[petsc-dev] libpetsc.so.3.12: undefined symbol: hypre_ParCSRMatrixCompleteClone

Sat Oct 19 16:38:35 CDT 2019

The fix will be in petsc-3.12.1. Its currently at 0e6427aaee0f47968cf0ac27aab894e1846afdba

or you can upgrade to hypre-2.18.1

Satish

On Sat, 19 Oct 2019, Antonio Trande via petsc-dev wrote:

> 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)
> 
> 