| Summary: | sci-libs/arpack-3.8.0 - configure: error: could not compile a Fortran MPI test program | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | CONFIRMED --- | ||
| Severity: | normal | CC: | frp.bissey, kernelpanic |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge-info.txt
emerge-history.txt.bz2 environment etc.portage.tar.bz2 logs.tar.bz2 sci-libs:arpack-3.8.0:20230111-183258.log temp.tar.bz2 tentative ebuils using cmake instead of autotools |
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Description
Toralf Förster
2023-01-11 19:01:22 UTC
Created attachment 848259 [details]
emerge-info.txt
Created attachment 848261 [details]
emerge-history.txt.bz2
Created attachment 848263 [details]
environment
Created attachment 848265 [details]
etc.portage.tar.bz2
Created attachment 848267 [details]
logs.tar.bz2
Created attachment 848269 [details]
sci-libs:arpack-3.8.0:20230111-183258.log
Created attachment 848271 [details]
temp.tar.bz2
This is interesting configure:26960: mpif77 -o conftest -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 conftest.f -lmpi >&5 /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_view' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_byte_offset' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_position_shared' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_position' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_delete' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_group' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_type_extent' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_atomicity' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_preallocate' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_size' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_info' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `MPI_File_f2c' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_seek' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_open' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_seek_shared' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_Register_datarep' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `MPI_File_c2f' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_close' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_get_amode' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_set_size' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_set_view' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_set_atomicity' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_sync' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpifort.so: undefined reference to `PMPI_File_set_info' collect2: error: ld returned 1 exit status From what I can see in the logs, mpi is provided by mpich, and it looks like libmpifort.so is underlinked and mpif77 doesn't provide the right extra libraries or possibly provide them out of order. What options has mpich been compiled with? Locally ldd -r doesn't report any missing symbols on libifort.so but "nm -D" does show "PMPI_File_get_get_view" as undefined. However it is part of a family of entries with various capitalisation and underscores, so it is probably aliased to another symbol somewhere. 17-1-j4-20230105-065844 /var/tmp/tb # emerge -qpvO mpich [ebuild R ] sys-cluster/mpich-3.4.3 USE="cxx fortran threads -doc -mpi-threads -romio" ABI_X86="(64) -32 (-x32)" Created attachment 911002 [details]
tentative ebuils using cmake instead of autotools
I have the same problem using openmpi.
I tried to build arpack outside the ebuild system; building with autotools it fails; but building arpack with cmake compiles and links fine.
The suggested ebuild is rather simple, and does not consider the switch for EIGEN nor INTEGER64; it seems to work, though.
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