir/Makefile
config.status: creating share/lib/hoc/mview/Makefile
config.status: creating share/lib/hoc/chanbild/Makefile
config.status: creating share/lib/hoc/import3d/Makefile
config.status: creating share/lib/auditscripts/Makefile
config.status: creating share/lib/nrn.defaults
config.status: creating bin/Makefile
config.status: creating bin/nrnocmodl
config.status: creating bin/nrnivmodl
config.status: creating bin/neurondemo
config.status: creating bin/nrngui
config.status: creating bin/bbswork.sh
config.status: creating bin/mos2nrn2.sh
config.status: creating bin/hel2mos1.sh
config.status: creating share/examples/Makefile
config.status: creating share/examples/ivoc/Makefile
config.status: creating share/examples/nrniv/Makefile
config.status: creating share/examples/nrniv/cable/Makefile
config.status: creating share/examples/nrniv/kkin/Makefile
config.status: creating share/examples/nrniv/netcon/Makefile
config.status: creating share/examples/nrniv/netsyn/Makefile
config.status: creating share/examples/nrniv/nmodl/Makefile
config.status: creating share/examples/nrniv/nrnoc/Makefile
config.status: creating share/examples/nrniv/randomsyn/Makefile
config.status: creating share/examples/nrniv/soma/Makefile
config.status: creating share/examples/nrniv/vrecorder/Makefile
config.status: creating share/examples/nrniv/xmech/Makefile
config.status: creating share/demo/Makefile
config.status: creating share/demo/release/Makefile
config.status: creating share/demo/dend3/Makefile
config.status: creating share/demo/sync/Makefile
config.status: creating src/nrnpython/setup.py
RefactoringTool: Skipping implicit fixer: buffer
RefactoringTool: Skipping implicit fixer: idioms
RefactoringTool: Skipping implicit fixer: set_literal
RefactoringTool: Skipping implicit fixer: ws_comma
RefactoringTool: Refactored src/nrnpython/setup.py
--- src/nrnpython/setup.py (original)
+++ src/nrnpython/setup.py (refactored)
@@ -18,10 +18,10 @@
     nrn_srcdir = '../../' + nrn_srcdir
 
 if nrnpython_pyver!=get_python_version():
-    print "Error:"
-    print "NEURON configure time python: "+nrnpython_exec+"  "+ nrnpython_pyver
-    print "Python presently executing setup.py: "+sys.executable+"   "+ get_python_version()
-    print "These do not match, and they should!"
+    print("Error:")
+    print("NEURON configure time python: "+nrnpython_exec+"  "+ nrnpython_pyver)
+    print("Python presently executing setup.py: "+sys.executable+"   "+ get_python_version())
+    print("These do not match, and they should!")
     sys.exit(1)
 
 
RefactoringTool: Files that were modified:
RefactoringTool: src/nrnpython/setup.py
config.status: creating config.h
config.status: config.h is unchanged
config.status: creating nmodlconf.h
config.status: nmodlconf.h is unchanged
config.status: creating nrnconf.h
config.status: nrnconf.h is unchanged
config.status: creating src/nrnoc/nrnconfigargs.h
config.status: src/nrnoc/nrnconfigargs.h is unchanged
config.status: creating src/oc/nrnmpiuse.h
config.status: src/oc/nrnmpiuse.h is unchanged
config.status: creating src/oc/nrnrtuse.h
config.status: src/oc/nrnrtuse.h is unchanged
config.status: creating src/oc/nrnpthread.h
config.status: src/oc/nrnpthread.h is unchanged
config.status: creating src/parallel/bbsconf.h
config.status: src/parallel/bbsconf.h is unchanged
config.status: creating src/nrnjava/njconf.h
config.status: src/nrnjava/njconf.h is unchanged
config.status: creating src/nrncvode/nrnneosm.h
config.status: src/nrncvode/nrnneosm.h is unchanged
config.status: creating src/ivos/ivstream.h
config.status: src/ivos/ivstream.h is unchanged
config.status: creating src/sundials/sundials_config.h
config.status: src/sundials/sundials_config.h is unchanged
config.status: creating src/nrnpython/nrnpython_config.h
config.status: src/nrnpython/nrnpython_config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
however, when i entered

Code: Select all

sudo make
i got the following:

Code: Select all

make  all-recursive
make[1]: Entering directory `/home/mutlu/neuron/nrn'
Making all in src
make[2]: Entering directory `/home/mutlu/neuron/nrn/src'
Making all in memacs
make[3]: Entering directory `/home/mutlu/neuron/nrn/src/memacs'
source='ansi.c' object='ansi.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o ansi.lo ansi.c
source='basic.c' object='basic.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o basic.lo basic.c
source='bind.c' object='bind.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o bind.lo bind.c
source='buffer.c' object='buffer.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o buffer.lo buffer.c
source='display.c' object='display.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o display.lo display.c
source='file.c' object='file.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o file.lo file.c
source='fileio.c' object='fileio.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o fileio.lo fileio.c
source='line.c' object='line.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o line.lo line.c
source='lock.c' object='lock.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o lock.lo lock.c
source='main1.c' object='main1.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o main1.lo main1.c
source='random.c' object='random.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o random.lo random.c
source='region.c' object='region.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o region.lo region.c
source='search.c' object='search.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o search.lo search.c
source='spawn.c' object='spawn.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o spawn.lo spawn.c
source='tcap.c' object='tcap.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o tcap.lo tcap.c
source='termio.c' object='termio.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o termio.lo termio.c
source='window.c' object='window.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o window.lo window.c
source='word.c' object='word.lo' libtool=yes \
        DEPDIR=.deps depmode=none /bin/bash ../../depcomp \
        /bin/bash ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython     -g -O2 -c -o word.lo word.c
/bin/bash ../../libtool --tag=CC   --mode=link gcc  -g -O2   -o libmemacs.la -rpath /opt/nrn-7.2/x86_64/lib ansi.lo basic.lo bind.lo buffer.lo display.lo file.lo fileio.lo line.lo lock.lo main1.lo random.lo region.lo search.lo spawn.lo tcap.lo termio.lo window.lo word.lo -lncurses -lm -ldl
libtool: link: `ansi.lo' is not a valid libtool object
make[3]: *** [libmemacs.la] Error 1
make[3]: Leaving directory `/home/mutlu/neuron/nrn/src/memacs'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/mutlu/neuron/nrn/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/mutlu/neuron/nrn'
make: *** [all] Error 2
i suppose there's a problem with generating "ansi.lo", but i'm not sure.

does anyone know how to cope with this?

hines
Site Admin
Posts: 1580
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON with Python 3.1 installation

Post by hines » Sat Feb 26, 2011 6:36 pm

start with a fresh directory and try 'make' instead of 'sudo make'. If that succeeds then you can do
the next step 'sudo make install'.

hines
Site Admin
Posts: 1580
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON with Python 3.1 installation

Post by hines » Sat Feb 26, 2011 6:39 pm

By the way, the current version of NEURON for Python 3.1 has a memory leak for strings passed from Python to NEURON.
I have not yet been able to figure out a way to avoid it.

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