[petsc-dev] configure failed after update of OSX

Barry Smith bsmith at mcs.anl.gov
Mon Jan 27 13:36:22 CST 2014


    Classic. Anyway here is where MPICH goes wrong; if you want to know WHY it is looking for the .la file that goes beyond me. 

Error running make; make install on MPICH: Could not execute "cd /Users/markadams/Codes/petsc/arch-macosx-gnu-g/externalpackages/mpich-3.0.4-106 && /usr/bin/make -j 7 all":
/usr/bin/make  all-recursive
Making all in src/mpl
  CC       mplstr.lo
  CC       mpltrmem.lo
  CC       mplenv.lo
  CCLD     libmpl.la
Making all in src/openpa
Making all in src
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
  CC       opa_primitives.lo
  CC       opa_queue.lo
  CCLD     libopa.la
Making all in test
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
Making all in src/mpi/romio
  CC       mpi-io/close.lo
  CC       mpi-io/delete.lo
  CC       mpi-io/file_c2f.lo
  CC       mpi-io/file_f2c.lo
  CC       mpi-io/fsync.lo
  CC       mpi-io/get_amode.lo
  CC       mpi-io/get_atom.lo
  CC       mpi-io/get_bytoff.lo
  CC       mpi-io/get_extent.lo
  CC       mpi-io/get_group.lo
  CC       mpi-io/get_info.lo
  CC       mpi-io/get_posn.lo
  CC       mpi-io/get_posn_sh.lo
  CC       mpi-io/get_size.lo
  CC       mpi-io/iread_at.lo
  CC       mpi-io/iread.lo
  CC       mpi-io/get_view.lo
  CC       mpi-io/iread_sh.lo
  CC       mpi-io/iwrite.lo
  CC       mpi-io/iwrite_at.lo
  CC       mpi-io/iwrite_sh.lo
  CC       mpi-io/open.lo
  CC       mpi-io/prealloc.lo
  CC       mpi-io/rd_atallb.lo
  CC       mpi-io/rd_atalle.lo
  CC       mpi-io/read.lo
  CC       mpi-io/read_all.lo
  CC       mpi-io/read_allb.lo
  CC       mpi-io/read_alle.lo
  CC       mpi-io/read_at.lo
  CC       mpi-io/read_atall.lo
  CC       mpi-io/read_ord.lo
  CC       mpi-io/read_ordb.lo
  CC       mpi-io/read_orde.lo
  CC       mpi-io/read_sh.lo
  CC       mpi-io/register_datarep.lo
  CC       mpi-io/seek.lo
  CC       mpi-io/seek_sh.lo
  CC       mpi-io/set_atom.lo
  CC       mpi-io/set_info.lo
  CC       mpi-io/set_size.lo
  CC       mpi-io/set_view.lo
  CC       mpi-io/wr_atallb.lo
  CC       mpi-io/wr_atalle.lo
  CC       mpi-io/write.lo
  CC       mpi-io/write_all.lo
  CC       mpi-io/write_allb.lo
  CC       mpi-io/write_alle.lo
  CC       mpi-io/write_at.lo
  CC       mpi-io/write_atall.lo
  CC       mpi-io/write_ord.lo
  CC       mpi-io/write_ordb.lo
  CC       mpi-io/write_orde.lo
  CC       mpi-io/write_sh.lo
  CC       mpi-io/glue/mpich/mpio_file.lo
  CC       mpi-io/glue/mpich/mpio_err.lo
  CC       mpi-io/mpich_fileutil.lo
  CC       mpi-io/mpir-mpioinit.lo
  CC       mpi-io/mpiu_greq.lo
  CC       mpi-io/mpiu_external32.lo
  CC       adio/ad_nfs/ad_nfs_read.lo
  CC       adio/ad_nfs/ad_nfs_open.lo
  CC       adio/ad_nfs/ad_nfs_write.lo
  CC       adio/ad_nfs/ad_nfs_done.lo
  CC       adio/ad_nfs/ad_nfs_fcntl.lo
  CC       adio/ad_nfs/ad_nfs_iread.lo
  CC       adio/ad_nfs/ad_nfs_iwrite.lo
  CC       adio/ad_nfs/ad_nfs_wait.lo
  CC       adio/ad_nfs/ad_nfs_setsh.lo
  CC       adio/ad_nfs/ad_nfs_getsh.lo
  CC       adio/ad_nfs/ad_nfs.lo
  CC       adio/ad_nfs/ad_nfs_resize.lo
  CC       adio/ad_nfs/ad_nfs_features.lo
  CC       adio/ad_testfs/ad_testfs_close.lo
  CC       adio/ad_testfs/ad_testfs_read.lo
  CC       adio/ad_testfs/ad_testfs_rdcoll.lo
  CC       adio/ad_testfs/ad_testfs_wrcoll.lo
  CC       adio/ad_testfs/ad_testfs_open.lo
  CC       adio/ad_testfs/ad_testfs_write.lo
  CC       adio/ad_testfs/ad_testfs_done.lo
  CC       adio/ad_testfs/ad_testfs_fcntl.lo
  CC       adio/ad_testfs/ad_testfs_iread.lo
  CC       adio/ad_testfs/ad_testfs_iwrite.lo
  CC       adio/ad_testfs/ad_testfs_wait.lo
  CC       adio/ad_testfs/ad_testfs_flush.lo
  CC       adio/ad_testfs/ad_testfs_seek.lo
  CC       adio/ad_testfs/ad_testfs_resize.lo
  CC       adio/ad_testfs/ad_testfs_hints.lo
  CC       adio/ad_testfs/ad_testfs_delete.lo
  CC       adio/ad_testfs/ad_testfs.lo
  CC       adio/ad_ufs/ad_ufs.lo
  CC       adio/ad_ufs/ad_ufs_open.lo
  CC       adio/common/ad_aggregate.lo
  CC       adio/common/ad_aggregate_new.lo
  CC       adio/common/ad_close.lo
  CC       adio/common/ad_coll_build_req_new.lo
  CC       adio/common/ad_coll_exch_new.lo
  CC       adio/common/ad_darray.lo
  CC       adio/common/ad_delete.lo
  CC       adio/common/ad_done.lo
  CC       adio/common/ad_done_fake.lo
  CC       adio/common/ad_end.lo
  CC       adio/common/ad_fcntl.lo
  CC       adio/common/ad_features.lo
  CC       adio/common/ad_flush.lo
  CC       adio/common/ad_fstype.lo
  CC       adio/common/ad_get_sh_fp.lo
  CC       adio/common/ad_hints.lo
  CC       adio/common/ad_init.lo
  CC       adio/common/ad_io_coll.lo
  CC       adio/common/ad_iopen.lo
  CC       adio/common/ad_iread.lo
  CC       adio/common/ad_iread_fake.lo
  CC       adio/common/ad_iwrite.lo
  CC       adio/common/ad_iwrite_fake.lo
  CC       adio/common/ad_open.lo
  CC       adio/common/ad_opencoll.lo
  CC       adio/common/ad_opencoll_failsafe.lo
  CC       adio/common/ad_opencoll_scalable.lo
  CC       adio/common/ad_prealloc.lo
  CC       adio/common/ad_read.lo
  CC       adio/common/ad_read_coll.lo
  CC       adio/common/ad_read_str.lo
  CC       adio/common/ad_read_str_naive.lo
  CC       adio/common/ad_resize.lo
  CC       adio/common/ad_seek.lo
  CC       adio/common/ad_set_sh_fp.lo
  CC       adio/common/ad_set_view.lo
  CC       adio/common/ad_subarray.lo
  CC       adio/common/ad_wait.lo
  CC       adio/common/ad_wait_fake.lo
  CC       adio/common/ad_write.lo
  CC       adio/common/ad_write_coll.lo
  CC       adio/common/ad_write_nolock.lo
  CC       adio/common/ad_write_str.lo
  CC       adio/common/ad_write_str_naive.lo
  CC       adio/common/adi_close.lo
  CC       adio/common/byte_offset.lo
  CC       adio/common/cb_config_list.lo
  CC       adio/common/eof_offset.lo
  CC       adio/common/error.lo
  CC       adio/common/flatten.lo
  CC       adio/common/get_fp_posn.lo
  CC       adio/common/greq_fns.lo
  CC       adio/common/heap-sort.lo
  CC       adio/common/iscontig.lo
  CC       adio/common/lock.lo
  CC       adio/common/malloc.lo
  CC       adio/common/shfp_fname.lo
  CC       adio/common/status_setb.lo
  CC       adio/common/strfns.lo
  CC       adio/common/system_hints.lo
  CC       mpi-io/libpromio_la-close.lo
  CC       mpi-io/libpromio_la-delete.lo
  CC       mpi-io/libpromio_la-file_c2f.lo
  CC       mpi-io/libpromio_la-file_f2c.lo
  CC       mpi-io/libpromio_la-fsync.lo
  CC       mpi-io/libpromio_la-get_amode.lo
  CC       mpi-io/libpromio_la-get_atom.lo
  CC       mpi-io/libpromio_la-get_bytoff.lo
  CC       mpi-io/libpromio_la-get_extent.lo
  CC       mpi-io/libpromio_la-get_group.lo
  CC       mpi-io/libpromio_la-get_info.lo
  CC       mpi-io/libpromio_la-get_posn.lo
  CC       mpi-io/libpromio_la-get_posn_sh.lo
  CC       mpi-io/libpromio_la-get_size.lo
  CC       mpi-io/libpromio_la-get_view.lo
  CC       mpi-io/libpromio_la-iread.lo
  CC       mpi-io/libpromio_la-iread_at.lo
  CC       mpi-io/libpromio_la-iread_sh.lo
  CC       mpi-io/libpromio_la-iwrite.lo
  CC       mpi-io/libpromio_la-iwrite_at.lo
  CC       mpi-io/libpromio_la-iwrite_sh.lo
  CC       mpi-io/libpromio_la-open.lo
  CC       mpi-io/libpromio_la-prealloc.lo
  CC       mpi-io/libpromio_la-rd_atallb.lo
  CC       mpi-io/libpromio_la-rd_atalle.lo
  CC       mpi-io/libpromio_la-read.lo
  CC       mpi-io/libpromio_la-read_all.lo
  CC       mpi-io/libpromio_la-read_allb.lo
  CC       mpi-io/libpromio_la-read_alle.lo
  CC       mpi-io/libpromio_la-read_at.lo
  CC       mpi-io/libpromio_la-read_atall.lo
  CC       mpi-io/libpromio_la-read_ord.lo
  CC       mpi-io/libpromio_la-read_ordb.lo
  CC       mpi-io/libpromio_la-read_orde.lo
  CC       mpi-io/libpromio_la-read_sh.lo
  CC       mpi-io/libpromio_la-register_datarep.lo
  CC       mpi-io/libpromio_la-seek.lo
  CC       mpi-io/libpromio_la-seek_sh.lo
  CC       mpi-io/libpromio_la-set_atom.lo
  CC       mpi-io/libpromio_la-set_info.lo
  CC       mpi-io/libpromio_la-set_size.lo
  CC       mpi-io/libpromio_la-set_view.lo
  CC       mpi-io/libpromio_la-wr_atallb.lo
  CC       mpi-io/libpromio_la-wr_atalle.lo
  CC       mpi-io/libpromio_la-write.lo
  CC       mpi-io/libpromio_la-write_all.lo
  CC       mpi-io/libpromio_la-write_allb.lo
  CC       mpi-io/libpromio_la-write_alle.lo
  CC       mpi-io/libpromio_la-write_at.lo
  CC       mpi-io/libpromio_la-write_atall.lo
  CC       mpi-io/libpromio_la-write_ord.lo
  CC       mpi-io/libpromio_la-write_ordb.lo
  CC       mpi-io/libpromio_la-write_orde.lo
  CC       mpi-io/libpromio_la-write_sh.lo
  CCLD     libromio.la
  CCLD     libpromio.la
Making all in src/pm/hydra
Making all in ../../mpl
make[3]: Nothing to be done for `all'.
Making all in tools/topo/hwloc/hwloc
Making all in src
  CC       topology.lo
  CC       traversal.lo
  CC       distances.lo
  CC       components.lo
  CC       bind.lo
  CC       bitmap.lo
  CC       misc.lo
  CC       base64.lo
  CC       topology-noos.lo
  CC       topology-synthetic.lo
  CC       topology-custom.lo
  CC       topology-xml.lo
  CC       topology-xml-nolibxml.lo
  CC       topology-xml-libxml.lo
  CC       topology-darwin.lo
  CC       topology-x86.lo
  CCLD     libhwloc_embedded.lampi-io/mpiu_external32.c:123:14: warning: unused variable 'extent' [-Wunused-variable]
    MPI_Aint extent = 0;
1 warning generated.
adio/common/ad_coll_build_req_new.c:905:9: warning: unused variable 'cb_node_ct' [-Wunused-variable]
    int cb_node_ct = fd->hints->cb_nodes;
1 warning generated.
grep: /opt/local/lib/liblzma.la: No such file or directory
/opt/local/bin/gsed: can't read /opt/local/lib/liblzma.la: No such file or directory
libtool: link: `/opt/local/lib/liblzma.la' is not a valid libtool archive
make[4]: *** [libhwloc_embedded.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

On Jan 27, 2014, at 1:19 PM, Sean Farley <sean.michael.farley at gmail.com> wrote:

> bsmith at mcs.anl.gov writes:
>> On Jan 27, 2014, at 11:44 AM, Sean Farley <sean.michael.farley at gmail.com> wrote:
>>> bsmith at mcs.anl.gov writes:
>>>> I think resolved it by getting rid of some stuff that macports put in maybe
>>> I just *completely* revamped the mpi ports in macports and would like to
>>> know if these types of problems still exist.
>>  Sean,
>>    It wasn’t the MPI ports in macports. It was MPICH’s regular configure/make making mistakes because of some libraries in those directories that did not have corresponding .la files.
> Ah. One of Apple's employees made it his mission to get rid of .la files
> entirely:
> http://trac.macports.org/ticket/38010
> I don't know if I agree with it but if there are any errors due to it,
> please do file a bug. Though, this case seems to be MPICH's fault.

More information about the petsc-dev mailing list