Summary: | sci-mathematics/octave-3.0.3 fails to compile/link with gfortran warnings and MPI errors | ||
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Product: | Gentoo Linux | Reporter: | Ben Schwartz <bmschwar> |
Component: | Current packages | Assignee: | Gentoo Science Mathematics related packages <sci-mathematics> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | jlec |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Bug Depends on: | |||
Bug Blocks: | 302621 |
Description
Ben Schwartz
2009-10-08 18:21:18 UTC
You probably need to rebuild everything that linked with libgfortran.so.1, AFAIK, in gcc 4.3 it's libgfortran.so.3. Could you clarify that suggestion? I tried rebuilding gcc (with the fortran useflag), and then rebuilding octave, but got the exact same error. I was talking about revdep-rebuild. Looking at your error, it's probably blas, that needs rebuild, but probably more. Please report back if the Problem is still valid after fixing the libgfortran things of blas and friends. I rebuilt gcc, blas-atlas, blas-lapack, and openmpi. Now I get making DOCSTRINGS DOCSTRINGS is unchanged rm -f liboctinterp.so.3.0.3 ln -s liboctinterp.so liboctinterp.so.3.0.3 i686-pc-linux-gnu-g++ -I. -I.. -I../liboctave -I../src -I../libcruft/misc -DHAVE_CONFIG_H -mieee-fp -Wall -W -Wshadow -Wold-style-cast -O2 -march=i686 -pipe -rdynamic \ -L.. -fPIC -Wl,-O1 -o octave \ main.o \ -L../liboctave -L../libcruft -L../src -Wl,-rpath -Wl,/usr/lib/octave-3.0.3 \ -loctinterp -loctave -lcruft \ -lumfpack -lamd -lcamd -lcolamd \ -lcholmod -lccolamd -lcxsparse -llapack -lblas -lpthread -lcblas -latlas -lblas -latlas -lpthread \ -lfftw3 -lreadline -lncurses -ldl -lhdf5 -lz -lm -L/usr/lib/gcc/i686-pc-linux-gnu/4.3.2 -L/usr/lib/gcc/i686-pc-linux-gnu/4.3.2/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.3.2/../../.. -lhdf5 -lz -lgfortranbegin -lgfortran -lm ../src/liboctinterp.so: undefined reference to `ompi_mpi_comm_null' ../src/liboctinterp.so: undefined reference to `MPI_Topo_test' ../src/liboctinterp.so: undefined reference to `MPI_Group_excl' ../src/liboctinterp.so: undefined reference to `MPI_Type_create_subarray' ../src/liboctinterp.so: undefined reference to `MPI_Win_get_name' ../src/liboctinterp.so: undefined reference to `SEEK_SET' ../src/liboctinterp.so: undefined reference to `MPI_Graph_create' ../src/liboctinterp.so: undefined reference to `MPI_Op_free' ../src/liboctinterp.so: undefined reference to `MPI_Graph_neighbors' ../src/liboctinterp.so: undefined reference to `MPI_Grequest_complete' ../src/liboctinterp.so: undefined reference to `MPI_Comm_create' ../src/liboctinterp.so: undefined reference to `MPI_Win_test' ../src/liboctinterp.so: undefined reference to `MPI_Scan' ../src/liboctinterp.so: undefined reference to `MPI_Graphdims_get' ../src/liboctinterp.so: undefined reference to `MPI_Test_cancelled' ../src/liboctinterp.so: undefined reference to `MPI_Put' ../src/liboctinterp.so: undefined reference to `MPI_Bsend_init' ../src/liboctinterp.so: undefined reference to `MPI_Type_get_attr' ../src/liboctinterp.so: undefined reference to `MPI_Group_range_excl' ../src/liboctinterp.so: undefined reference to `MPI_Reduce_scatter' ../src/liboctinterp.so: undefined reference to `MPI_Info_get_valuelen' ../src/liboctinterp.so: undefined reference to `MPI_Irsend' ../src/liboctinterp.so: undefined reference to `MPI_Sendrecv_replace' ../src/liboctinterp.so: undefined reference to `MPI_Comm_remote_group' ../src/liboctinterp.so: undefined reference to `ompi_mpi_cxx_op_intercept' ../src/liboctinterp.so: undefined reference to `MPI_Ssend_init' ../src/liboctinterp.so: undefined reference to `MPI_Alltoallv' ../src/liboctinterp.so: undefined reference to `MPI_Scatter' ../src/liboctinterp.so: undefined reference to `MPI_Win_start' ../src/liboctinterp.so: undefined reference to `MPI_Cart_create' ../src/liboctinterp.so: undefined reference to `MPI_Accumulate' ../src/liboctinterp.so: undefined reference to `MPI_Scatterv' ../src/liboctinterp.so: undefined reference to `MPI_Request_get_status' ../src/liboctinterp.so: undefined reference to `MPI_Graph_neighbors_count' ../src/liboctinterp.so: undefined reference to `MPI_Iprobe' ../src/liboctinterp.so: undefined reference to `MPI_Probe' ../src/liboctinterp.so: undefined reference to `MPI_Type_delete_attr' ../src/liboctinterp.so: undefined reference to `MPI_Allgatherv' ../src/liboctinterp.so: undefined reference to `MPI_Issend' ../src/liboctinterp.so: undefined reference to `MPI_Comm_disconnect' ../src/liboctinterp.so: undefined reference to `MPI_Win_set_attr' ../src/liboctinterp.so: undefined reference to `MPI_Cart_sub' ../src/liboctinterp.so: undefined reference to `MPI_Win_wait' ../src/liboctinterp.so: undefined reference to `MPI_Win_complete' ../src/liboctinterp.so: undefined reference to `MPI_Graph_map' ../src/liboctinterp.so: undefined reference to `MPI_Comm_remote_size' ../src/liboctinterp.so: undefined reference to `MPI::Datatype::Free()' ../src/liboctinterp.so: undefined reference to `MPI_Send_init' ../src/liboctinterp.so: undefined reference to `MPI_Exscan' ../src/liboctinterp.so: undefined reference to `MPI_Status_set_cancelled' ../src/liboctinterp.so: undefined reference to `MPI_Rsend' ../src/liboctinterp.so: undefined reference to `MPI_Win_get_group' ../src/liboctinterp.so: undefined reference to `MPI_Type_get_true_extent' ../src/liboctinterp.so: undefined reference to `MPI_Bsend' ../src/liboctinterp.so: undefined reference to `MPI_Get' ../src/liboctinterp.so: undefined reference to `MPI_Cartdim_get' ../src/liboctinterp.so: undefined reference to `MPI_Win_lock' ../src/liboctinterp.so: undefined reference to `MPI_Cart_coords' ../src/liboctinterp.so: undefined reference to `MPI_Type_create_indexed_block' ../src/liboctinterp.so: undefined reference to `MPI_Win_fence' ../src/liboctinterp.so: undefined reference to `MPI_Type_get_extent' ../src/liboctinterp.so: undefined reference to `MPI_Type_dup' ../src/liboctinterp.so: undefined reference to `MPI::Win::Set_errhandler(MPI::Errhandler const&)' ../src/liboctinterp.so: undefined reference to `MPI_Group_rank' ../src/liboctinterp.so: undefined reference to `MPI_Cart_rank' ../src/liboctinterp.so: undefined reference to `MPI_Start' ../src/liboctinterp.so: undefined reference to `MPI_Ibsend' ../src/liboctinterp.so: undefined reference to `MPI_Type_create_resized' ../src/liboctinterp.so: undefined reference to `MPI::Comm::Set_errhandler(MPI::Errhandler const&)' ../src/liboctinterp.so: undefined reference to `MPI_Type_create_hindexed' ../src/liboctinterp.so: undefined reference to `MPI_Group_size' ../src/liboctinterp.so: undefined reference to `MPI_Op_create' ../src/liboctinterp.so: undefined reference to `MPI_Info_get_nthkey' ../src/liboctinterp.so: undefined reference to `ompi_op_set_cxx_callback' ../src/liboctinterp.so: undefined reference to `MPI_Request_free' ../src/liboctinterp.so: undefined reference to `MPI_Ssend' ../src/liboctinterp.so: undefined reference to `MPI_Test' ../src/liboctinterp.so: undefined reference to `MPI_Intercomm_create' ../src/liboctinterp.so: undefined reference to `MPI_Comm_spawn_multiple' ../src/liboctinterp.so: undefined reference to `MPI_Info_get_nkeys' ../src/liboctinterp.so: undefined reference to `MPI_Win_delete_attr' ../src/liboctinterp.so: undefined reference to `MPI_Recv_init' ../src/liboctinterp.so: undefined reference to `MPI_Type_set_attr' ../src/liboctinterp.so: undefined reference to `MPI::Comm::Comm()' ../src/liboctinterp.so: undefined reference to `MPI_Type_create_hvector' ../src/liboctinterp.so: undefined reference to `MPI_Rsend_init' ../src/liboctinterp.so: undefined reference to `MPI_Win_post' ../src/liboctinterp.so: undefined reference to `MPI_Attr_delete' ../src/liboctinterp.so: undefined reference to `MPI_Type_get_name' ../src/liboctinterp.so: undefined reference to `MPI_Comm_get_name' ../src/liboctinterp.so: undefined reference to `MPI_Comm_spawn' ../src/liboctinterp.so: undefined reference to `MPI_Type_set_name' ../src/liboctinterp.so: undefined reference to `MPI_Win_set_name' ../src/liboctinterp.so: undefined reference to `MPI_Cart_shift' ../src/liboctinterp.so: undefined reference to `MPI_Comm_accept' ../src/liboctinterp.so: undefined reference to `MPI_Status_set_elements' ../src/liboctinterp.so: undefined reference to `MPI_Win_call_errhandler' ../src/liboctinterp.so: undefined reference to `MPI_Comm_connect' ../src/liboctinterp.so: undefined reference to `MPI_Intercomm_merge' ../src/liboctinterp.so: undefined reference to `MPI_Group_range_incl' ../src/liboctinterp.so: undefined reference to `MPI_Graph_get' ../src/liboctinterp.so: undefined reference to `MPI_Cart_get' ../src/liboctinterp.so: undefined reference to `MPI::Win::Free()' ../src/liboctinterp.so: undefined reference to `MPI_Cart_map' ../src/liboctinterp.so: undefined reference to `MPI_Win_unlock' ../src/liboctinterp.so: undefined reference to `MPI_Alltoallw' collect2: ld returned 1 exit status make[2]: *** [octave] Error 1 The gfortran errors have gone away, but the MPI errors remain. I think is this something to fix from the maintainers. Please provide emerge -vp sci-mathematics/octave This is not octave's fault I think because octave doesn't know and care about MPI and this must hence come from some of the libraries it links against. Please try rebuilding all packages that liboctinterp.so links against, such as hdf5, umfpack and friends, etc. and see if that helps. Thanks, Markus This should be fixed now in the latest octave 3.2.4. Thanks, Markus |