Error compiling nrniv - caused by bbsrcli.cpp?

Post Reply
tyrell_turing
Posts: 4
Joined: Fri Jan 24, 2014 5:33 pm

Error compiling nrniv - caused by bbsrcli.cpp?

Post by tyrell_turing » Wed Feb 26, 2014 4:04 pm

Hi there,

I am trying to compile NEURON on a Dell XPS Ultrabook running Ubuntu 12.10. I had no problems compiling and installing InterViews, but I am having a real tough time with an error I'm getting when compiling NEURON itself. The error appears when compiling in the nrniv directory. In particular, I get the following error:

Code: Select all

$ sudo make

... everything fine through here...

Making all in nrniv
make[3]: Entering directory `/usr/local/neuron/nrn/src/nrniv'
/bin/bash ../../libtool --tag=CXX   --mode=compile g++ -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  -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I/usr/local/neuron/iv/include  -I../../src/parallel -I../../src/nrnmpi -I/include -I. -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1  -pthread -g -O2 -MT bbsrcli.lo -MD -MP -MF .deps/bbsrcli.Tpo -c -o bbsrcli.lo bbsrcli.cpp
libtool: compile:  g++ -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 -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I/usr/local/neuron/iv/include -I../../src/parallel -I../../src/nrnmpi -I/include -I. -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -pthread -g -O2 -MT bbsrcli.lo -MD -MP -MF .deps/bbsrcli.Tpo -c bbsrcli.cpp  -fPIC -DPIC -o .libs/bbsrcli.o
In file included from bbsrcli.cpp:5:0:
../parallel/bbsrcli.cpp: In member function 'virtual char* BBSClient::upkpickle(size_t*)':
../parallel/bbsrcli.cpp:90:9: error: 's' was not declared in this scope
make[3]: *** [bbsrcli.lo] Error 1
make[3]: Leaving directory `/usr/local/neuron/nrn/src/nrniv'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/usr/local/neuron/nrn/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/neuron/nrn'
make: *** [all] Error 2
For the record, I am trying to compile everything in a directory /usr/local/neuron where I have put both iv and nrn. When I run configure for the NEURON compilation everything seems fine, though there are a few minor error messages. I had ignored them because everything seemed okay (Makefiles were generated, etc), but now I'm wondering if there were problems. Here's the output from my configure:

Code: Select all

$ sudo ./configure --prefix=/usr/local/neuron/nrn/ --with-iv=/usr/local/neuron/iv
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
CYGWIN=no
MINGW=no
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++... gcc3
sh: 0: Can't open /home/blake/neuron/nrn/hg2nrnversion_h.sh
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... gcc3
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 cos in -lm... yes
checking for cython... cython
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 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 how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-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 gcc object... ok
checking for sysroot... no
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 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 how to run the C++ preprocessor... g++ -E
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... (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... 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 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 g++ accepts -g... (cached) yes
checking dependency style of g++... (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-7.3 and later... ok
The signal function does not need a cast for the handler
checking /usr/include/pvm3.h usability... yes
checking /usr/include/pvm3.h presence... yes
checking for /usr/include/pvm3.h... yes
sed: can't read /usr/conf/.def: No such file or directory
PVM_XTRA_LIBS=
checking for pvm_parent in -lpvm3... yes
checking for pvm_pkmesg in -lpvm3... yes

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/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/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/nrnsetupmingw.nsi
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 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
I'm wondering now, is the problem I'm having at all related to these messages from configure?

Code: Select all

...
sed: can't read /usr/conf/.def: No such file or directory
PVM_XTRA_LIBS=
checking for pvm_parent in -lpvm3... yes
checking for pvm_pkmesg in -lpvm3... yes

do SIGPOLL and I_GETSIG work: no
But see config.log to see why it failed.
...
When I look at the bbsrcli.cpp file, there is indeed a string 's' that is being returned by BBSClient::upkpickle() though it is not declared. I'm assuming this is not just a bug in the code? But then, where does this 's' variable get defined?

Does anyone have any ideas? Any help would be greatly appreciated.

Thanks,

Blake

ted
Site Admin
Posts: 5591
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Error compiling nrniv - caused by bbsrcli.cpp?

Post by ted » Wed Feb 26, 2014 9:51 pm

Which source code are you using and for which version of NEURON?
From the standard distribution's gzipped tar files, from one of the alpha versions, or are you using the latest from the mercurial repository?

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: Error compiling nrniv - caused by bbsrcli.cpp?

Post by hines » Thu Feb 27, 2014 7:31 pm

All of the PVM dependent files are vestigial and have been superseded by MPI versions of those files.
The problem is manifested because of the accident that your machine has PVM installed and you are not building a parallel version ( --with-paranrn)
I'll have to change the configuration files so that under no circumstances will the PVM dependent files be used.
Untli then, try the work around of adding 'use_mpi=abc' as a configure argument and try to rebuild from a fresh set of
sources.

I'm a little worried about that 'sed' error. But if the above works, there is no reason to pursue it.

tyrell_turing
Posts: 4
Joined: Fri Jan 24, 2014 5:33 pm

Re: Error compiling nrniv - caused by bbsrcli.cpp?

Post by tyrell_turing » Sun Mar 02, 2014 3:49 pm

Thanks both of you for your help! PVM was indeed the cause of the problem. I no longer needed PVM, so I just removed it from my computer and then everything compiled just fine.

Thanks again,

Blake

Post Reply