Compiling NEURON on a cluster

[Sandrine]

Hello Ted, Michael,

We attempt to compile neuron on a cluster
http://www-sop.inria.fr/parallel/hardware.en.html in order to run large
simulations
http://www-sop.inria.fr/members/Sandrin ... tal-07.pdf

System characteristics
Linux FC7 2.4.21-52.ELsmp #1 SMP Mon Nov 26 18:58:58 EST 2007
x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-59)
mpich2-gnu-1.0.3-3 libtool-1.4.3-6
and experiment the following caveats, very likely due to some bad
install on our side:
with nrniv : Assertion failed: file symbol.c, line 239 nrn-run.sh: line
5: 21397 Segmentation fault (core dumped)
with nrnoc: StringFunctions is not a template

what was wrong on our side ?

Attached the run log and the configure log:

run log:

export PATH=$PATH:/export/home/vthierry/nrn/x86_64/bin
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/home/vthierry/nrn/lib:/export/home/vthierry/nrn/x86_64/lib
cd generatedNEURON

nrniv Project_evol_temp_test.hoc
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Assertion failed: file symbol.c, line 239
nrn-run.sh: line 5: 21397 Segmentation fault (core dumped) nrniv
Project_evol_temp_test.hoc


nrnoc Project_evol_temp_test.hoc
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

loading membrane mechanisms from x86_64/.libs/libnrnmech.so
dlopen failed -
/export/home/vthierry/nrn/x86_64/lib/libivoc.so.0: undefined symbol:
_ZNK10ivResource3refEv
nrnoc: StringFunctions is not a template
in stdlib.hoc near line 72
hoc_sf_ = new StringFunctions()
^
xopen("stdlib.hoc")
execute1("{xopen("stdlib.hoc")}")
load_file("stdlib.hoc")
xopen("stdgui.hoc")
and others
nrnoc: Segmentation violation
in stdlib.hoc near line 72
^

configure log

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
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 for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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++... gcc3
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 ANSI C... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for flex... flex
checking for yywrap in -lfl... yes
checking lex output file root... lex.yy
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... 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 whether stripping libraries is possible... yes
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 if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
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
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... 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
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 static flag -static works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 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
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking for mpic++... mpic++
checking for mpi.h... 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... disabled
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... yes
checking varargs.h presence... yes
checking for varargs.h... yes
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... yes
checking stream.h presence... yes
checking for stream.h... yes
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 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
disable everything depending on x11
Not compiling with interviews.
Building nrniv only with classes that do not depend on InterViews.
The signal function does not need a cast for the handler

do SIGPOLL and I_GETSIG work: yes
checking whether the compiler supports Standard Template Library... yes
NRNOC_X11 = 0
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/nrnpython/setup.py
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 share/Makefile
config.status: creating bin/nrnoc_makefile
config.status: creating bin/nrniv_makefile
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 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/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


Sincerely,
Sandrine.

[ted]

We attempt to compile neuron

What happens when you execute
nrniv
at the system command prompt?

What happens when you execute
nrnoc
at the system command prompt?

Does Project_evol_temp_test.hoc use any mechanisms that are defined by mod files, which must be compiled with mknrndll?

--Ted

[Sandrine]

>nrniv

NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16

Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008

See http://www.neuron.yale.edu/credits.html



Assertion failed: file symbol.c, line 239

nrn-run.sh: line 4: 24934 Segmentation fault (core dumped) nrniv


> nrnoc

NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16

Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008

See http://www.neuron.yale.edu/credits.html



loading membrane mechanisms from x86_64/.libs/libnrnmech.so

dlopen failed -

x86_64/.libs/libnrnmech.so: undefined symbol: nrn_actual_v

oc>



after running nrnivmodl



while before we got:



NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16

Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008

See http://www.neuron.yale.edu/credits.html



loading membrane mechanisms from x86_64/.libs/libnrnmech.so

dlopen failed -

/export/home/vthierry/nrn/x86_64/lib/libivoc.so.0: undefined symbol:
_ZNK10ivResource3refEv

oc>



while setting:

export PATH=$PATH:$HOME/nrn/x86_64/bin

export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/nrn/lib:$HOME/nrn/x86_64/lib




Does Project_evol_temp_test.hoc use any mechanisms that are defined by mod
files, which must be compiled with mknrndll?

I can not find mknrndll installed (is it like nrnivmodl??) but notice that i am under linux not mswin.

Sandrine.

[ted]

I can not find mknrndll installed (is it like nrnivmodl??) but notice that i am under linux not mswin.

Sorry, I meant nrnivmodl. So, does Project_evol_temp_test.hoc use any mechanisms that are defined by mod files, which must be compiled with nrnivmodl?

The output from configure, which you included in your original message, suggests that configure succeeded. What was the command line that you used to run configure? (something like
./configure
with some command line switches--what were they?)

Did make and make install succeed? What were the last ~10 lines of output produced by each of these commands?

[Sandrine]

Dear Ted,
Thanks to the ``write questions´´ you asked we very carrefully rerun install/compil using mpich2 (we could have used openmpi or other platforms like lam/mpi etc.. but this one seems the best) and got a sane compilation and install while nrniv and nrnoc alone works well. We have zipped install scripts and logs.
We however have still undefined symbol with nrnoc:
loading membrane mechanisms from x86_64/.libs/libnrnmech.so
dlopen failed -
x86_64/.libs/libnrnmech.so: undefined symbol: nrn_actual_v
nrnoc: StringFunctions is not a template
while with nrniv a syntax error is announced (while we do not get it on with other nrn). I send to you by email the Log details are in the ZIP and the source.

So that we still need help . . !

Sincerely


The ``empty test´´:

[vthierry@nef-devel ~]$ export PATH=$PATH:$HOME/nrn/x86_64/bin
[vthierry@nef-devel ~]$ export LD_LIBRARY_PATH=$HOME/nrn/lib:$HOME/nrn/x86_64/lib:$LD_LIBRARY_PATH
[vthierry@nef-devel ~]$ nrniv
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

oc>
[vthierry@nef-devel ~]$ nrnoc
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

oc>

[hines]

Forget about nrnoc. That is now so limited as to be useless since it does not contain any c++ classes such
as NetCon and Cvode. It continues to exist only as an intermediate stage in the build process and I only
care that it compiles not if it works.
The problem with nrniv is a bit of a puzzle since your configure log says:
checking for posix_memalign... yes
and the assertion error at line 239 in symbol.c is

Code: Select all

#if HAVE_MEMALIGN
        assert(posix_memalign(memptr, 64, size) == 0);
#else

Try manually editing the configure created nrnconf.h file in directory you type 'make' and change
#define HAVE_POSIX_MEMALIGN 1
to
#undef HAVE_POSIX_MEMALIGN
and then
make clean
make
make install
It should not matter that you bypass this since it is only needed for good thread performance.
If this does not fix things, then be sure to specify the exact configure line you used.