[petsc-dev] libpetsc.so.3.12: undefined symbol: hypre_ParCSRMatrixCompleteClone
Antonio Trande
anto.trande at gmail.com
Sat Oct 19 14:53:30 CDT 2019
Hi all.
Following error appears by executing 'petsc4py-3.12.0' tests:
+ /usr/bin/python3 setup.py test
running test
Traceback (most recent call last):
File "setup.py", line 270, in <module>
main()
File "setup.py", line 267, in main
run_setup()
File "setup.py", line 119, in run_setup
setup(packages = ['petsc4py',
File "/usr/lib/python3.8/site-packages/setuptools/__init__.py", line
145, in setup
return distutils.core.setup(**attrs)
File "/usr/lib64/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib64/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib64/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "setup.py", line 258, in run_testsuite
err = main(args)
File "test/runtests.py", line 203, in main
package = import_package(options, pkgname)
File "test/runtests.py", line 85, in import_package
package.init(args, arch=options.arch)
File "build/lib.linux-x86_64-3.8/petsc4py/__init__.py", line 42, in init
PETSc = petsc4py.lib.ImportPETSc(arch)
File "build/lib.linux-x86_64-3.8/petsc4py/lib/__init__.py", line 29,
in ImportPETSc
return Import('petsc4py', 'PETSc', path, arch)
File "build/lib.linux-x86_64-3.8/petsc4py/lib/__init__.py", line 73,
in Import
module = import_module(pkg, name, path, arch)
File "build/lib.linux-x86_64-3.8/petsc4py/lib/__init__.py", line 58,
in import_module
with f: return imp.load_module(fullname, f, fn, info)
File "/usr/lib64/python3.8/imp.py", line 242, in load_module
return load_dynamic(name, filename, file)
File "/usr/lib64/python3.8/imp.py", line 342, in load_dynamic
return _load(spec)
File "<frozen importlib._bootstrap>", line 702, in _load
File "<frozen importlib._bootstrap>", line 657, in _load_unlocked
File "<frozen importlib._bootstrap>", line 556, in module_from_spec
File "<frozen importlib._bootstrap_external>", line 1101, in create_module
File "<frozen importlib._bootstrap>", line 219, in
_call_with_frames_removed
ImportError: /usr/lib64/mpich/lib/libpetsc.so.3.12: undefined symbol:
hypre_ParCSRMatrixCompleteClone
This is a clear undefined symbol of PETSc-3.12.0 compiled on Fedora 32
(devel branch) with MPICH-3.3.1 and Hypre-2.18.0
$ ldd -r /usr/lib64/mpich/lib/libHYPRE.so
linux-vdso.so.1 (0x00007ffed55f3000)
libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007fce15135000)
libsuperlu_dist.so.1 => /usr/lib64/mpich/lib/libsuperlu_dist.so.1
(0x00007fce1504d000)
libm.so.6 => /lib64/libm.so.6 (0x00007fce14f06000)
libmpi.so.12 => /usr/lib64/mpich/lib/libmpi.so.12 (0x00007fce14bfd000)
libc.so.6 => /lib64/libc.so.6 (0x00007fce14a34000)
libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007fce14792000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fce14596000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007fce1455c000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fce14542000)
/lib64/ld-linux-x86-64.so.2 (0x00007fce1785b000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fce14520000)
librt.so.1 => /lib64/librt.so.1 (0x00007fce14515000)
libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007fce144c8000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007fce1447c000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fce14475000)
libltdl.so.7 => /lib64/libltdl.so.7 (0x00007fce14469000)
$ ldd -r /usr/lib64/mpich/lib/libpetsc.so.3.12.0
linux-vdso.so.1 (0x00007ffc46bfb000)
libHYPRE.so.2.1 => /usr/lib64/mpich/lib/libHYPRE.so.2.1
(0x00007f8c4d67a000)
libdmumps-5.2.so => /usr/lib64/mpich/lib/libdmumps-5.2.so
(0x00007f8c4d458000)
libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f8c4b140000)
libptscotch.so.1 => /usr/lib64/mpich/lib/libptscotch.so.1
(0x00007f8c4b0f6000)
libscotch.so.1 => /usr/lib64/mpich/lib/libscotch.so.1 (0x00007f8c4b06b000)
libptscotcherr.so.1 => /usr/lib64/mpich/lib/libptscotcherr.so.1
(0x00007f8c4b066000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8c4b042000)
libhdf5.so.103 => /usr/lib64/mpich/lib/libhdf5.so.103 (0x00007f8c4ac82000)
libcgns.so.3.4 => /lib64/libcgns.so.3.4 (0x00007f8c4abaa000)
libm.so.6 => /lib64/libm.so.6 (0x00007f8c4aa63000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f8c4a91d000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f8c4a916000)
libmpi.so.12 => /usr/lib64/mpich/lib/libmpi.so.12 (0x00007f8c4a60b000)
libc.so.6 => /lib64/libc.so.6 (0x00007f8c4a442000)
libsuperlu_dist.so.1 => /usr/lib64/mpich/lib/libsuperlu_dist.so.1
(0x00007f8c4a35a000)
libmumps_common-5.2.so => /usr/lib64/mpich/lib/libmumps_common-5.2.so
(0x00007f8c4a308000)
libmpiblacs.so.2 => /usr/lib64/mpich/lib/libmpiblacs.so.2
(0x00007f8c4a2d5000)
libscalapack.so.2 => /usr/lib64/mpich/lib/libscalapack.so.2
(0x00007f8c49ce6000)
libmetis.so.0 => /lib64/libmetis.so.0 (0x00007f8c49c78000)
libmpifort.so.12 => /usr/lib64/mpich/lib/libmpifort.so.12
(0x00007f8c49bf3000)
libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f8c49951000)
libscotcherr.so.1 => /lib64/libscotcherr.so.1 (0x00007f8c4994c000)
libz.so.1 => /lib64/libz.so.1 (0x00007f8c49932000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f8c4991e000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f8c498f3000)
/lib64/ld-linux-x86-64.so.2 (0x00007f8c4edf7000)
libsz.so.2 => /lib64/libsz.so.2 (0x00007f8c498ee000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f8c498c3000)
librt.so.1 => /lib64/librt.so.1 (0x00007f8c498b8000)
libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007f8c4986b000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f8c4984f000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f8c49655000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f8c4961b000)
libpord-5.2.so => /usr/lib64/mpich/lib/libpord-5.2.so (0x00007f8c49602000)
libesmumps.so.1 => /lib64/libesmumps.so.1 (0x00007f8c495fb000)
libpcre2-posix.so.2 => /lib64/libpcre2-posix.so.2 (0x00007f8c495f4000)
libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f8c495aa000)
libaec.so.0 => /lib64/libaec.so.0 (0x00007f8c495a0000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f8c4959a000)
libltdl.so.7 => /lib64/libltdl.so.7 (0x00007f8c4958e000)
libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f8c494fe000)
undefined symbol: hypre_ParCSRMatrixCompleteClone
(/usr/lib64/mpich/lib/libpetsc.so.3.12.0)
--
---
Antonio Trande
Fedora Project
mailto 'sagitter at fedoraproject dot org'
GPG key: 0x6e0331dd1699e4d7
GPG key server: https://keys.openpgp.org/
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