[gmx-developers] Automake

[aherz]

Hey,

> So when you've edited a Makefile.am, run automake yourself in the
> top-level directory by hand (or use the bootstrap script described
> here http://wiki.gromacs.org/index.php/Compiling_CVS), then configure
> however you want to, and you should be fine.
>
> The behaviour you observe above is actually a good thing - if someone
> edits Makefile.am then various dependencies should get observed and
> the whole tree should rebuild itself. It seems that the re-configure
> isn't working properly (but you haven't described it well enough for
> me to be sure). If so, it's probably not worth fixing, since there is
> the above work-around.
>

I edit the Makefile.am, then I run aclocal (outputs nothing) followed by
automake in the top-level directory which outputs:

include/Makefile.am:131: variable `_SOURCES' is defined but no program or
include/Makefile.am:131: library has `' as canonic name (possible typo)

afterwards I run configure which outputs the same stuff as usually:

checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
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 how to create a ustar tar archive... gnutar
checking for cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cc -E
checking whether cc accepts -O3... yes
checking whether cc accepts -funroll-all-loops... yes
checking whether cc accepts  -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -funroll-all-loops... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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 whether byte ordering is bigendian... no
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 4
checking for long long int... yes
checking size of long long int... 8
checking for off_t... yes
checking size of off_t... 4
checking that size_t can hold pointers... yes
checking floating-point format... IEEE754 (little-endian byte and word
order)
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by cc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from cc object... ok
checking for dlfcn.h... yes
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... no
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/bin/ld) supports shared
libraries... yes
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 if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... yes
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for rpc/xdr.h... yes
checking for xdr_float in -lnsl... yes
checking for working memcmp... yes
checking return type of signal handlers... void
checking for off_t... (cached) yes
checking for vprintf... yes
checking for _doprnt... no
checking if malloc debugging is wanted... no
checking for strcasecmp... yes
checking for strdup... yes
checking for bool... no
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 libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for main in -lxml2... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for inline... inline
checking whether your compiler can handle assembly files (*.s)... yes
checking whether as fully supports ia32 SSE... yes
checking whether as fully supports ia32 3DNow! instructions... yes
checking whether byte ordering is bigendian... (cached) no
checking if the compiler supports gcc inline assembly... yes
checking if the compiler supports MSVC inline assembly... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/gmxlib/Makefile
config.status: creating src/gmxlib/gmx_blas/Makefile
config.status: creating src/gmxlib/gmx_lapack/Makefile
config.status: creating src/gmxlib/nonbonded/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile
config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile
config.status: creating include/Makefile
config.status: creating include/types/Makefile
config.status: creating src/mdlib/Makefile
config.status: creating src/kernel/Makefile
config.status: creating src/tools/Makefile
config.status: creating src/ngmx/Makefile
config.status: creating src/contrib/Makefile
config.status: creating scripts/Makefile
config.status: creating admin/Makefile
config.status: creating share/Makefile
config.status: creating share/tutor/Makefile
config.status: creating share/tutor/gmxdemo/Makefile
config.status: creating share/tutor/nmr1/Makefile
config.status: creating share/tutor/nmr2/Makefile
config.status: creating share/tutor/water/Makefile
config.status: creating share/tutor/mixed/Makefile
config.status: creating share/tutor/methanol/Makefile
config.status: creating share/tutor/speptide/Makefile
config.status: creating share/template/Makefile
config.status: creating share/top/Makefile
config.status: creating share/html/Makefile
config.status: creating share/html/images/Makefile
config.status: creating share/html/online/Makefile
config.status: creating man/Makefile
config.status: creating man/man1/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands

* On most platforms you can save 10X space with dynamic libraries, although
  the binaries might be less portable. Why not try --enable-shared ?



Finally I try to compile which gives me:

Making all in include
make[1]: Betrete Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/include'
Making all in .
make[2]: Betrete Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/include'
make[2]: Für das Ziel »all-am« ist nichts zu tun.
make[2]: Verlasse Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/include'
Making all in types
make[2]: Betrete Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/include/types'
make[2]: Für das Ziel »all« ist nichts zu tun.
make[2]: Verlasse Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/include/types'
make[1]: Verlasse Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/include'
Making all in src
make[1]: Betrete Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src'
make  all-recursive
make[2]: Betrete Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src'
Making all in gmxlib
make[3]: Betrete Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib'
Making all in nonbonded
make[4]: Betrete Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib/nonbonded'
Making all in nb_kernel_ia32_sse
make[5]: Betrete Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib/nonbonded/nb_kernel_ia32_sse'
/bin/bash ../../../../libtool   --mode=compile cc  -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -c -o nb_kernel010_ia32_sse.lo nb_kernel010_ia32_sse.s
../../../../libtool: line 833: X--mode=compile: command not found
../../../../libtool: line 1000: *** Warning: inferring the mode of
operation is deprecated.: command not found
../../../../libtool: line 1001: *** Future versions of Libtool will
require --mode=MODE be specified.: command not found
../../../../libtool: line 1144: Xcc: command not found
../../../../libtool: line 1144: X-O3: command not found
../../../../libtool: line 1144: X-fomit-frame-pointer: command not found
../../../../libtool: line 1144: X-finline-functions: command not found
../../../../libtool: line 1144: X-Wall: command not found
../../../../libtool: line 1144: X-Wno-unused: command not found
../../../../libtool: line 1144: X-funroll-all-loops: command not found
../../../../libtool: line 1144: X-c: command not found
../../../../libtool: line 1197: Xnb_kernel010_ia32_sse.lo: command not found
../../../../libtool: line 1202: libtool: compile: cannot determine name
of library object from `': command not found
make[5]: *** [nb_kernel010_ia32_sse.lo] Fehler 1
make[5]: Verlasse Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib/nonbonded/nb_kernel_ia32_sse'
make[4]: *** [all-recursive] Fehler 1
make[4]: Verlasse Verzeichnis
'/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib/nonbonded'
make[3]: *** [all-recursive] Fehler 1
make[3]: Verlasse Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src/gmxlib'
make[2]: *** [all-recursive] Fehler 1
make[2]: Verlasse Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src'
make[1]: *** [all] Fehler 2
make[1]: Verlasse Verzeichnis '/home/aherz/cvs/gromacs-4.0.2-T37/src'
make: *** [all-recursive] Fehler 1

Whereas running configure (with the same options) on the files contained
in the original tar.gz and then compiling works fine.

Any ideas??

Thx,
Alex