<div dir="ltr"><div dir="ltr">On Thu, Aug 27, 2020 at 2:50 PM Blaise A Bourdin <<a href="mailto:bourdin@lsu.edu">bourdin@lsu.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
Hi,
<div><br>
</div>
<div>I am trying to build firedrake using intel compilers, mpi, and python. I compiled petsc using the following options, and petsc4py is installed by firedrake-install (see the compilation options below)</div>
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<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font face="SourceCodePro-Regular">./configure --with-mpi-dir=$MPI_HOME --CFLAGS='-std=c11 -D_GNU_SOURCE' --CXXFLAGS='' --FFLAGS='' --COPTFLAGS='-O3 -xCASCADELAKE -g' --FOPTFLAGS='-O3 -xCASCADELAKE -g' --CXXOPTFLAGS='-O3
-xCASCADELAKE -g' --with-c++-support --with-c-support --with-fortran --with-fortran-bindings=0 --with-cxx-dialect=C++11 --download-ptscotch --download-hdf5=<a href="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.bz2" target="_blank">https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.bz2</a>
--download-hypre --download-superlu_dist --download-metis --download-parmetis --download-scalapack --download-mumps --download-chaco --download-ml --download-eigen=<a href="https://github.com/eigenteam/eigen-git-mirror/archive/3.3.3.tar.gz" target="_blank">https://github.com/eigenteam/eigen-git-mirror/archive/3.3.3.tar.gz</a>
--download-sowing=0</font></div>
</blockquote>
<div><br>
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<div><br>
</div>
<div>Here is what I get when trying to import petsc4py:</div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font face="SourceCodePro-Regular">(firedrake) mef90:firedrake$ python3</font></div>
<div><font face="SourceCodePro-Regular">Python 3.7.7 (default, Jun 26 2020, 05:10:03) </font></div>
<div><font face="SourceCodePro-Regular">[GCC 7.3.0] :: Intel(R) Corporation on linux</font></div>
<div><font face="SourceCodePro-Regular">Type "help", "copyright", "credits" or "license" for more information.</font></div>
<div><font face="SourceCodePro-Regular">Intel(R) Distribution for Python is brought to you by Intel Corporation.</font></div>
<div><font face="SourceCodePro-Regular">Please check out: <a href="https://software.intel.com/en-us/python-distribution" target="_blank">
https://software.intel.com/en-us/python-distribution</a></font></div>
<div><font face="SourceCodePro-Regular">>>> import petsc4py</font></div>
<div><font face="SourceCodePro-Regular">>>> petsc4py.init()</font></div>
<div><font face="SourceCodePro-Regular">Traceback (most recent call last):</font></div>
<div><font face="SourceCodePro-Regular"> File "<stdin>", line 1, in <module></font></div>
<div><font face="SourceCodePro-Regular"> File "/home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/__init__.py", line 42, in init</font></div>
<div><font face="SourceCodePro-Regular"> PETSc = petsc4py.lib.ImportPETSc(arch)</font></div>
<div><font face="SourceCodePro-Regular"> File "/home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc</font></div>
<div><font face="SourceCodePro-Regular"> return Import('petsc4py', 'PETSc', path, arch)</font></div>
<div><font face="SourceCodePro-Regular"> File "/home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 73, in Import</font></div>
<div><font face="SourceCodePro-Regular"> module = import_module(pkg, name, path, arch)</font></div>
<div><font face="SourceCodePro-Regular"> File "/home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/lib/__init__.py", line 58, in import_module</font></div>
<div><font face="SourceCodePro-Regular"> with f: return imp.load_module(fullname, f, fn, info)</font></div>
<div><font face="SourceCodePro-Regular"> File "/share/apps/intel-2020.2/intelpython3/lib/python3.7/imp.py", line 242, in load_module</font></div>
<div><font face="SourceCodePro-Regular"> return load_dynamic(name, filename, file)</font></div>
<div><font face="SourceCodePro-Regular"> File "/share/apps/intel-2020.2/intelpython3/lib/python3.7/imp.py", line 342, in load_dynamic</font></div>
<div><font face="SourceCodePro-Regular"> return _load(spec)</font></div>
<div><font face="SourceCodePro-Regular"> File "<frozen importlib._bootstrap>", line 696, in _load</font></div>
<div><font face="SourceCodePro-Regular"> File "<frozen importlib._bootstrap>", line 670, in _load_unlocked</font></div>
<div><font face="SourceCodePro-Regular"> File "<frozen importlib._bootstrap>", line 583, in module_from_spec</font></div>
<div><font face="SourceCodePro-Regular"> File "<frozen importlib._bootstrap_external>", line 1043, in create_module</font></div>
<div><font face="SourceCodePro-Regular"> File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed</font></div>
<div><font face="SourceCodePro-Regular">ImportError: /home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake/<a href="http://PETSc.cpython-37m-x86_64-linux-gnu.so" target="_blank">PETSc.cpython-37m-x86_64-linux-gnu.so</a>: undefined symbol: PetscPartitionerInitializePackage</font></div></blockquote></div></blockquote><div><br></div><div>I have this symbol:</div><div><br></div><div>master $:/PETSc3/petsc/petsc-dev$ nm -o arch-master-debug/lib/libpetsc.dylib | grep PetscPartitionerInitializePackage<br>arch-master-debug/lib/libpetsc.dylib: 0000000000e07f90 T _PetscPartitionerInitializePackage<br></div><div><br></div><div>Can you run</div><div><br></div><div> nm -o /home/blaise/Development/firedrake/lib/python3.7/site-packages/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake/<a href="http://PETSc.cpython-37m-x86_64-linux-gnu.so" target="_blank">PETSc.cpython-37m-x86_64-linux-gnu.so</a> | grep PetscPartitionerInitializePackage</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
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</blockquote>
The relevant part of the firedrake-install.log are below.<br>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
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<div><font face="SourceCodePro-Regular">2020-08-27 12:48:23,861 INFO Installing petsc4py/</font></div>
<div><font face="SourceCodePro-Regular">2020-08-27 12:48:23,882 DEBUG Running command '/home/blaise/Development/firedrake/bin/python -m pip install --no-binary mpi4py,randomgen,islpy --no-deps -vvv --ignore-installed petsc4py/'</font></div>
<div><font face="SourceCodePro-Regular">2020-08-27 12:50:32,017 DEBUG Using pip 20.2.2 from /home/blaise/Development/firedrake/lib/python3.7/site-packages/pip (python 3.7)</font></div>
<div><font face="SourceCodePro-Regular">Non-user install because user site-packages disabled</font></div>
<div><font face="SourceCodePro-Regular">Created temporary directory: /tmp/pip-ephem-wheel-cache-5540399x</font></div>
<div><font face="SourceCodePro-Regular">Created temporary directory: /tmp/pip-req-tracker-jo7ho6yz</font></div>
<div><font face="SourceCodePro-Regular">Initialized build tracking at /tmp/pip-req-tracker-jo7ho6yz</font></div>
<div><font face="SourceCodePro-Regular">Created build tracker: /tmp/pip-req-tracker-jo7ho6yz</font></div>
<div><font face="SourceCodePro-Regular">Entered build tracker: /tmp/pip-req-tracker-jo7ho6yz</font></div>
<div><font face="SourceCodePro-Regular">Created temporary directory: /tmp/pip-install-e3u5z76o</font></div>
<div><font face="SourceCodePro-Regular">Processing ./petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> Created temporary directory: /tmp/pip-req-build-r3agmgty</font></div>
<div><font face="SourceCodePro-Regular"> Added <a>
file:///home/blaise/Development/firedrake/src/petsc4py</a> to build tracker '/tmp/pip-req-tracker-jo7ho6yz'</font></div>
<div><font face="SourceCodePro-Regular"> Running setup.py (path:/tmp/pip-req-build-r3agmgty/setup.py) egg_info for package from <a>file:///home/blaise/Development/firedrake/src/petsc4py</a></font></div>
<div><font face="SourceCodePro-Regular"> Created temporary directory: /tmp/pip-pip-egg-info-dctmtwx0</font></div>
<div><font face="SourceCodePro-Regular"> Running command python setup.py egg_info</font></div>
<div><font face="SourceCodePro-Regular"> running egg_info</font></div>
<div><font face="SourceCodePro-Regular"> creating /tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info</font></div>
<div><font face="SourceCodePro-Regular"> writing /tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/PKG-INFO</font></div>
<div><font face="SourceCodePro-Regular"> writing dependency_links to /tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/dependency_links.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing requirements to /tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/requires.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing top-level names to /tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/top_level.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing manifest file '/tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> reading manifest file '/tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> reading manifest template 'MANIFEST.in'</font></div>
<div><font face="SourceCodePro-Regular"> writing manifest file '/tmp/pip-pip-egg-info-dctmtwx0/petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> Source in /tmp/pip-req-build-r3agmgty has version 3.13.0, which satisfies requirement petsc4py==3.13.0 from <a>file:///home/blaise/Development/firedrake/src/petsc4py</a></font></div>
<div><font face="SourceCodePro-Regular"> Removed petsc4py==3.13.0 from
<a>file:///home/blaise/Development/firedrake/src/petsc4py</a> from build tracker '/tmp/pip-req-tracker-jo7ho6yz'</font></div>
<div><font face="SourceCodePro-Regular">Building wheels for collected packages: petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> Created temporary directory: /tmp/pip-wheel-0o0xldo2</font></div>
<div><font face="SourceCodePro-Regular"> Building wheel for petsc4py (setup.py): started</font></div>
<div><font face="SourceCodePro-Regular"> Destination directory: /tmp/pip-wheel-0o0xldo2</font></div>
<div><font face="SourceCodePro-Regular"> Running command /home/blaise/Development/firedrake/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-r3agmgty/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-r3agmgty/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"',
open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-0o0xldo2</font></div>
<div><font face="SourceCodePro-Regular"> running bdist_wheel</font></div>
<div><font face="SourceCodePro-Regular"> running build</font></div>
<div><font face="SourceCodePro-Regular"> running build_src</font></div>
<div><font face="SourceCodePro-Regular"> cythonizing 'petsc4py.PETSc.pyx' -> 'petsc4py.PETSc.c'</font></div>
<div><font face="SourceCodePro-Regular"> /home/blaise/Development/firedrake/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later
release! File: include/petsc4py/PETSc.pxd</font></div>
<div><font face="SourceCodePro-Regular"> tree = Parsing.p_module(s, pxd, full_module_name)</font></div>
<div><font face="SourceCodePro-Regular"> cythonizing 'libpetsc4py/libpetsc4py.pyx' -> 'libpetsc4py/libpetsc4py.c'</font></div>
<div><font face="SourceCodePro-Regular"> /home/blaise/Development/firedrake/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later
release! File: /tmp/pip-req-build-r3agmgty/src/libpetsc4py/libpetsc4py.pyx</font></div>
<div><font face="SourceCodePro-Regular"> tree = Parsing.p_module(s, pxd, full_module_name)</font></div>
<div><font face="SourceCodePro-Regular"> running build_py</font></div>
<div><font face="SourceCodePro-Regular"> creating build</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/PETSc.py -> build/lib.linux-x86_64-3.7/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/__main__.py -> build/lib.linux-x86_64-3.7/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> copying src/lib/__init__.py -> build/lib.linux-x86_64-3.7/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7/petsc4py/include</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/numpy.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/__init__.pxd -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/include/petsc4py/__init__.pyx -> build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/PETSc.pxd -> build/lib.linux-x86_64-3.7/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying src/lib/petsc.cfg -> build/lib.linux-x86_64-3.7/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> running build_ext</font></div>
<div><font face="SourceCodePro-Regular"> PETSC_DIR: /opt/HPC/petsc-maint</font></div>
<div><font face="SourceCodePro-Regular"> PETSC_ARCH: RHEL7-intel2020.2-impi-firedrake</font></div>
<div><font face="SourceCodePro-Regular"> version: 3.13.4 release</font></div>
<div><font face="SourceCodePro-Regular"> integer-size: 32-bit</font></div>
<div><font face="SourceCodePro-Regular"> scalar-type: real</font></div>
<div><font face="SourceCodePro-Regular"> precision: double</font></div>
<div><font face="SourceCodePro-Regular"> language: CONLY</font></div>
<div><font face="SourceCodePro-Regular"> compiler: /share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc</font></div>
<div><font face="SourceCodePro-Regular"> linker: /share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc</font></div>
<div><font face="SourceCodePro-Regular"> building 'PETSc' extension</font></div>
<div><font face="SourceCodePro-Regular"> creating build/temp.linux-x86_64-3.7</font></div>
<div><font face="SourceCodePro-Regular"> creating build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake</font></div>
<div><font face="SourceCodePro-Regular"> creating build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake/src</font></div>
<div><font face="SourceCodePro-Regular"> /share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc -pthread -B /share/apps/intel-2020.2/intelpython3/compiler_compat -Wl,--sysroot=/ -std=c11 -D_GNU_SOURCE -fPIC -O3 -xCASCADELAKE
-g -fPIC -L/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/lib -I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include -I/share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/include -I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include/eigen3
-I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include -I/opt/HPC/petsc-maint/include -Isrc/include -I/home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include -I/home/blaise/Development/firedrake/include -I/share/apps/intel-2020.2/intelpython3/include/python3.7m
-c src/PETSc.c -o build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake/src/PETSc.o</font></div>
<div><font face="SourceCodePro-Regular"> In file included from /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h(12),</font></div>
<div><font face="SourceCodePro-Regular"> from /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h(4),</font></div>
<div><font face="SourceCodePro-Regular"> from src/include/petsc4py/numpy.h(11),</font></div>
<div><font face="SourceCodePro-Regular"> from src/petsc4py.PETSc.c(612),</font></div>
<div><font face="SourceCodePro-Regular"> from src/PETSc.c(4):</font></div>
<div><font face="SourceCodePro-Regular"> /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h(84): warning #2650: attributes ignored here</font></div>
<div><font face="SourceCodePro-Regular"> NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),</font></div>
<div><font face="SourceCodePro-Regular"> ^</font></div>
<div><font face="SourceCodePro-Regular"><br>
</font></div>
<div><font face="SourceCodePro-Regular"> In file included from src/petsc4py.PETSc.c(619),</font></div>
<div><font face="SourceCodePro-Regular"> from src/PETSc.c(4):</font></div>
<div><font face="SourceCodePro-Regular"> src/include/initpkg.h(23): warning #266: function "PetscPartitionerInitializePackage" declared implicitly</font></div>
<div><font face="SourceCodePro-Regular"> ierr = PetscPartitionerInitializePackage();CHKERRQ(ierr);</font></div>
<div><font face="SourceCodePro-Regular"> ^</font></div>
<div><font face="SourceCodePro-Regular"><br>
</font></div>
<div><font face="SourceCodePro-Regular"> In file included from src/PETSc.c(4):</font></div>
<div><font face="SourceCodePro-Regular"> src/petsc4py.PETSc.c(294008): warning #266: function "PetscPartitionerReset" declared implicitly</font></div>
<div><font face="SourceCodePro-Regular"> __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(PetscPartitionerReset(__pyx_v_self->part)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(54, 55, __pyx_L1_error)</font></div>
<div><font face="SourceCodePro-Regular"> ^</font></div>
<div><font face="SourceCodePro-Regular"><br>
</font></div>
<div><font face="SourceCodePro-Regular"> /share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc -pthread -B /share/apps/intel-2020.2/intelpython3/compiler_compat -Wl,--sysroot=/ -std=c11 -D_GNU_SOURCE -fPIC -O3 -xCASCADELAKE
-g -fPIC -L/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/lib -I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include -I/share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/include -I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include/eigen3
-I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include -I/opt/HPC/petsc-maint/include -Isrc/include -I/home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include -I/home/blaise/Development/firedrake/include -I/share/apps/intel-2020.2/intelpython3/include/python3.7m
-c src/libpetsc4py.c -o build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake/src/libpetsc4py.o</font></div>
<div><font face="SourceCodePro-Regular"> In file included from /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h(12),</font></div>
<div><font face="SourceCodePro-Regular"> from /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h(4),</font></div>
<div><font face="SourceCodePro-Regular"> from src/include/petsc4py/numpy.h(11),</font></div>
<div><font face="SourceCodePro-Regular"> from src/libpetsc4py/libpetsc4py.c(612),</font></div>
<div><font face="SourceCodePro-Regular"> from src/libpetsc4py.c(6):</font></div>
<div><font face="SourceCodePro-Regular"> /home/blaise/Development/firedrake/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h(84): warning #2650: attributes ignored here</font></div>
<div><font face="SourceCodePro-Regular"> NPY_CHAR NPY_ATTR_DEPRECATE("Use NPY_STRING"),</font></div>
<div><font face="SourceCodePro-Regular"> ^</font></div>
<div><font face="SourceCodePro-Regular"><br>
</font></div>
<div><font face="SourceCodePro-Regular"> creating build/lib.linux-x86_64-3.7/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake</font></div>
<div><font face="SourceCodePro-Regular"> /share/apps/intel-2020.2/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc -pthread -B /share/apps/intel-2020.2/intelpython3/compiler_compat -Wl,--sysroot=/ -std=c11 -D_GNU_SOURCE -fPIC -O3 -xCASCADELAKE
-g -shared -L/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/lib -I/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/include -L/share/apps/intel-2020.2/intelpython3/lib -Wl,-rpath=/share/apps/intel-2020.2/intelpython3/lib -Wl,--no-as-needed -Wl,--sysroot=/
build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake/src/PETSc.o build/temp.linux-x86_64-3.7/RHEL7-intel2020.2-impi-firedrake/src/libpetsc4py.o -L/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/lib -Wl,-rpath,/opt/HPC/petsc-maint/RHEL7-intel2020.2-impi-firedrake/lib
-lpetsc -o build/lib.linux-x86_64-3.7/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake/<a href="http://PETSc.cpython-37m-x86_64-linux-gnu.so" target="_blank">PETSc.cpython-37m-x86_64-linux-gnu.so</a></font></div>
<div><font face="SourceCodePro-Regular"> writing build/lib.linux-x86_64-3.7/petsc4py/lib/petsc.cfg</font></div>
<div><font face="SourceCodePro-Regular"> installing to build/bdist.linux-x86_64/wheel</font></div>
<div><font face="SourceCodePro-Regular"> running install</font></div>
<div><font face="SourceCodePro-Regular"> running install_lib</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/PETSc.py -> build/bdist.linux-x86_64/wheel/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/__init__.py -> build/bdist.linux-x86_64/wheel/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/__main__.py -> build/bdist.linux-x86_64/wheel/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/lib/__init__.py -> build/bdist.linux-x86_64/wheel/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/lib/petsc.cfg -> build/bdist.linux-x86_64/wheel/petsc4py/lib</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake/<a href="http://PETSc.cpython-37m-x86_64-linux-gnu.so" target="_blank">PETSc.cpython-37m-x86_64-linux-gnu.so</a> -> build/bdist.linux-x86_64/wheel/petsc4py/lib/RHEL7-intel2020.2-impi-firedrake</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py/include</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/numpy.h -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/petsc4py.h -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/petsc4py.PETSc.h -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/petsc4py.PETSc_api.h -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/petsc4py.i -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/PETSc.pxd -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/__init__.pxd -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/include/petsc4py/__init__.pyx -> build/bdist.linux-x86_64/wheel/petsc4py/include/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> copying build/lib.linux-x86_64-3.7/petsc4py/PETSc.pxd -> build/bdist.linux-x86_64/wheel/petsc4py</font></div>
<div><font face="SourceCodePro-Regular"> running install_egg_info</font></div>
<div><font face="SourceCodePro-Regular"> running egg_info</font></div>
<div><font face="SourceCodePro-Regular"> creating petsc4py.egg-info</font></div>
<div><font face="SourceCodePro-Regular"> writing petsc4py.egg-info/PKG-INFO</font></div>
<div><font face="SourceCodePro-Regular"> writing dependency_links to petsc4py.egg-info/dependency_links.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing requirements to petsc4py.egg-info/requires.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing top-level names to petsc4py.egg-info/top_level.txt</font></div>
<div><font face="SourceCodePro-Regular"> writing manifest file 'petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> reading manifest file 'petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> reading manifest template 'MANIFEST.in'</font></div>
<div><font face="SourceCodePro-Regular"> writing manifest file 'petsc4py.egg-info/SOURCES.txt'</font></div>
<div><font face="SourceCodePro-Regular"> Copying petsc4py.egg-info to build/bdist.linux-x86_64/wheel/petsc4py-3.13.0-py3.7.egg-info</font></div>
<div><font face="SourceCodePro-Regular"> running install_scripts</font></div>
<div><font face="SourceCodePro-Regular"> adding license file "LICENSE.rst" (matched pattern "LICEN[CS]E*")</font></div>
<div><font face="SourceCodePro-Regular"> creating build/bdist.linux-x86_64/wheel/petsc4py-3.13.0.dist-info/WHEEL</font></div>
<div><font face="SourceCodePro-Regular"> creating '/tmp/pip-wheel-0o0xldo2/petsc4py-3.13.0-cp37-cp37m-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/PETSc.pxd'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/PETSc.py'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/__init__.py'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/__main__.py'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/PETSc.pxd'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/__init__.pxd'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/__init__.pyx'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/numpy.h'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/petsc4py.PETSc.h'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/petsc4py.PETSc_api.h'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/petsc4py.h'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/include/petsc4py/petsc4py.i'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/lib/__init__.py'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/lib/petsc.cfg'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py/lib/RHEL7-intel2020.2-impi-firedrake/<a href="http://PETSc.cpython-37m-x86_64-linux-gnu.so" target="_blank">PETSc.cpython-37m-x86_64-linux-gnu.so</a>'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py-3.13.0.dist-info/LICENSE.rst'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py-3.13.0.dist-info/METADATA'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py-3.13.0.dist-info/WHEEL'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py-3.13.0.dist-info/top_level.txt'</font></div>
<div><font face="SourceCodePro-Regular"> adding 'petsc4py-3.13.0.dist-info/RECORD'</font></div>
<div><font face="SourceCodePro-Regular"> removing build/bdist.linux-x86_64/wheel</font></div>
<div><font face="SourceCodePro-Regular"> Building wheel for petsc4py (setup.py): finished with status 'done'</font></div>
<div><font face="SourceCodePro-Regular"> Created wheel for petsc4py: filename=petsc4py-3.13.0-cp37-cp37m-linux_x86_64.whl size=4287046 sha256=95604a089946004038f4268d38948c35a5372a2cedaa9df21e354d68231cb99a</font></div>
<div><font face="SourceCodePro-Regular"> Stored in directory: /tmp/pip-ephem-wheel-cache-5540399x/wheels/88/a6/a9/78aff17157d1fedc3a047afc3f1c84462e68ea89775758cd2e</font></div>
<div><font face="SourceCodePro-Regular">Successfully built petsc4py</font></div>
<div><font face="SourceCodePro-Regular">Installing collected packages: petsc4py</font></div>
<div><font face="SourceCodePro-Regular"><br>
</font></div>
<div><font face="SourceCodePro-Regular">Successfully installed petsc4py-3.13.0</font></div>
<div><font face="SourceCodePro-Regular">Removed build tracker: '/tmp/pip-req-tracker-jo7ho6yz'</font></div>
</blockquote>
<div><br>
<div><br>
</div>
<div>Any idea?</div>
<div><br>
</div>
<div>Blaise</div>
<div><br>
</div>
<div><br>
</div>
<div>-- <br>
A.K. & Shirley Barton Professor of Mathematics<br>
Adjunct Professor of Mechanical Engineering<br>
Adjunct of the Center for Computation & Technology<br>
Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA<br>
Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web <a href="http://www.math.lsu.edu/~bourdin" target="_blank">http://www.math.lsu.edu/~bourdin</a></div>
<br>
</div>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>