Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

acnavasolive
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Joined: Mon Feb 19, 2018 11:02 am
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Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Wed Sep 12, 2018 7:34 am

Hi everyone!

I want to use the parallel version of NEURON, so I uninstalled my old one to start from the beginning. I have an Ubuntu 16.04.

I started installing MPICH.
Then, following the main instructions for IV:

Code: Select all

# Compiling iv:
$ ./configure --prefix=`pwd`
$ make
$ make install
and then for NEURON:

Code: Select all

$ ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-paranrn --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python
$ make
I had the following messages...
- for './configure' it seemed ok:

Code: Select all

andrea@inrc-mprida-14:~/neuron/nrn$ ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-paranrn --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python
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... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for style of include used by make... GNU
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.22... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
CYGWIN=no
MINGW=no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
Not trying to build rpms for your system (use --enable-rpm-rules to override) 
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) gawk
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking whether ln -s works... yes
checking for cos in -lm... yes
Python binary found (/home/andrea/anaconda3/envs/py27/bin/python)
checking nrnpython configuration... get_python_version()  '2.7'
sys.version_info[0]  '2'
get_python_inc(0)  '/home/andrea/anaconda3/envs/py27/include/python2.7'
get_config_var('LIBS')  '-lpthread -ldl  -lutil'
get_config_var('LIBRARY')  'libpython2.7.a'
get_config_var('LIBDIR')  '/home/andrea/anaconda3/envs/py27/lib'
get_config_var('LIBS')  '-lpthread -ldl  -lutil'
get_config_var('MODLIBS')  '' returning ''
checking if python include files and libraries work... yes
checking for python... python
checking for cython... yes
checking for cython... cython
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking for mpic++... mpic++
checking for mpi.h... yes
checking how to print strings... printf
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 mpicc... /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 how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
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 dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
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 for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC -DPIC
checking if mpicc PIC flag -fPIC -DPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc 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... yes
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 how to run the C++ preprocessor... mpic++ -E
checking for ld used by mpic++... /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 mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpic++ option to produce PIC... -fPIC -DPIC
checking if mpic++ PIC flag -fPIC -DPIC works... yes
checking if mpic++ static flag -static works... no
checking if mpic++ supports -c -o file.o... yes
checking if mpic++ supports -c -o file.o... (cached) yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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... yes
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... 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_CC=mpicc
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 int64_t... 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 for mallinfo... 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 mpic++ accepts -g... (cached) yes
checking dependency style of mpic++... (cached) gcc3
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-7.4 and later... ok
The signal function does not need a cast for the handler

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
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/modlunit/Makefile
config.status: creating src/nmodl/Makefile
config.status: creating src/nrnpython/Makefile
config.status: creating src/mswin/nrncygso.sh
config.status: creating src/nrnpython/setup.py
config.status: creating share/lib/python/neuron/rxd/geometry3d/Makefile
config.status: creating share/lib/python/neuron/rxd/geometry3d/setup.py
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/Random123/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/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/mac/macdist.pkgproj
config.status: creating src/mac/postinstall.sh
config.status: creating src/mswin/nrnsetup.nsi
config.status: creating src/mswin/lib/mknrndll.mak
config.status: creating src/mswin/nrnsetupmingw.nsi
config.status: creating src/mswin/EnvVarUpdate.nsh
config.status: creating src/mswin/AddToPath.nsh
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/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 share/lib/python/neuron/Makefile
config.status: creating share/lib/python/neuron/rxd/Makefile
config.status: creating config.h
config.status: creating nmodlconf.h
config.status: nmodlconf.h is unchanged
config.status: creating src/nrnpython/nrnpython_config.h
config.status: src/nrnpython/nrnpython_config.h is unchanged
config.status: creating nrnconf.h
config.status: nrnconf.h is unchanged
config.status: creating src/nrnoc/nrnconfigargs.h
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: executing depfiles commands
config.status: executing libtool commands
- but for 'make':

Code: Select all

andrea@inrc-mprida-14:~/neuron/nrn$ make
make  all-recursive
make[1]: Entering directory '/home/andrea/neuron/nrn'
Making all in src
make[2]: Entering directory '/home/andrea/neuron/nrn/src'
Making all in memacs
make[3]: Entering directory '/home/andrea/neuron/nrn/src/memacs'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/memacs'
Making all in modlunit
make[3]: Entering directory '/home/andrea/neuron/nrn/src/modlunit'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/modlunit'
Making all in nmodl
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nmodl'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nmodl'
Making all in sparse
make[3]: Entering directory '/home/andrea/neuron/nrn/src/sparse'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/sparse'
Making all in sparse13
make[3]: Entering directory '/home/andrea/neuron/nrn/src/sparse13'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/sparse13'
Making all in scopmath
make[3]: Entering directory '/home/andrea/neuron/nrn/src/scopmath'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/scopmath'
Making all in Random123
make[3]: Entering directory '/home/andrea/neuron/nrn/src/Random123'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/Random123'
Making all in nrnmpi
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nrnmpi'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrnmpi'
Making all in oc
make[3]: Entering directory '/home/andrea/neuron/nrn/src/oc'
make  all-am
make[4]: Entering directory '/home/andrea/neuron/nrn/src/oc'
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/oc'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/oc'
Making all in nrnoc
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nrnoc'
if test -d ../../.git ; then \
	sh ../../git2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
                if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
                        echo "nrnversion.h not changed" ; \
                        rm ./nrnversion.h.tmp ; \
                else \
                        mv ./nrnversion.h.tmp ./nrnversion.h ; \
                        echo "updated nrnversion.h" ; \
                fi \
elif test -d ../../.hg ; then \
	sh ../../hg2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
	if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
		echo "nrnversion.h not changed" ; \
		rm ./nrnversion.h.tmp ; \
	else \
		mv ./nrnversion.h.tmp ./nrnversion.h ; \
		echo "updated nrnversion.h" ; \
	fi \
else \
	if test -d ../../.svn && svnversion ../.. ; then \
		if test "`svnversion ../..`" != "`sed -n 's/.*SVN_CHANGESET.*(\([^)]*\).*/\1/p' ./nrnversion.h`" ; then \
   			sh ../../svn2nrn_h.sh ../.. > ./nrnversion.h.tmp; \
   			if test -s ./nrnversion.h.tmp ; then \
			mv ./nrnversion.h.tmp ./nrnversion.h ; \
   			fi ; \
   			echo "updated nrnversion.h" ; \
		else \
			echo "nrnversion.h not changed" ; \
		fi \
	fi \
fi
make  all-am
make[4]: Entering directory '/home/andrea/neuron/nrn/src/nrnoc'
if test -d ../../.git ; then \
	sh ../../git2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
                if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
                        echo "nrnversion.h not changed" ; \
                        rm ./nrnversion.h.tmp ; \
                else \
                        mv ./nrnversion.h.tmp ./nrnversion.h ; \
                        echo "updated nrnversion.h" ; \
                fi \
elif test -d ../../.hg ; then \
	sh ../../hg2nrnversion_h.sh ../.. > ./nrnversion.h.tmp ; \
	if cmp ./nrnversion.h.tmp ./nrnversion.h ; then \
		echo "nrnversion.h not changed" ; \
		rm ./nrnversion.h.tmp ; \
	else \
		mv ./nrnversion.h.tmp ./nrnversion.h ; \
		echo "updated nrnversion.h" ; \
	fi \
else \
	if test -d ../../.svn && svnversion ../.. ; then \
		if test "`svnversion ../..`" != "`sed -n 's/.*SVN_CHANGESET.*(\([^)]*\).*/\1/p' ./nrnversion.h`" ; then \
   			sh ../../svn2nrn_h.sh ../.. > ./nrnversion.h.tmp; \
   			if test -s ./nrnversion.h.tmp ; then \
			mv ./nrnversion.h.tmp ./nrnversion.h ; \
   			fi ; \
   			echo "updated nrnversion.h" ; \
		else \
			echo "nrnversion.h not changed" ; \
		fi \
	fi \
fi
/bin/bash ../../libtool  --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnpython -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials  -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi   -g -O2 -MT nrnversion.lo -MD -MP -MF .deps/nrnversion.Tpo -c -o nrnversion.lo nrnversion.c
libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnpython -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -DCABLE=1 -DOOP=1 -I../../src/oc -I../../src/oc -I../../src/scopmath -I../../src/sparse13 -I../../src/nrnmpi -g -O2 -MT nrnversion.lo -MD -MP -MF .deps/nrnversion.Tpo -c nrnversion.c  -fPIC -DPIC -o .libs/nrnversion.o
mv -f .deps/nrnversion.Tpo .deps/nrnversion.Plo
/bin/bash ../../libtool  --tag=CC   --mode=link mpicc  -g -O2   -o libnrnoc.la -rpath /home/andrea/neuron/nrn/x86_64/lib hh.lo feature.lo passive.lo stim.lo syn.lo vclmp.lo apcount.lo svclmp.lo oclmp.lo xmech.lo netstim.lo intfire1.lo intfire2.lo intfire4.lo expsyn.lo exp2syn.lo ppmark.lo pattern.lo cabcode.lo capac.lo clamp.lo eion.lo extcelln.lo fadvance.lo fstim.lo init.lo nrnnemo.lo point.lo psection.lo solve.lo synapse.lo treeset.lo hoc_init.lo code.lo hoc_oop.lo seclist.lo method3.lo hocprax.lo secref.lo ldifus.lo hocusr.lo nrnversion.lo nrntimeout.lo passive0.lo  -lm -ldl
libtool: link: rm -fr  .libs/libnrnoc.la .libs/libnrnoc.lai .libs/libnrnoc.so .libs/libnrnoc.so.0 .libs/libnrnoc.so.0.0.0
libtool: link: mpicc -shared  -fPIC -DPIC  .libs/hh.o .libs/feature.o .libs/passive.o .libs/stim.o .libs/syn.o .libs/vclmp.o .libs/apcount.o .libs/svclmp.o .libs/oclmp.o .libs/xmech.o .libs/netstim.o .libs/intfire1.o .libs/intfire2.o .libs/intfire4.o .libs/expsyn.o .libs/exp2syn.o .libs/ppmark.o .libs/pattern.o .libs/cabcode.o .libs/capac.o .libs/clamp.o .libs/eion.o .libs/extcelln.o .libs/fadvance.o .libs/fstim.o .libs/init.o .libs/nrnnemo.o .libs/point.o .libs/psection.o .libs/solve.o .libs/synapse.o .libs/treeset.o .libs/hoc_init.o .libs/code.o .libs/hoc_oop.o .libs/seclist.o .libs/method3.o .libs/hocprax.o .libs/secref.o .libs/ldifus.o .libs/hocusr.o .libs/nrnversion.o .libs/nrntimeout.o .libs/passive0.o   -lm -ldl  -g -O2   -Wl,-soname -Wl,libnrnoc.so.0 -o .libs/libnrnoc.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libnrnoc.so.0" && ln -s "libnrnoc.so.0.0.0" "libnrnoc.so.0")
libtool: link: (cd ".libs" && rm -f "libnrnoc.so" && ln -s "libnrnoc.so.0.0.0" "libnrnoc.so")
libtool: link: ( cd ".libs" && rm -f "libnrnoc.la" && ln -s "../libnrnoc.la" "libnrnoc.la" )
/bin/bash ../../libtool  --tag=CC   --mode=link mpicc  -g -O2   -o nrnoc ocmain.o nrnnoiv.o ocnoiv.o cprop.o ../oc/modlreg.o libnrnoc.la ../oc/liboc.la ../memacs/libmemacs.la ../scopmath/libscopmath.la ../sparse13/libsparse13.la ../nrnmpi/libnrnmpi.la -lreadline -lncurses  -lm -ldl
libtool: link: mpicc -g -O2 -o .libs/nrnoc ocmain.o nrnnoiv.o ocnoiv.o cprop.o ../oc/modlreg.o  ./.libs/libnrnoc.so ../oc/.libs/liboc.so ../memacs/.libs/libmemacs.so ../scopmath/.libs/libscopmath.so ../sparse13/.libs/libsparse13.so ../nrnmpi/.libs/libnrnmpi.so -lreadline -lncurses -lm -ldl -Wl,-rpath -Wl,/home/andrea/neuron/nrn/x86_64/lib
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/nrnoc'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrnoc'
Making all in nrnpython
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nrnpython'
if test inithoc.cpp -ot ../../src/nrnpython/inithoc.cpp ; then \
	cp ../../src/nrnpython/inithoc.cpp inithoc.cpp ; \
fi
make  all-am
make[4]: Entering directory '/home/andrea/neuron/nrn/src/nrnpython'
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/nrnpython'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrnpython'
Making all in sundials
make[3]: Entering directory '/home/andrea/neuron/nrn/src/sundials'
make  all-recursive
make[4]: Entering directory '/home/andrea/neuron/nrn/src/sundials'
Making all in shared
make[5]: Entering directory '/home/andrea/neuron/nrn/src/sundials/shared'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/home/andrea/neuron/nrn/src/sundials/shared'
Making all in cvodes
make[5]: Entering directory '/home/andrea/neuron/nrn/src/sundials/cvodes'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/home/andrea/neuron/nrn/src/sundials/cvodes'
Making all in ida
make[5]: Entering directory '/home/andrea/neuron/nrn/src/sundials/ida'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/home/andrea/neuron/nrn/src/sundials/ida'
make[5]: Entering directory '/home/andrea/neuron/nrn/src/sundials'
make[5]: Leaving directory '/home/andrea/neuron/nrn/src/sundials'
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/sundials'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/sundials'
Making all in mesch
make[3]: Entering directory '/home/andrea/neuron/nrn/src/mesch'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/mesch'
Making all in gnu
make[3]: Entering directory '/home/andrea/neuron/nrn/src/gnu'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/gnu'
Making all in ivoc
make[3]: Entering directory '/home/andrea/neuron/nrn/src/ivoc'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/ivoc'
Making all in nrncvode
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nrncvode'
make  all-am
make[4]: Entering directory '/home/andrea/neuron/nrn/src/nrncvode'
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/nrncvode'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrncvode'
Making all in parallel
make[3]: Entering directory '/home/andrea/neuron/nrn/src/parallel'
make  all-am
make[4]: Entering directory '/home/andrea/neuron/nrn/src/parallel'
make[4]: Leaving directory '/home/andrea/neuron/nrn/src/parallel'
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/parallel'
Making all in nrniv
make[3]: Entering directory '/home/andrea/neuron/nrn/src/nrniv'
/bin/bash ../../libtool  --tag=CXX   --mode=link mpic++  -D_GLIBCXX_USE_CXX11_ABI=0   -o nrniv nvkludge.o ../ivoc/nrnmain.o ../ivoc/ivocmain.o ../oc/modlreg.o ../oc/ockludge.o ../nrnoc/libnrnoc.la ../oc/liboc.la libnrniv.la ../ivoc/libivoc.la ../oc/liboc.la ../nrnmpi/libnrnmpi.la     ../gnu/libneuron_gnu.la ../scopmath/libscopmath.la ../sparse13/libsparse13.la ../sundials/libsundials.la ../memacs/libmemacs.la ../mesch/libmeschach.la  /home/andrea/neuron/iv/x86_64/lib/libIVhines.la  ../nrnpython/libnrnpython.la -L/home/andrea/anaconda3/envs/py27/lib -lpython2.7 -lpthread -ldl  -lutil  -R/home/andrea/anaconda3/envs/py27/lib -lreadline -lncurses  -lm -ldl
libtool: link: mpic++ -D_GLIBCXX_USE_CXX11_ABI=0 -o .libs/nrniv nvkludge.o ../ivoc/nrnmain.o ../ivoc/ivocmain.o ../oc/modlreg.o ../oc/ockludge.o  ../nrnoc/.libs/libnrnoc.so ./.libs/libnrniv.so ../ivoc/.libs/libivoc.so ../oc/.libs/liboc.so ../nrnmpi/.libs/libnrnmpi.so ../gnu/.libs/libneuron_gnu.so ../scopmath/.libs/libscopmath.so ../sparse13/.libs/libsparse13.so ../sundials/.libs/libsundials.so ../memacs/.libs/libmemacs.so ../mesch/.libs/libmeschach.so /home/andrea/neuron/iv/x86_64/lib/libIVhines.so ../nrnpython/.libs/libnrnpython.so -L/home/andrea/anaconda3/envs/py27/lib -lpython2.7 -lpthread -lutil -lreadline -lncurses -lm -ldl -Wl,-rpath -Wl,/home/andrea/neuron/nrn/x86_64/lib -Wl,-rpath -Wl,/home/andrea/neuron/iv/x86_64/lib -Wl,-rpath -Wl,/home/andrea/anaconda3/envs/py27/lib
./.libs/libnrniv.so: undefined reference to `VTT for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
Makefile:743: recipe for target 'nrniv' failed
make[3]: *** [nrniv] Error 1
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrniv'
Makefile:516: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/andrea/neuron/nrn/src'
Makefile:653: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/andrea/neuron/nrn'
Makefile:511: recipe for target 'all' failed
make: *** [all] Error 2

there were several errors:

collect2: error: ld returned 1 exit status

Makefile:743: recipe for target 'nrniv' failed
make[3]: *** [nrniv] Error 1
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrniv'

Makefile:516: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/andrea/neuron/nrn/src'

Makefile:653: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/andrea/neuron/nrn'

Makefile:511: recipe for target 'all' failed
make: *** [all] Error 2



I tried searching for similar errors in the forum, as this one:
viewtopic.php?t=3880
so I added CXXFLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' to the configure:

Code: Select all

./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-paranrn --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python CXXFLAGS='-D_GLIBCXX_USE_CXX11_ABI=0'
but I still have the same errors.

What should I do to solve them?

Thanks in advance!! :D

Andrea

ted
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Location: Yale University School of Medicine
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by ted » Wed Sep 12, 2018 4:34 pm

First question: what neuron source code did you use? Did you get
https://neuron.yale.edu/ftp/neuron/vers ... 6.2.tar.gz
or did you get the latest development code from the github repository?

Second question: whichever one you got, did you get it after August 15?


ted
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by ted » Thu Sep 13, 2018 9:55 am

Use 7.6 instead. Get the source code from the links at https://neuron.yale.edu/neuron/getstd

acnavasolive
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Fri Sep 14, 2018 4:19 am

I downloaded the 7.6 version and again, there was no problems with the iv installation, and the same errors when I tried to compile NEURON:

collect2: error: ld returned 1 exit status
Makefile:746: recipe for target 'nrniv' failed
make[3]: *** [nrniv] Error 1
make[3]: Leaving directory '/home/andrea/neuron/nrn/src/nrniv'

Makefile:518: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/andrea/neuron/nrn/src'

Makefile:655: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/andrea/neuron/nrn'

Makefile:513: recipe for target 'all' failed
make: *** [all] Error 2

hines
Site Admin
Posts: 1517
Joined: Wed May 18, 2005 3:32 pm

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by hines » Fri Sep 14, 2018 11:44 am

do
which mpicc
which mpic++
which mpicxx
which mpiexe
all seem to come from the same place?

The interviews installation seemed to work. But can you verify by launching
$HOME/neuron/iv/x86_64/bin/idraw

I'm going to guess that the mpich installation has a problem. Do things compile with
make dist_clean
./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python --disable-rx3d
make -j
make install
x86_64/bin/nrniv -python
import neuron
neuron.test()

ted
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Location: Yale University School of Medicine
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by ted » Fri Sep 14, 2018 11:55 am

Apropos of mpicc etc.--
under CentOS 7.x (and probably Red Hat 7.x as well), mpicc ends up in /usr/lib64/mpich-3.2/bin. I had to add this to PATH myself.

acnavasolive
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Mon Sep 17, 2018 5:39 am

Hi!

Yes, all mpicc, mpic++, mpicxx and mpiexec are in /usr/bin/

Also, the interviews installation was ok, since $HOME/neuron/iv/x86_64/bin/idraw worked. There was just an error message: "invalid font name -*-Symbol-*-12-*-*-*-*-*-*-*, substituting fixed font", but except for that, it was alright.



The configure,

Code: Select all

$ ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/home/andrea/anaconda3/envs/py27/bin/python --disable-rx3d > /home/andrea/configure.txt
made two warnings:
  • config.status: WARNING: 'bin/nrnoc_makefile.in' seems to ignore the --datarootdir setting
  • config.status: WARNING: 'bin/nrniv_makefile.in' seems to ignore the --datarootdir setting
along with the configure messages, that can be seen in the configure.txt file in here:
https://www.dropbox.com/sh/ifvzb94sgn0z ... pEgja?dl=0

Compilation failed again.

Code: Select all

$ make -j > /home/andrea/make.txt
Compilation messages can be seen in the make.txt file in here:
https://www.dropbox.com/sh/ifvzb94sgn0z ... pEgja?dl=0
and terminal messages were:

Code: Select all

Translating hh.mod into hh.c
Translating passive.mod into passive.c
Translating feature.mod into feature.c
Notice: VERBATIM blocks are not thread safe
Translating stim.mod into stim.c
Translating vclmp.mod into vclmp.c
Translating svclmp.mod into svclmp.c
Translating apcount.mod into apcount.c
Translating syn.mod into syn.c
Translating oclmp.mod into oclmp.c
Notice: VERBATIM blocks are not thread safe
Notice: LINEAR is not thread safe.
Translating xmech.mod into xmech.c
Translating netstim.mod into netstim.c
Translating intfire2.mod into intfire2.c
Translating intfire1.mod into intfire1.c
Translating intfire4.mod into intfire4.c
Translating ppmark.mod into ppmark.c
Translating exp2syn.mod into exp2syn.c
Translating expsyn.mod into expsyn.c
Translating pattern.mod into pattern.c
Notice: Use of POINTER is not thread safe.
Notice: VERBATIM blocks are not thread safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
Thread Safe
In file included from /home/andrea/anaconda3/envs/py27/include/python2.7/Python.h:8:0,
                 from ./nrnwrap_Python.h:9,
                 from grids.h:11,
                 from rxd.c:5:
/home/andrea/anaconda3/envs/py27/include/python2.7/pyconfig.h:1190:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from rxd.c:2:
/usr/include/features.h:228:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
In file included from /home/andrea/anaconda3/envs/py27/include/python2.7/Python.h:8:0,
                 from ./nrnwrap_Python.h:9,
                 from grids.h:11,
                 from rxd_extracellular.c:5:
/home/andrea/anaconda3/envs/py27/include/python2.7/pyconfig.h:1190:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from rxd_extracellular.c:2:
/usr/include/features.h:228:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
In file included from /home/andrea/anaconda3/envs/py27/include/python2.7/Python.h:8:0,
                 from ./nrnwrap_Python.h:9,
                 from grids.h:11,
                 from rxd_vol.c:4:
/home/andrea/anaconda3/envs/py27/include/python2.7/pyconfig.h:1190:0: warning: "_POSIX_C_SOURCE" redefined
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from rxd_vol.c:2:
/usr/include/features.h:228:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')
./.libs/libnrniv.so: undefined reference to `VTT for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/andrea/neuron/iv/x86_64/lib/libIVhines.so: undefined reference to `VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
./.libs/libnrniv.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make[3]: *** [nrniv] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

hines
Site Admin
Posts: 1517
Joined: Wed May 18, 2005 3:32 pm

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by hines » Mon Sep 17, 2018 10:18 am

It is easier to see the relationship between stderr and stdout by making available the interleaved output in a single file via
make >& temp

But no need to do that in this case as it is undoubtedly similar to your first message.
We already suspect that the problem is related to your mpich installation. It was not specified how you installed mpich. I have an mpich
installation on my machine and it works well. But I installed it in $HOME/soft as I have to deal with multiple installations of mpi. And my
default installation is openmpi from ubuntu's 'sudo apt install openmpi_dev'. (I may not be remembering this exactly so try 'apt search openmpi'
to get the correct name.
I think is is worth trying again with the openmpi installation to see if the problem goes away. If so we can pursue the issue with mpich but I would
need to know the mpich version you are using. Their downloads page says for the stable version 3.2.1

acnavasolive
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Mon Sep 17, 2018 11:43 am

I installed mpich with:

Code: Select all

sudo apt install mpich
and I have just uninstalled it with:

Code: Select all

sudo apt remove mpich
To install it again, I did as you said:

Code: Select all

$ sudo apt install libopenmpi-dev

Leyendo lista de paquetes... Hecho
Creando arbol de dependencias       
Leyendo la informacion de estado... Hecho
libopenmpi-dev ya esta en su version mas reciente (1.10.2-8ubuntu1).
0 actualizados, 0 nuevos se instalaran, 0 para eliminar y 331 no actualizados.
I found out that I had already openmpi.

hines
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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by hines » Mon Sep 17, 2018 2:51 pm

I found out that I had already openmpi.
Nothing wrong with that in principle. So for nrn
make distclean
./configure ... # just like you did before
make -j install

and does that succeed?

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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Tue Sep 18, 2018 4:15 am

No... it fails again, same errors.
Here there are the resulted files from the >&:
https://www.dropbox.com/sh/ifvzb94sgn0z ... pEgja?dl=0

There is also information about my current version of OpenMPI in ompi_info.txt

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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Tue Sep 18, 2018 6:41 am

I am a beginner with OpenMPI, so I can't really do much with it right now, but I have been trying to check if it worked ok running easy examples. Here it is what I did:

Code: Select all

$ mpirun -np 4 mpi_hello_world
--------------------------------------------------------------------------
[[3509,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: inrc-mprida-14

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
Hello world from processor inrc-mprida-14, rank 1 out of 4 processors
Hello world from processor inrc-mprida-14, rank 3 out of 4 processors
Hello world from processor inrc-mprida-14, rank 0 out of 4 processors
Hello world from processor inrc-mprida-14, rank 2 out of 4 processors
[inrc-mprida-14:23909] 3 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics
[inrc-mprida-14:23909] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
But as I am working with just one machine:

Code: Select all

$ mpirun -np 4 -mca btl ^openib mpi_hello_world
Hello world from processor inrc-mprida-14, rank 0 out of 4 processors
Hello world from processor inrc-mprida-14, rank 1 out of 4 processors
Hello world from processor inrc-mprida-14, rank 3 out of 4 processors
Hello world from processor inrc-mprida-14, rank 2 out of 4 processors
I don't know if this information helps in any way.

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

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by hines » Tue Sep 18, 2018 8:23 am

The openmpi is working. But I missed the fact in your earlier message that the problem has nothing to do with mpi as linking fails even
in the absence of --with-paranrn. That makes me wonder if you have an incomplete g++ development environment or one that has inconsistent
libraries. The build environment I use on ubuntu 16.4 is

Code: Select all

# Install build tools needed to compile and link NEURON
# ubuntu example

base="build-essential libreadline-dev libx11-dev libxext-dev
  libncurses-dev zlib1g-dev"
bld="git automake libtool flex bison"
mpi="libopenmpi-dev" # if desire parallel
py="python3-dev python3-scipy cython3" # and/or python-dev etc.

sudo apt install $base $bld $mpi $py
Since you arleady have python you can leave that part out. In fact, just try base and see if anything installs or is updated.

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Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Post by acnavasolive » Tue Sep 18, 2018 8:44 am

Oh! I haven't noticed that either.

Code: Select all

$ base="build-essential libreadline-dev libx11-dev libxext-dev libncurses-dev zlib1g-dev"
$ sudo apt install $base
Leyendo lista de paquetes... Hecho
Creando árbol de dependencias       
Leyendo la información de estado... Hecho
Nota, seleccionando «libncurses5-dev» en lugar de «libncurses-dev»
build-essential ya está en su versión más reciente (12.1ubuntu2).
libncurses5-dev ya está en su versión más reciente (6.0+20160213-1ubuntu1).
libreadline-dev ya está en su versión más reciente (6.3-8ubuntu2).
libxext-dev ya está en su versión más reciente (2:1.3.3-1).
fijado libxext-dev como instalado manualmente.
libx11-dev ya está en su versión más reciente (2:1.6.3-1ubuntu2.1).
zlib1g-dev ya está en su versión más reciente (1:1.2.8.dfsg-2ubuntu4.1).
0 actualizados, 0 nuevos se instalarán, 0 para eliminar y 321 no actualizados.
No updated, nor installed libraries.

However, I tried the other two, bld and mpi and bison, flex, libbison-dev and libfl-dev have been installed.

Code: Select all

$ sudo apt install $bld $mpi
Leyendo lista de paquetes... Hecho
Creando árbol de dependencias       
Leyendo la información de estado... Hecho
automake ya está en su versión más reciente (1:1.15-4ubuntu1).
fijado automake como instalado manualmente.
libtool ya está en su versión más reciente (2.4.6-0.1).
fijado libtool como instalado manualmente.
libopenmpi-dev ya está en su versión más reciente (1.10.2-8ubuntu1).
git ya está en su versión más reciente (1:2.7.4-0ubuntu1.4).
Se instalarán los siguientes paquetes adicionales:
  libbison-dev libfl-dev
Paquetes sugeridos:
  bison-doc
Se instalarán los siguientes paquetes NUEVOS:
  bison flex libbison-dev libfl-dev
0 actualizados, 4 nuevos se instalarán, 0 para eliminar y 321 no actualizados.
Se necesita descargar 900 kB de archivos.
Se utilizarán 2.692 kB de espacio de disco adicional después de esta operación.
¿Desea continuar? [S/n] S
Des:1 http://es.archive.ubuntu.com/ubuntu xenial/main amd64 libfl-dev amd64 2.6.0-11 [12,5 kB]
Des:2 http://es.archive.ubuntu.com/ubuntu xenial/main amd64 flex amd64 2.6.0-11 [290 kB]
Des:3 http://es.archive.ubuntu.com/ubuntu xenial/main amd64 libbison-dev amd64 2:3.0.4.dfsg-1 [338 kB]
Des:4 http://es.archive.ubuntu.com/ubuntu xenial/main amd64 bison amd64 2:3.0.4.dfsg-1 [259 kB]
Descargados 900 kB en 0s (1.470 kB/s)
Seleccionando el paquete libfl-dev:amd64 previamente no seleccionado.
(Leyendo la base de datos ... 387927 ficheros o directorios instalados actualmente.)
Preparando para desempaquetar .../libfl-dev_2.6.0-11_amd64.deb ...
Desempaquetando libfl-dev:amd64 (2.6.0-11) ...
Seleccionando el paquete flex previamente no seleccionado.
Preparando para desempaquetar .../flex_2.6.0-11_amd64.deb ...
Desempaquetando flex (2.6.0-11) ...
Seleccionando el paquete libbison-dev:amd64 previamente no seleccionado.
Preparando para desempaquetar .../libbison-dev_2%3a3.0.4.dfsg-1_amd64.deb ...
Desempaquetando libbison-dev:amd64 (2:3.0.4.dfsg-1) ...
Seleccionando el paquete bison previamente no seleccionado.
Preparando para desempaquetar .../bison_2%3a3.0.4.dfsg-1_amd64.deb ...
Desempaquetando bison (2:3.0.4.dfsg-1) ...
Procesando disparadores para libc-bin (2.23-0ubuntu10) ...
Procesando disparadores para install-info (6.1.0.dfsg.1-5) ...
Procesando disparadores para doc-base (0.10.7) ...
Procesando 1 archivo doc-base añadido...
Registrando documentos con scrollkeeper...
Procesando disparadores para man-db (2.7.5-1) ...
Configurando libfl-dev:amd64 (2.6.0-11) ...
Configurando flex (2.6.0-11) ...
Configurando libbison-dev:amd64 (2:3.0.4.dfsg-1) ...
Configurando bison (2:3.0.4.dfsg-1) ...
update-alternatives: utilizando /usr/bin/bison.yacc para proveer /usr/bin/yacc (yacc) en modo automático
Procesando disparadores para libc-bin (2.23-0ubuntu10) ...
Shall I try installing NEURON again?

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