On 4/9/13 9:41 AM, Viv Kendon wrote: > On Tue, 9 Apr 2013, Alexander Hansen wrote: > >> On 4/9/13 8:04 AM, Viv Kendon wrote: >>> On Tue, 9 Apr 2013, Alexander Hansen wrote: >>> >>>> On 4/9/13 3:42 AM, Viv Kendon wrote: >>>>> On Sun, 7 Apr 2013, Alexander Hansen wrote: >>>>> >>>>>> On 4/7/13 1:51 PM, Viv Kendon wrote: >>>>>>> I think this is the relevant part of the logs, if not, I have the >>>>>>> rest >>>>>>> of it. >>>>>>> >>>>>>> make[2]: Entering directory >>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpa >>>>>>> ck-ng-3.1.3/PARPACK' >>>>>>> /bin/sh ../libtool --tag=F77 --mode=link /sw/bin/mpif77 -g -O2 >>>>>>> -no-undefined >>>>>>> -version-info 2:0 -Wl,-dead_strip_dylibs -L/sw/lib >>>>>>> -L/sw/lib/openmpi -o >>>>>>> libparpa >>>>>>> ck.la -rpath /sw/lib ../SRC/libarpacksrc.la >>>>>>> ../UTIL/libarpackutil.la >>>>>>> ../PARPACK >>>>>>> /SRC/MPI/libparpacksrcmpi.la >>>>>>> ../PARPACK/UTIL/MPI/libparpackutilmpi.la >>>>>>> -ltatlas - >>>>>>> ltatlas >>>>>>> libtool: link: /sw/bin/gfortran-fsf-4.8 -dynamiclib -o >>>>>>> .libs/libparpack.2.dylib >>>>>>> -Wl,-force_load ../SRC/.libs/libarpacksrc.a -Wl,-force_load >>>>>>> ../UTIL/.libs/lib >>>>>>> arpackutil.a -Wl,-force_load >>>>>>> ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a >>>>>>> -Wl,-fo >>>>>>> rce_load ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a -L/sw/lib >>>>>>> -L/sw/lib/open >>>>>>> mpi -ltatlas -O2 -Wl,-dead_strip_dylibs -install_name >>>>>>> /sw/lib/libparpack.2.d >>>>>>> ylib -compatibility_version 3 -current_version 3.0 >>>>>>> -Wl,-single_module >>>>>>> Undefined symbols for architecture x86_64: >>>>>>> "_mpi_allreduce_", referenced from: >>>>>>> _psgetv0_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o) >>>>>>> _psnaitr_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o) >>>>>>> _psnaup2_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o) >>>>>>> _pssaitr_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o) >>>>>>> _pssaup2_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o) >>>>>>> _psnorm2_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o) >>>>>>> _pdgetv0_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o) >>>>>>> ... >>>>>>> "_mpi_comm_rank_", referenced from: >>>>>>> _psnaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o) >>>>>>> _pssaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o) >>>>>>> _pdnaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o) >>>>>>> _pdsaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o) >>>>>>> _pcnaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o) >>>>>>> _pcgetv0_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o) >>>>>>> _pznaupd_ in >>>>>>> libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o) >>>>>>> ... >>>>>>> ld: symbol(s) not found for architecture x86_64 >>>>>>> collect2: error: ld returned 1 exit status >>>>>>> make[2]: *** [libparpack.la] Error 1 >>>>>>> make[2]: Leaving directory >>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK' >>>>>>> >>>>>>> >>>>>>> make[1]: *** [all-recursive] Error 1 >>>>>>> make[1]: Leaving directory >>>>>>> `/sw/src/fink.build/arpack-ng-mpi-atlas-3.1.3-1/arpack-ng-3.1.3/PARPACK' >>>>>>> >>>>>>> >>>>>>> make: *** [all-recursive] Error 1 >>>>>>> ### execution of /tmp/fink.ZL1fo failed, exit code 2 >>>>>>> >>>>>>> Package manager version: 0.34.7 >>>>>>> Distribution version: selfupdate-rsync Sun Apr 7 20:33:31 2013, >>>>>>> 10.7, >>>>>>> x86_64 >>>>>>> Trees: local/main stable/main >>>>>>> Xcode.app: 4.6.1 >>>>>>> Xcode command-line tools: 4.6.0.0.1.1362189000 >>>>>>> Max. Fink build jobs: 4 >>>>>>> >>>>>>> >>>>>>> open-mpi updated to 1.6.4-2 just prior to this failure. >>>>>>> >>>>>>> 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 >>>>>>> >>>>>> >>>>>> Thanks for the report. It looks like arpack-ng upstream tweaked the >>>>>> parallel library build, and I naively didn't test that. A fixed >>>>>> version should be available shortly via selfupdate. >>>>> >>>>> I think what is failing now is that it is looking for the wrong source >>>>> package name? >>>>> >>>>> curl --connect-timeout 30 -f -L -A 'fink/0.34.7' -O >>>>> http://distfiles.master.finkmirrors.net/arpack-ng-mpi-3.1.3.tar.gz >>>>> % Total % Received % Xferd Average Speed Time Time Time >>>>> Current >>>>> Dload Upload Total Spent Left >>>>> Speed >>>>> 0 0 0 0 0 0 0 0 --:--:-- --:--:-- >>>>> --:--:-- 0 >>>>> curl: (22) The requested URL returned error: 404 >>>>> >>>>> i.e., -mpi shouldn't be in there? >>>>> >>>> Oops. I just checked in a fix which should be available via >>>> 'selfupdate' shortly. >>> >>> It is still 404: >>> >>> curl --connect-timeout 30 -f -L -A 'fink/0.34.7' -O >>> http://distfiles.master.finkmirrors.net/arpack-3.1.3.tar.gz >>> % Total % Received % Xferd Average Speed Time Time Time >>> Current >>> Dload Upload Total Spent Left >>> Speed >>> ^M 0 0 0 0 0 0 0 0 --:--:-- --:--:-- >>> --:--:-- 0^M 0 0 0 0 0 0 0 0 --:--:-- >>> 0:00:01 --:--:-- 0 >>> curl: (22) The requested URL returned error: 404 >>> >>> >>> On my other machine I have to following sources: >>> >>> arpack-ng-3.1.3.tar.gz arpack-ng_3.1.2.tar.gz arpack_3.0.1.tar.gz >>> arpack-ng_3.1.0.tar.gz arpack-patch.tar.gz arpack_3.0.2.tar.gz >>> arpack-ng_3.1.1.tar.gz arpack96.tar.gz >>> >>> So it seems to have sometimes had -ng and sometimes not, but maybe it >>> needs it now? >>> >>> 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 >>> >> >> Sorry about that--I wasn't fully awake yet. I put up a new version >> _and_ verified that it fetches the tarball. :-) > > Thanks, downloads and builds fine now -- almost there, failed at the > last hurdle: > > /sw/bin/dpkg-lockwait -r fink-buildlock-arpack-ng-mpi-atlas-3.1.3-2 > (Reading database ... 274697 files and directories currently installed.) > Removing fink-buildlock-arpack-ng-mpi-atlas-3.1.3-2 ... > Failed: Error performing percent expansion: unknown % expansion or > nesting too deep: "(%type_raw[-mpi] = -mpi) /sw/lib/libparpack.2.dylib > 3.0.0 arpack-ng-mpi-atlas-shlibs (>=3.1.0-1)" > (/sw/fink/dists/stable/main/finkinfo/sci/arpack-ng-mpi.info "Shlibs") > > 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 >
Fixed now. The irony is that the packaging issues are due to the MPI build not working _without_ atlas or lapack342. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Fink-users mailing list [email protected] List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
