On Tue, 9 Apr 2013, Alexander Hansen wrote: > 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") >> > Fixed now. The irony is that the packaging issues are due to the MPI > build not working _without_ atlas or lapack342.
Installed now, many thanks! -- Viv ________________________________________________ Dr Viv Kendon http://quantum.leeds.ac.uk/~viv tel: +44 113 343 4864 Physics and Astronomy Quantum Information Group University of Leeds ------------------------------------------------------------------------------ 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
