On Sun, Apr 07, 2013 at 10:21:25PM +0100, Viv Kendon wrote:
> ...but it worked on 10.7 client. I tried to diff the two build logs, but
> that's messy, and I'm still not sure what the failure actually is.
> Ostensibly it is:
>
> chmod -R a-x /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/*
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/libcblas.dylib'
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/libf77blas.dylib'
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/liblapack.dylib'
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/libptcblas.dylib'
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/libptf77blas.dylib'
> chmod: cannot operate on dangling symlink
> `/sw/src/fink.build/root-atlas-3.10.1-
> 1/sw/lib/libptlapack.dylib'
> ### execution of /tmp/fink.zzyP6 failed, exit code 1
> ### execution of /tmp/fink.JV6pj failed, exit code 1
>
> but obviously this means something went wrong earlier. Working backwards
> through the log, there is:
>
> cp /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libsatlas.dll
> /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/.
> cp: cannot stat
> `/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libsatlas.dll'
> : No such file or directory
> make[1]: [install_lib] Error 1 (ignored)
> cp /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libtatlas.dll
> /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/.
> cp: cannot stat
> `/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libtatlas.dll'
> : No such file or directory
> make[1]: [install_lib] Error 1 (ignored)
> cp /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libsatlas.so
> /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/.
> cp: cannot stat
> `/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libsatlas.so':
> No such file or directory
> make[1]: [install_lib] Error 1 (ignored)
> cp /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libtatlas.so
> /sw/src/fink.build/root-atlas-3.10.1-1/sw/lib/.
> cp: cannot stat
> `/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libtatlas.so': No such
> file or directory
> make[1]: [install_lib] Error 1 (ignored)
>
> and there is
>
> /sw/src/fink.build/atlas-3.10.1-1/gcc -DL2SIZE=4194304
> -I/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/include
> -I/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/../ATLAS//include
> -I/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/../ATLAS//include/contrib
> -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Core2
> -DATL_CPUMHZ=3000 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS
> -DATL_GAS_x8664 -m64 -DATL_DYLIBS -DATL_FULL_LAPACK -DATL_NCPU=8 -fPIC
> -fomit-frame-pointer -O3 -m64 -mfpmath=sse -m64 -fPIC -o xtune_aff
> tune_aff.o ATL_goparallel_noaff.o \
> ATL_goparallel_aff.o ATL_log2tlaunch_noaff.o
> ATL_log2tlaunch.o \
> ATL_thread_start_noaff.o ATL_thread_start.o
> /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/lib/libatlas.a -lpthread -lm
> ld: duplicate symbol _ATL_goparallel_noaff in ATL_goparallel_aff.o and
> ATL_goparallel_noaff.o
> collect2: error: ld returned 1 exit status
> make[4]: *** [xtune_aff] Error 1
> make[4]: Leaving directory
> `/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/tune/threads'
> make[3]: [IThreadTune] Error 2 (ignored)
>
> and
>
> /sw/src/fink.build/atlas-3.10.1-1/gcc -DL2SIZE=4194304
> -I/sw/src/fink.build/atla
> s-3.10.1-1/darwin_bld/include
> -I/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/../
> ATLAS//include
> -I/sw/src/fink.build/atlas-3.10.1-1/darwin_bld/../ATLAS//include/
> contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX
> -DATL_ARCH_Core2
> -DATL_CPUMHZ=3000 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS
> -DATL_GAS_x86
> 64 -m64 -DATL_DYLIBS -DATL_FULL_LAPACK -DATL_NCPU=8 -fPIC
> -fomit-frame-pointer -
> O3 -m64 -mfpmath=sse -m64 -o xprobe_aff probe_aff.o atlconf_misc.o
> -lpthread -lm
> rm res/probe.out
> rm: cannot remove `res/probe.out': No such file or directory
> make[4]: [IRun_aff] Error 1 (ignored)
>
> and many like this:
>
> /sw/src/fink.build/atlas-3.10.1-1/ATLAS/ar2 d
> /sw/src/fink.build/atlas-3.10.1-1/
> darwin_bld/lib/libatlas.a ATL_cgerk__2.o ATL_cgerk__3.o
> ATL_cgerk__900003.o ATL_
> cgerk__900001.o ATL_cgerk__900006.o ATL_cgerk__900004.o ATL_cgerk__1.o
> ar: ATL_cgerk__2.o: not found in archive
> ar: ATL_cgerk__3.o: not found in archive
> ar: ATL_cgerk__900003.o: not found in archive
> ar: ATL_cgerk__900001.o: not found in archive
> ar: ATL_cgerk__900006.o: not found in archive
> ar: ATL_cgerk__900004.o: not found in archive
> ar: ATL_cgerk__1.o: not found in archive
> make[4]: [killlib] Error 1 (ignored)
>
> and several like this:
>
> /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/bin/xsubstr -o ATL_tMpFiLe
> -i
> /sw/src/fink.build/atlas-3.10.1-1/darwin_bld/../ATLAS//tune/blas/gemm/CASES/zcases.fl
> g \
> -s '^gcc' 'gcc-fsf-4.8 -fPIC -fomit-frame-pointer -O3 -m64
> -mfpmath=s
> se -m64 -fPIC' -s ' gcc' ' gcc-fsf-4.8 -fPIC -fomit-frame-pointer -O3
> -m64 -mfpm
> ath=sse -m64 -fPIC'
> ./xuserflag -i ATL_tMpFiLe -o zcases.flg
> gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march='
> instead
> FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= switch
> int main(){}
> ^
> cc1: error: unrecognized command line option "-maltivec"
> cc1: error: unrecognized command line option "-mabi=altivec"
> gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march='
> instead
> FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= switch
> int main(){}
> ^
> gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march='
> instead
> FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= switch
> int main(){}
> ^
> gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march='
> instead
> FlagCheck.c:1:0: error: bad value (ultrasparc) for -mtune= switch
> int main(){}
> ^
> gcc-fsf-4.8: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march='
> instead
> FlagCheck.c:1:0: error: bad value (970) for -mtune= switch
> int main(){}
> ^
> gcc-fsf-4.8: error: unrecognized command line option '-mips4'
> gcc-fsf-4.8: error: unrecognized command line option '-mips4'
> gcc-fsf-4.8: error: unrecognized command line option '-mips4'
> gcc-fsf-4.8: error: unrecognized command line option '-mips4'
> gcc-fsf-4.8: error: unrecognized command line option '-mvsx'
> gcc-fsf-4.8: error: unrecognized command line option '-mfpu=vfpv3'
>
> But I think they almost all occur in the successful build log as well.
>
> I can supply the whole log if necessary, let me know.
You will have to provide the full compressed log. The atlas build is quite
ugly as it's makfiles often try compiles and copies that will fail until
it the appropriate one succeeds. I suspect you will find some sort of
error in the linkages of libsatlas.dylib and libtatlas.dylib. Afterwards
you might also try removing the atlas package before you build the newer one
and see if that helps.
Jack
>
> Package manager version: 0.34.7
> Distribution version: selfupdate-rsync Sun Apr 7 20:26:24 2013, 10.6,
> x86_64
> Trees: local/main local/crypto stable/main stable/crypto unstable/main
> unstable/crypto
> Xcode.app: 3.2.6
> Xcode command-line tools: 3.2.6
> atlas-3.10.1-1 is set to build with only one job.
>
> TIA,
> -- Viv
> ________________________________________________
> Dr Viv Kendon http://quantum.leeds.ac.uk/~viv
> tel: +44 113 343 4864 Physics and Astronomy
> Quantum Information Group University of Leeds
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