Hi Floriane, On 08/02/18 10:26, Floriane Gidel [RPG] wrote:
Dear Lawrence,
When I run the attached file TOC2.py on a remote machine with a firedrake version updated from one week ago, I get the error that I sent to you in my previous email. When I run it on my laptop with an old version of Firedrake, it runs for a while and then stops with the error:
Hmm, I just tried with an up-to-date Firedrake here (firedrake-status says): Firedrake Configuration: petsc_int_type: int32 mpicc: mpicc packages: [] disable_ssh: True honour_pythonpath: False show_petsc_configure_options: False adjoint: False cache_dir: /data/lmitche1/tmp/firedrake/.cache slope: False package_manager: False slepc: False minimal_petsc: False Additions: None Environment: PETSC_ARCH: arch-linux2-c-opt PYTHONPATH: None PETSC_DIR: /data/lmitche1/src/deps/petsc Status of components: --------------------------------------------------------------------------- |Package |Branch |Revision |Modified | --------------------------------------------------------------------------- |COFFEE |master |5bb1b30 |False | |FInAT |master |ef12759 |False | |PyOP2 |master |8a918cf |False | |fiat |master |f2b2511 |False | |firedrake |master |d53aaa8 |False | |h5py |firedrake |c1e4a81 |False | |islpy |master |bc69e45 |False | |libspatialindex |master |4768bf3 |True | |petsc4py |firedrake |3f09f6d |False | |tsfc |master |d7da9dc |False | |ufl |master |50bbef8 |False | --------------------------------------------------------------------------- And I get no errors. I don't think much has changed recently, but can you please post the output of firedrake-status just to see if there are any differences. ...
[math-mc1096:02125] mca_sharedfp_sm_file_open: Error, unable to open file for mmap: /tmp/OMPIO_h_232.h5_-43450367_.sm
Exception petsc4py.PETSc.Error: 76 in 'petsc4py.PETSc.Object.__dealloc__' ignored
Traceback (most recent call last):
File "TOC2.py", line 84, in <module>
dumb_file_medium = DumbCheckpoint(save_path+"medium/h_"+str(i_dt), mode=FILE_READ)
File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 65, in __init__
self.new_file()
File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 144, in new_file
comm=self.comm)
File "PETSc/Viewer.pyx", line 365, in petsc4py.PETSc.ViewerHDF5.create (src/petsc4py.PETSc.c:76259)
petsc4py.PETSc.Error: error code 76
[0] PetscObjectDestroy() line 69 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/sys/objects/destroy.c
[0] PetscViewerDestroy() line 100 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/sys/classes/viewer/interface/view.c
[0] PetscViewerDestroy_HDF5() line 49 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/sys/classes/viewer/impls/hdf5/hdf5v.c
[0] PetscViewerFileClose_HDF5() line 39 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/sys/classes/viewer/impls/hdf5/hdf5v.c
I think this is somehow an indication that some files were not correctly closed. I tried on my Mac laptop (also with the same firedrake indicated above), and didn't see any problems. A bit of a mystery! Lawrence