(Deleted) AttributeError: module 'fenics' has no attribute 'HDF5File'


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10 months ago by
Hey

I installed fenics from source as suggested on https://fenicsproject.org/download/, including support for HDF5.

However, when i try:  outFile = HDF5File(mesh.mpi_comm(), 'filename.h5')
it gives: AttributeError: module 'fenics' has no attribute 'HDF5File'

I rechecked the cmake configuration for dolfin and it is able to detect HDF5 package on my system. Pasting a snippet of the 'cmake .." execution below.
I am new to using fenics. Primarily, I want to be able to write and read function outputs from a solver. From the information I have gathered, one can do this by working with hdf5 format.
In case there better ways to achieve that, please let me know. Thanks.

...
HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Checking for Trilinos
-- Unable to find Trilinos (>= 12.4.0)
-- Trilinos could not be found
-- 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.


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>
Community: FEniCS Project

1 Answer


0
10 months ago by
What do you get with has_hdf5() and has_hdf5_parallel() in dolfin?
Both give me 'False'. Although I am able to store and retrieve data using XDMF format now which solves my purpose, I would still like to know how to fix this issue with HDF5.
written 10 months ago by Pratyuksh Bansal  
Could anyone please suggest what would be the best way to store reference solutions and then be able to load them later during post-processing? I tried the checkpoint writing with XDMF but it does not help, I am unable to load the information that I saved. Thank you for your time.
written 9 months ago by Pratyuksh Bansal  
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