- edited description
PETSC_TEST_RUNS Fails
Issue #900
wontfix
Hello All,
I'm stuck on a funny petsc issue when compiling dolfin from the master branch. cmake says that PETSC_TEST_RUNS fails. I tried tracking this down in the cmake files, but became a little confused. What does this error mean? What strategies can I use to overcome it?
When I test my petsc installation everything looks fine. I pasted dolfin's cmake output and the output of petsc's test.
cmake output
#!
~/dolfin/build $ rm -rf *
~/dolfin/build $ PETSC_DIR=/usr/local/petsc/ cmake ..
-- The C compiler identification is AppleClang 8.0.0.8000042
-- The CXX compiler identification is AppleClang 8.0.0.8000042
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found MPI_C: /usr/local/Cellar/open-mpi/2.1.1/lib/libmpi.dylib
-- Found MPI_CXX: /usr/local/Cellar/open-mpi/2.1.1/lib/libmpi.dylib
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- timer
-- filesystem
-- program_options
-- iostreams
-- system
-- regex
-- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "3.2.8")
-- Found PythonInterp: /usr/local/bin/python3 (found suitable version "3.6.2", minimum required is "3")
-- Found PythonLibs: /usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6m.dylib (found suitable exact version "3.6.2")
-- NumPy header version 1.12.0 found
-- Found PY_ply: /usr/local/lib/python3.6/site-packages/ply
-- Found SWIG: /usr/local/bin/swig (found version "3.0.12")
-- Found UFC: /usr/local/lib/python3.6/site-packages/ffc/backends/ufc (Required is at least version "2017.2")
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Checking for one of the modules 'craypetsc_real;PETSc'
-- Test PETSC_TEST_RUNS with shared library linking - Failed
-- Test PETSC_TEST_RUNS static linking - Failed
-- Check size of PetscInt
-- Check size of PetscInt - done
-- PETSc could not be configured. (missing: PETSC_TEST_RUNS) (found suitable version "3.7.6", minimum required is "3.7")
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: /usr/local/bin/libparmetis.dylib;/usr/local/bin/libmetis.dylib (Required is at least version "4.0.2")
-- Checking for package 'SCOTCH-PT'
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing: SCOTCH_LIBRARIES SCOTCH_INCLUDE_DIRS SCOTCH_TEST_RUNS)
-- Checking for package 'AMD'
-- Looking for dgemm_
-- Looking for dgemm_ - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /System/Library/Frameworks/Accelerate.framework
-- Looking for cheev_
-- Looking for cheev_ - found
-- Performing test CHOLMOD_TEST_RUNS - Success
-- Performing test UMFPACK_TEST_RUNS - Success
-- Found UMFPACK: /usr/local/lib/libumfpack.dylib;/usr/local/lib/libamd.dylib;/System/Library/Frameworks/Accelerate.framework;/usr/local/lib/libcholmod.dylib;/usr/local/lib/libamd.dylib;/usr/local/lib/libcamd.dylib;/usr/local/lib/libcolamd.dylib;/usr/local/lib/libccolamd.dylib;/usr/local/lib/libsuitesparseconfig.dylib;/usr/local/bin/libparmetis.dylib;/usr/local/bin/libmetis.dylib;/System/Library/Frameworks/Accelerate.framework;/System/Library/Frameworks/Accelerate.framework;/System/Library/Frameworks/Accelerate.framework;/usr/local/lib/libsuitesparseconfig.dylib
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /System/Library/Frameworks/Accelerate.framework
-- Performing test CHOLMOD_TEST_RUNS - Success
-- Found CHOLMOD: /usr/local/lib/libcholmod.dylib;/usr/local/lib/libamd.dylib;/usr/local/lib/libcamd.dylib;/usr/local/lib/libcolamd.dylib;/usr/local/lib/libccolamd.dylib;/usr/local/lib/libsuitesparseconfig.dylib;/usr/local/bin/libparmetis.dylib;/usr/local/bin/libmetis.dylib;/System/Library/Frameworks/Accelerate.framework;/System/Library/Frameworks/Accelerate.framework;/System/Library/Frameworks/Accelerate.framework
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/local/Cellar/hdf5/1.10.1_1/lib/libhdf5.dylib;/usr/local/opt/szip/lib/libsz.dylib;/usr/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found version "1.10.1") found components: C
-- Checking for Trilinos
-- Unable to find Trilinos (>= 12.4.0)
-- Trilinos could not be found
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")
-- Checking for package 'Sphinx'
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'sphinx'
-- Could NOT find Sphinx (missing: SPHINX_VERSION_OK) (Required is at least version "1.1.0")
-- The following features have been enabled:
* BUILD_SHARED_LIBS, Build DOLFIN with shared libraries.
* DOLFIN_AUTO_DETECT_MPI, Detect MPI automatically (turn this off to use the MPI compiler wrappers directly via setting CXX, CXX, FC).
* DOLFIN_WITH_LIBRARY_VERSION, Build with library version information.
* DOLFIN_ENABLE_GTEST, Enable C++ unit tests with Google Test if DOLFIN_ENABLE_TESTING is true (requires Internet connection to download Google Test when first configured).
* DOLFIN_ENABLE_DOCS, Enable generation of documentation.
* CMAKE_INSTALL_RPATH_USE_LINK_PATH, Add paths to linker search and installed rpath.
* DOLFIN_ENABLE_MPI, Compile with support for MPI.
* DOLFIN_ENABLE_PETSC, Compile with support for PETSc.
* DOLFIN_ENABLE_PETSC4PY, Compile with support for PETSc4py.
* DOLFIN_ENABLE_SLEPC, Compile with support for SLEPc.
* DOLFIN_ENABLE_SLEPC4PY, Compile with support for SLEPc4py.
* DOLFIN_ENABLE_TRILINOS, Compile with support for Trilinos.
* DOLFIN_ENABLE_UMFPACK, Compile with support for UMFPACK.
* DOLFIN_ENABLE_CHOLMOD, Compile with support for CHOLMOD.
* DOLFIN_ENABLE_SCOTCH, Compile with support for SCOTCH.
* DOLFIN_ENABLE_PARMETIS, Compile with support for ParMETIS.
* DOLFIN_ENABLE_ZLIB, Compile with support for zlib.
* DOLFIN_ENABLE_PYTHON, Compile with support for Python.
* DOLFIN_ENABLE_SPHINX, Compile with support for Sphinx.
* DOLFIN_ENABLE_HDF5, Compile with support for HDF5.
* DOLFIN_ENABLE_VTK, Compile with support for VTK.
-- The following OPTIONAL packages have been found:
* MPI, Message Passing Interface (MPI)
Enables DOLFIN to run in parallel with MPI
* UMFPACK, Sparse LU factorization library, <http://faculty.cse.tamu.edu/davis/suitesparse.html>
* BLAS, Basic Linear Algebra Subprograms, <http://netlib.org/blas/>
* Threads
* CHOLMOD, Sparse Cholesky factorization library for sparse matrices, <http://faculty.cse.tamu.edu/davis/suitesparse.html>
* HDF5, Hierarchical Data Format 5 (HDF5), <https://www.hdfgroup.org/HDF5>
* ZLIB, Compression library, <http://www.zlib.net>
-- The following REQUIRED packages have been found:
* Boost, Boost C++ libraries, <http://www.boost.org>
* Eigen3 (required version >= 3.2.8), Lightweight C++ template library for linear algebra, <http://eigen.tuxfamily.org>
* PythonInterp (required version >= 3), Interactive high-level object-oriented language, <http://www.python.org>
Needed for the Python interface to DOLFIN
* PythonLibs (required version == 3.6.2), Include paths and libraries for Python
* NumPy, Array processing for numbers, strings, records, and objects in Python., <http://www.numpy.org>
Needed for the Python interface to DOLFIN
* SWIG, Tool to wrap C/C++ libraries in high-level languages, <http://swig.org>
Needed for the Python interface to DOLFIN
* UFC (required version >= 2017.2), Unified language for form-compilers (part of FFC), <https://bitbucket.org/fenics-project/ffc>
* PkgConfig
-- The following features have been disabled:
* CMAKE_USE_RELATIVE_PATHS, Use relative paths in makefiles and projects.
* DOLFIN_ENABLE_CODE_COVERAGE, Enable code coverage.
* DOLFIN_ENABLE_TESTING, Enable testing.
* DOLFIN_ENABLE_BENCHMARKS, Enable benchmark programs.
* DOLFIN_SKIP_BUILD_TESTS, Skip build tests for testing usability of dependency packages.
* DOLFIN_DEPRECATION_ERROR, Turn deprecation warnings into errors.
* DOLFIN_IGNORE_PETSC4PY_VERSION, Ignore version of PETSc4py.
* DOLFIN_ENABLE_OPENMP, Compile with support for OpenMP.
-- The following OPTIONAL packages have not been found:
* PETSc (required version >= 3.7), Portable, Extensible Toolkit for Scientific Computation, <https://www.mcs.anl.gov/petsc/>
Enables the PETSc linear algebra backend
* SCOTCH, Programs and libraries for graph, mesh and hypergraph partitioning, <https://www.labri.fr/perso/pelegrin/scotch>
Enables parallel graph partitioning
* Sphinx (required version >= 1.1.0), Python documentation generator, <http://www.sphinx-doc.org>
Needed to build documentation
--
-- Generating SWIG interface.
-- --------------------------
--------------------------------------------
WARNING: Missing doxygen, producing dummy docstrings
Generating dummy docstrings...
Writing /Users/jquick/dolfin/dolfin/swig/common/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/parameter/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/log/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/mesh/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/generation/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/geometry/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/refinement/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/graph/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/la/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/nls/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/function/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/math/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/ale/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/fem/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/multistage/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/adaptivity/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/plot/docstrings.i
Writing /Users/jquick/dolfin/dolfin/swig/io/docstrings.i
--
-- Generating demo source files from reStructuredText
-- --------------------------------------------------
extract written to /Users/jquick/dolfin/demo/documented/auto-adaptive-poisson/python/demo_auto-adaptive-poisson.py
extract written to /Users/jquick/dolfin/demo/documented/biharmonic/python/demo_biharmonic.py
extract written to /Users/jquick/dolfin/demo/documented/built-in-meshes/python/demo_built-in-meshes.py
extract written to /Users/jquick/dolfin/demo/documented/cahn-hilliard/python/demo_cahn-hilliard.py
extract written to /Users/jquick/dolfin/demo/documented/eigenvalue/python/demo_eigenvalue.py
extract written to /Users/jquick/dolfin/demo/documented/hyperelasticity/python/demo_hyperelasticity.py
extract written to /Users/jquick/dolfin/demo/documented/maxwell-eigenvalues/python/demo_maxwell-eigenvalues.py
extract written to /Users/jquick/dolfin/demo/documented/mixed-poisson/python/demo_mixed-poisson.py
extract written to /Users/jquick/dolfin/demo/documented/nonlinear-poisson/python/demo_nonlinear-poisson.py
extract written to /Users/jquick/dolfin/demo/documented/nonmatching-interpolation/python/demo_nonmatching-interpolation.py
extract written to /Users/jquick/dolfin/demo/documented/poisson/python/demo_poisson.py
extract written to /Users/jquick/dolfin/demo/documented/singular-poisson-rst/python/demo_singular-poisson-rst.py
extract written to /Users/jquick/dolfin/demo/documented/auto-adaptive-poisson/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/biharmonic/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/built-in-meshes/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/eigenvalue/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/hyperelasticity/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/mixed-poisson/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/nonmatching-interpolation/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/poisson/cpp/main.cpp
extract written to /Users/jquick/dolfin/demo/documented/auto-adaptive-poisson/cpp/AdaptivePoisson.ufl
extract written to /Users/jquick/dolfin/demo/documented/biharmonic/cpp/Biharmonic.ufl
extract written to /Users/jquick/dolfin/demo/documented/eigenvalue/cpp/StiffnessMatrix.ufl
extract written to /Users/jquick/dolfin/demo/documented/hyperelasticity/cpp/HyperElasticity.ufl
extract written to /Users/jquick/dolfin/demo/documented/mixed-poisson/cpp/MixedPoisson.ufl
extract written to /Users/jquick/dolfin/demo/documented/nonmatching-interpolation/cpp/P1.ufl
extract written to /Users/jquick/dolfin/demo/documented/nonmatching-interpolation/cpp/P3.ufl
extract written to /Users/jquick/dolfin/demo/documented/poisson/cpp/Poisson.ufl
CMake Deprecation Warning at demo/CMakeLists.txt:7 (cmake_policy):
The OLD behavior for policy CMP0004 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Found PythonInterp: /usr/local/bin/python3 (found version "3.6.2")
-- Performing Test HAVE_NO_MULTLINE
-- Performing Test HAVE_NO_MULTLINE - Success
-- Disabling generation of documentation because Sphinx is missing.
TRUE
1
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/jquick/dolfin/build
PETSC Test Output
~/install_petsc/petsc $ make PETSC_DIR=/usr/local/petsc PETSC_ARCH="" test
Running test examples to verify correct installation
Using PETSC_DIR=/usr/local/petsc and PETSC_ARCH=
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
PMIx has detected a temporary directory name that results
in a path that is too long for the Unix domain socket:
Temp dir: /var/folders/xv/t_q3wz391xggz8cpdh36ng_sqg9_wg/T/openmpi-sessions-1861528463@JQUICK-24176S_0/8395
Try setting your TMPDIR environmental variable to point to
something shorter in length
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI processes
See http://www.mcs.anl.gov/petsc/documentation/faq.html
PMIx has detected a temporary directory name that results
in a path that is too long for the Unix domain socket:
Temp dir: /var/folders/xv/t_q3wz391xggz8cpdh36ng_sqg9_wg/T/openmpi-sessions-1861528463@JQUICK-24176S_0/8388
Try setting your TMPDIR environmental variable to point to
something shorter in length
Possible error running Fortran example src/snes/examples/tutorials/ex5f with 1 MPI process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
PMIx has detected a temporary directory name that results
in a path that is too long for the Unix domain socket:
Temp dir: /var/folders/xv/t_q3wz391xggz8cpdh36ng_sqg9_wg/T/openmpi-sessions-1861528463@JQUICK-24176S_0/8566
Try setting your TMPDIR environmental variable to point to
something shorter in length
Completed test examples
=========================================
Now to evaluate the computer systems you plan use - do:
make PETSC_DIR=/usr/local/petsc PETSC_ARCH= streams
Comments (2)
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reporter -
- changed status to wontfix
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