Hi,
Running the following script works fine in serial but fails to run in parallel:
from dolfin import *
filename = "mesh3d.h5"
# Write to file
mesh0 = UnitCubeMesh(10, 10, 10)
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "w")
mesh_file.write(mesh0, "/my_mesh")
mesh_file.close()
# Read from file
mesh1 = Mesh()
mesh_file = HDF5File(mesh0.mpi_comm(), filename, "r")
mesh_file.read(mesh1, "/my_mesh", False)
mesh_file.close()
The error message is attached. Any idea what the problem could be?
Johannes
johannr@debian-t420s:tmp$ mpirun -np 2 python test.py
Number of global vertices: 1331
Number of global cells: 6000
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5F.c line 1512 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
#001: H5F.c line 1290 in H5F_open(): unable to open file: time = Wed Feb 4 09:47:47 2015
, name = 'mesh3d.h5', tent_flags = 13
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 985 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#004: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_ERR_OTHER: known error not in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5F.c line 1512 in H5Fcreate(): unable to create file
major: File accessibilty
minor: Unable to open file
#001: H5F.c line 1290 in H5F_open(): unable to open file: time = Wed Feb 4 09:47:47 2015
, name = 'mesh3d.h5', tent_flags = 13
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 985 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#004: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_ERR_OTHER: known error not in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 811 in H5Gclose(): not a group
major: Invalid arguments to routine
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 811 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 811 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 811 in H5Gclose(): not a group
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5G.c line 811 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 240 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 2591 in H5Aexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 244 in H5Acreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 929 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 2288 in H5Aclose(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 1078 in H5Oclose(): not a valid file object ID (dataset, group, or datatype)
major: Invalid arguments to routine
minor: Unable to release object
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 644 in H5Oget_info_by_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 285 in H5Gcreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5G.c line 811 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 165 in H5Dcreate2(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Shyper.c line 6593 in H5Sselect_hyperslab(): not a data space
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5Dio.c line 225 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 257 in H5D__pre_write(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 415 in H5Dclose(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5S.c line 391 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 240 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 2591 in H5Aexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 244 in H5Acreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 929 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 2288 in H5Aclose(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 1078 in H5Oclose(): not a valid file object ID (dataset, group, or datatype)
major: Invalid arguments to routine
minor: Unable to release object
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 240 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 2591 in H5Aexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 244 in H5Acreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 929 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5A.c line 2288 in H5Aclose(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5O.c line 1078 in H5Oclose(): not a valid file object ID (dataset, group, or datatype)
major: Invalid arguments to routine
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 240 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 2591 in H5Aexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 244 in H5Acreate2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 929 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5A.c line 2288 in H5Aclose(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5O.c line 1078 in H5Oclose(): not a valid file object ID (dataset, group, or datatype)
major: Invalid arguments to routine
minor: Unable to release object
minor: Unable to release object
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5F.c line 2049 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5F.c line 2049 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5F.c line 1594 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5F.c line 1290 in H5F_open(): unable to open file: time = Wed Feb 4 09:47:47 2015
, name = 'mesh3d.h5', tent_flags = 0
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5F.c line 1594 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5F.c line 1290 in H5F_open(): unable to open file: time = Wed Feb 4 09:47:47 2015
, name = 'mesh3d.h5', tent_flags = 0
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 985 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 985 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
minor: Some MPI function failed
#004: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_ERR_OTHER: known error not in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
#003: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#004: H5FDmpio.c line 1064 in H5FD_mpio_open(): MPI_ERR_OTHER: known error not in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 340 in H5Dopen2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5S.c line 780 in H5Sget_simple_extent_ndims(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5L.c line 813 in H5Lexists(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
Traceback (most recent call last):
File "test.py", line 16, in <module>
mesh_file.read(mesh1, "/my_mesh", False)
Exception: std::bad_alloc
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
#000: H5F.c line 2049 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 340 in H5Dopen2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5D.c line 461 in H5Dget_space(): not a dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5S.c line 780 in H5Sget_simple_extent_ndims(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type
Traceback (most recent call last):
File "test.py", line 16, in <module>
mesh_file.read(mesh1, "/my_mesh", False)
Exception: std::bad_alloc
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
#000: H5F.c line 2049 in H5Fclose(): not a file ID
major: Invalid arguments to routine
minor: Inappropriate type
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
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