Re: [Fink-beginners] Openmpi fails to build
> On Nov 18, 2016, at 21:08, Marc Boxerman wrote: > > I cannot update openmpi. Here’s the output immediately before and at the > error: > > -I/sw/include > /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 > -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT > adio/ad_nfs/ad_nfs_features.lo -MD -MP -MF > adio/ad_nfs/.deps/ad_nfs_features.Tpo -c adio/ad_nfs/ad_nfs_features.c > -fno-common -DPIC -o adio/ad_nfs/.libs/ad_nfs_features.o -I. -I./adio/include > -I./../../../../../opal/include -I./../../../../../ompi/include -I./include > -I./mpi-io -I./adio/include -I./include > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include > -I/sw/include > libtool: error: Failed to create 'mpi-io/.libs' > make[4]: *** [Makefile:3396: mpi-io/get_posn.lo] Error 1 > libtool: error: Failed to create 'mpi-io/.libs' > make[4]: *** [Makefile:3396: mpi-io/get_size.lo] Error 1 > libtool: error: Failed to create 'mpi-io/.libs' > make[4]: *** [Makefile:3396: mpi-io/iread.lo] Error 1 > make[4]: Leaving directory > '/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio' > make[3]: *** [all-recursive] Error 1 > make[2]: *** [all-recursive] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 > ### execution of /tmp/fink.zJauj failed, exit code 2 > ### execution of /tmp/fink.x0WgO failed, exit code 2 > Removing runtime build-lock... > Removing build-lock package... > /sw/bin/dpkg-lockwait -r fink-buildlock-openmpi-1.10.4-1 > (Reading database ... 265512 files and directories currently installed.) > Removing fink-buildlock-openmpi-1.10.4-1 ... > Failed: phase compiling: openmpi-1.10.4-1 failed > > I’m still running El Capitan. > > Thank you for any assistance, > > Marc > How many build jobs is fink set up for? If it’s more than one could you make an another attempt with only one job? The output kind of looks like there might have been an earlier failure in another build thread. -- Alexander Hansen, Ph.D. Fink User Liaison -- ___ Fink-beginners mailing list Fink-beginners@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.beginners Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-beginners
Re: [Fink-beginners] Openmpi fails to build
You’re right. Fink updated openmpi and openmpi-shlibs together. Fink will not let me update openmpi without also updating openmpi-shlibs. I tried updating only openmpi-shlibs. It also fails The output suggests fink was also attempting to update openmpi? -1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include -I/sw/include /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/ad_testfs/ad_testfs_open.lo -MD -MP -MF adio/ad_testfs/.deps/ad_testfs_open.Tpo -c adio/ad_testfs/ad_testfs_open.c -fno-common -DPIC -o adio/ad_testfs/.libs/ad_testfs_open.o -I. -I./adio/include -I./../../../../../opal/include -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include -I./include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io -I/sw/src/fink.build/openmpi-1.10.4-1/open/sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/ad_ufs/ad_ufs_open.lo -MD -MP -MF adio/ad_ufs/.deps/ad_ufs_open.Tpo -c adio/ad_ufs/ad_ufs_open.c -fno-common -DPIC -o adio/ad_ufs/.libs/ad_ufs_open.o -I. -I./adio/include -I./../../../../../opal/include -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include -I./include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/r4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include -I/sw/include /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_fcntl.lo -MD -MP -MF adio/common/.deps/ad_fcntl.Tpo -c adio/common/ad_fcntl.c -fno-common -DPIC -o adio/common/.libs/ad_fcntl.o -I. -I./adio/include -I./../../../../../opal/include -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include -I./include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/a/sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_end.lo -MD -MP -MF adio/common/.deps/ad_end.Tpo -c adio/common/ad_end.c -fno-common -DPIC -o adio/common/.libs/ad_end.o -I. -I./adio/include -I./../../../../../opal/include -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include -I./include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/inclmpi-1.10.4/ompi/mca/io/romio/romio/adio/include -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2
Re: [Fink-beginners] Openmpi fails to build
> On Nov 20, 2016, at 16:46, Marc Boxerman wrote: > > You’re right. Fink updated openmpi and openmpi-shlibs together. Fink will > not let me update openmpi without also updating openmpi-shlibs. I tried > updating only openmpi-shlibs. It also fails The output suggests fink was > also attempting to update openmpi? There is no possible way in the current packaging to build one without the other because they’re built as part of the same procedure. In principle we could build them separately, but there’s really not a circumstance where there is a gain from building the headers and other build-time items in a separate operation for the same version of a package. > > -1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include > -I/sw/include > /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 > -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT > adio/ad_testfs/ad_testfs_open.lo -MD -MP -MF > adio/ad_testfs/.deps/ad_testfs_open.Tpo -c adio/ad_testfs/ad_testfs_open.c > -fno-common -DPIC -o adio/ad_testfs/.libs/ad_testfs_open.o -I. > -I./adio/include -I./../../../../../opal/include > -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include > -I./include > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io > -I/sw/src/fink.build/openmpi-1.10.4-1/open/sw/bin/flag-sort: /usr/bin/clang > -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing > -DHAVE_ROMIOCONF_H -MT adio/ad_ufs/ad_ufs_open.lo -MD -MP -MF > adio/ad_ufs/.deps/ad_ufs_open.Tpo -c adio/ad_ufs/ad_ufs_open.c -fno-common > -DPIC -o adio/ad_ufs/.libs/ad_ufs_open.o -I. -I./adio/include > -I./../../../../../opal/include -I./../../../../../ompi/include -I./include > -I./mpi-io -I./adio/include -I./include > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/r4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include > -I/sw/include > /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 > -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_fcntl.lo > -MD -MP -MF adio/common/.deps/ad_fcntl.Tpo -c adio/common/ad_fcntl.c > -fno-common -DPIC -o adio/common/.libs/ad_fcntl.o -I. -I./adio/include > -I./../../../../../opal/include -I./../../../../../ompi/include -I./include > -I./mpi-io -I./adio/include -I./include > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/a/sw/bin/flag-sort: > /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG > -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_end.lo -MD -MP -MF > adio/common/.deps/ad_end.Tpo -c adio/common/ad_end.c -fno-common -DPIC -o > adio/common/.libs/ad_end.o -I. -I./adio/include > -I./../../../../../opal/include -I./../../../../../ompi/include -I./include > -I./mpi-io -I./adio/include -I./include > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. > > -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal
Re: [Fink-beginners] Openmpi fails to build
Alexander, I had a feeling the packages could not be built separately. I’m using Xcode 8.1. But as you know, I’m not able to install the newest version of command line tools because I’m not on 10.12. My version of command line tools is 7.3.1.0.1.1461711523. Marc > On Nov 20, 2016, at 11:33 PM, Alexander Hansen > wrote: > > >> On Nov 20, 2016, at 16:46, Marc Boxerman wrote: >> >> You’re right. Fink updated openmpi and openmpi-shlibs together. Fink will >> not let me update openmpi without also updating openmpi-shlibs. I tried >> updating only openmpi-shlibs. It also fails The output suggests fink was >> also attempting to update openmpi? > > There is no possible way in the current packaging to build one without the > other because they’re built as part of the same procedure. > > In principle we could build them separately, but there’s really not a > circumstance where there is a gain from building the headers and other > build-time items in a separate operation for the same version of a package. > >> >> -1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include >> -I/sw/include >> /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 >> -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT >> adio/ad_testfs/ad_testfs_open.lo -MD -MP -MF >> adio/ad_testfs/.deps/ad_testfs_open.Tpo -c adio/ad_testfs/ad_testfs_open.c >> -fno-common -DPIC -o adio/ad_testfs/.libs/ad_testfs_open.o -I. >> -I./adio/include -I./../../../../../opal/include >> -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include >> -I./include >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io >> -I/sw/src/fink.build/openmpi-1.10.4-1/open/sw/bin/flag-sort: /usr/bin/clang >> -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing >> -DHAVE_ROMIOCONF_H -MT adio/ad_ufs/ad_ufs_open.lo -MD -MP -MF >> adio/ad_ufs/.deps/ad_ufs_open.Tpo -c adio/ad_ufs/ad_ufs_open.c -fno-common >> -DPIC -o adio/ad_ufs/.libs/ad_ufs_open.o -I. -I./adio/include >> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include >> -I./mpi-io -I./adio/include -I./include >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/r4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include >> -I/sw/include >> /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 >> -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_fcntl.lo >> -MD -MP -MF adio/common/.deps/ad_fcntl.Tpo -c adio/common/ad_fcntl.c >> -fno-common -DPIC -o adio/common/.libs/ad_fcntl.o -I. -I./adio/include >> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include >> -I./mpi-io -I./adio/include -I./include >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../.. >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io >> >> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/a/sw/bin/flag-sort: >> /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG >> -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_end.lo -MD -MP >> -MF adio/common/.dep