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

_______________________________________________
firedrake mailing list
firedrake@imperial.ac.uk
https://mailman.ic.ac.uk/mailman/listinfo/firedrake