BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead

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selfdestructo
Posts: 32
Joined: Wed Oct 14, 2009 11:12 am

BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead

Post by selfdestructo » Tue Dec 04, 2018 5:39 am

Dear Neuron developers,

I'm experiencing some issues with the build.sh script and the configure step of NEURON on a cluster. I've compiled it previously on the same machine, so I'm a bit confused why it doesn't work now.

These are the loaded modules (seems pretty ordinary):

Code: Select all

$ module list

Currently Loaded Modules:
  1) StdEnv                                             (S)   9) imkl/2018.1.163-iimpi-2018a      17) Java/1.8.0_162                     25) Autotools/20170619-GCCcore-6.4.0 (H)
  2) GCCcore/6.4.0                                           10) intel/2018a                      18) Python/3.6.4-intel-2018a           26) libreadline/7.0-GCCcore-6.4.0    (H)
  3) binutils/2.28-GCCcore-6.4.0                        (H)  11) bzip2/1.0.6-GCCcore-6.4.0   (H)  19) libtool/2.4.6-GCCcore-6.4.0   (H)  27) Doxygen/1.8.13-GCCcore-6.4.0     (H)
  4) icc/2018.1.163-GCC-6.4.0-2.28                           12) zlib/1.2.11-GCCcore-6.4.0   (H)  20) flex/2.6.4-GCCcore-6.4.0      (H)  28) libyaml/0.1.7-GCCcore-6.4.0      (H)
  5) ifort/2018.1.163-GCC-6.4.0-2.28                         13) ncurses/6.0-GCCcore-6.4.0   (H)  21) Bison/3.0.4-GCCcore-6.4.0     (H)  29) MATLAB/2018a
  6) iccifort/2018.1.163-GCC-6.4.0-2.28                      14) GMP/6.1.2-GCCcore-6.4.0     (H)  22) CMake/3.10.1-GCCcore-6.4.0    (H)
  7) impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28      15) libffi/3.2.1-GCCcore-6.4.0  (H)  23) Automake/1.15.1-GCCcore-6.4.0 (H)
  8) iimpi/2018a                                             16) M4/1.4.18-GCCcore-6.4.0     (H)  24) Autoconf/2.69-GCCcore-6.4.0   (H)
Starting with a clean source tree (github@master, but version doesn't appear to matter) I get:

Code: Select all

$ git pull
$ git clean -fd
$ sh build.sh
which: no glibtoolize in (/cluster/home/espehage/.local/nrn/x86_64/bin/:/cluster/software/MATLAB/2018a:/cluster/software/MATLAB/2018a/bin:/cluster/software/Doxygen/1.8.13-GCCcore-6.4.0/bin:/cluster/software/libreadline/7.0-GCCcore-6.4.0/bin:/cluster/software/Autoconf/2.69-GCCcore-6.4.0/bin:/cluster/software/Automake/1.15.1-GCCcore-6.4.0/bin:/cluster/software/CMake/3.10.1-GCCcore-6.4.0/bin:/cluster/software/Bison/3.0.4-GCCcore-6.4.0/bin:/cluster/software/flex/2.6.4-GCCcore-6.4.0/bin:/cluster/software/libtool/2.4.6-GCCcore-6.4.0/bin:/cluster/software/Python/3.6.4-intel-2018a/bin:/cluster/home/espehage/.local/nrn/x86_64/bin:/cluster/software/Java/1.8.0_162:/cluster/software/Java/1.8.0_162/bin:/cluster/software/M4/1.4.18-GCCcore-6.4.0/bin:/cluster/software/ncurses/6.0-GCCcore-6.4.0/bin:/cluster/software/bzip2/1.0.6-GCCcore-6.4.0/bin:/cluster/software/imkl/2018.1.163-iimpi-2018a/mkl/bin:/cluster/software/imkl/2018.1.163-iimpi-2018a/bin:/cluster/software/impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28/bin64:/cluster/software/ifort/2018.1.163-GCC-6.4.0-2.28/compilers_and_libraries_2018.1.163/linux/bin/intel64:/cluster/software/icc/2018.1.163-GCC-6.4.0-2.28/compilers_and_libraries_2018.1.163/linux/bin/intel64:/cluster/software/binutils/2.28-GCCcore-6.4.0/bin:/cluster/software/GCCcore/6.4.0/bin:/node/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/cluster/bin:/cluster/home/espehage/.local/bin:/cluster/home/espehage/bin)
libtoolize -c -f -i
libtoolize: putting auxiliary files in '..'.
libtoolize: copying file '../config.guess'
libtoolize: copying file '../config.sub'
libtoolize: copying file '../install-sh'
libtoolize: copying file '../ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: You should add the contents of 'm4/libtool.m4' to 'aclocal.m4'.
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: You should add the contents of 'm4/ltoptions.m4' to 'aclocal.m4'.
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: You should add the contents of 'm4/ltsugar.m4' to 'aclocal.m4'.
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
libtoolize: You should add the contents of 'm4/lt~obsolete.m4' to 'aclocal.m4'.
configure.ac:21: installing '../compile'
configure.ac:16: installing '../missing'
BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead
src/gnu/Makefile.am: installing '../depcomp'
grep: depcomp: No such file or directory
sed: can't read depcomp: No such file or directory
Thing is, there are no install.sh script anywhere in the source tree. My typical configure step fails with no Makefile.in found, but I'm not sure if that is related to the build.sh issue:

Code: Select all

$ ./configure --prefix=$HOME/.local/nrn --without-iv --with-nrnpython --with-paranrn --with-mpi CC=gcc CXX=g++ MPICC=mpicc MPICXX=mpicxx
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/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-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
CYGWIN=no
MINGW=no
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... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking whether ln -s works... yes
checking for cos in -lm... yes
checking for python3... python3
Python binary found (/cluster/software/Python/3.6.4-intel-2018a/bin/python3)
checking nrnpython configuration... get_python_version()  '3.6'
sys.version_info[0]  '3'
get_python_inc(0)  '/cluster/software/Python/3.6.4-intel-2018a/include/python3.6m'
get_config_var('LIBS')  '-ldl -liomp5 -lpthread -lutil'
get_config_var('LIBRARY')  'libpython3.6m.a'
get_config_var('LIBDIR')  '/cluster/software/Python/3.6.4-intel-2018a/lib'
get_config_var('LIBS')  '-ldl -liomp5 -lpthread -lutil'
get_config_var('MODLIBS')  '/cluster/software/libreadline/7.0-GCCcore-6.4.0/lib/libreadline.a /cluster/software/ncurses/6.0-GCCcore-6.4.0/lib/libncurses.a'
checking if python include files and libraries work... yes
checking for cython3... no
checking for cython... cython
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking for mpic++... mpicxx
checking for mpi.h... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /cluster/software/binutils/2.28-GCCcore-6.4.0/bin/ld
checking if the linker (/cluster/software/binutils/2.28-GCCcore-6.4.0/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /cluster/software/binutils/2.28-GCCcore-6.4.0/bin/nm -B
checking the name lister (/cluster/software/binutils/2.28-GCCcore-6.4.0/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 3458764513820540925
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 /cluster/software/binutils/2.28-GCCcore-6.4.0/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 /cluster/software/binutils/2.28-GCCcore-6.4.0/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : 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... yes
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc linker (/cluster/software/binutils/2.28-GCCcore-6.4.0/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... 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... mpicxx -E
checking for ld used by mpicxx... /cluster/software/binutils/2.28-GCCcore-6.4.0/bin/ld -m elf_x86_64
checking if the linker (/cluster/software/binutils/2.28-GCCcore-6.4.0/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpicxx linker (/cluster/software/binutils/2.28-GCCcore-6.4.0/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpicxx option to produce PIC... -fPIC -DPIC
checking if mpicxx PIC flag -fPIC -DPIC works... yes
checking if mpicxx static flag -static works... yes
checking if mpicxx supports -c -o file.o... yes
checking if mpicxx supports -c -o file.o... (cached) yes
checking whether the mpicxx linker (/cluster/software/binutils/2.28-GCCcore-6.4.0/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 NCURSES... yes
checking which library has the termcap functions... using pkgconfig_ncurses
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... no
checking stropts.h presence... no
checking for stropts.h... no
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 mpicxx accepts -g... (cached) yes
checking dependency style of mpicxx... (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
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: 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: error: cannot find input file: `Makefile.in'
Any pointers to what may solve the problem?

Kind regards,
Espen

selfdestructo
Posts: 32
Joined: Wed Oct 14, 2009 11:12 am

Re: BUG.am: error: 'install.sh' is an anachronism; use 'install-sh' instead

Post by selfdestructo » Thu Dec 06, 2018 4:25 pm

Hi,
I found out why this happens. There was a file /<neuron-sources>/../install.sh confusing automake. Don't know why it would look for it in a location not in $PATH or outside of the NEURON source code directory.

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