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PETSC_TEST_RUNS Fails

Issue #900 wontfix
Julian Quick created an issue

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

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