hdf5 error

[christina-rice]

I am receiving a strange hdf5 error when running example codes. This seems to have occurred on other programs as well, but I am not sure how to specifically debug the HemoCell code as the general solution did not resolve the issue.

I have followed this thread suggestion to add to my .bashrc file "export HDF5_USE_FILE_LOCKING='FALSE'"

Additionally, I found this thread and this thread that suggests changing close()/flush()/MPI_finalize() or adding "--hdf5 …/HDF5" into the script, but I am not sure where to start editing HemoCell to make these changes.

Has anyone had this problem? How would you go about resolving it?

A sample of the error message:
'''
(readPositionsBloodCells) Particle count in file (PLT): 80.
(HemoCell) (Output) writing output at timestep 0 (0 s). Approx. performance: 0.00 s / iteration.
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
# 000: H5F.c line 350 in H5Fcreate(): unable to create file
major: File accessibility
minor: Unable to open file
# 001: H5Fint.c line 1670 in H5F_open(): unable to open file: time = Mon Nov 14 20:09:48 2022
, name = './output_9//hdf5/000000000000/RBC.000000000000.p.226.h5', tent_flags = 13
major: File accessibility
minor: Unable to open file
# 002: H5FD.c line 723 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
# 003: H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = './output_9//hdf5/000000000000/RBC.000000000000.p.226.h5', errno = 2, error message = 'No such file or directory', flags = 13, o_flags = 242
major: File accessibility
minor: Unable to open file
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
# 000: H5O.c line 101 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
# 001: H5Gloc.c line 228 in H5G_loc(): invalid location ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
# 000: H5O.c line 101 in H5Oopen(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
'''

[christina-rice]

I rebuilt HemoCell, and the simulation can run on one node with 36 tasks, but not multiple nodes.

[mojtabaAmiraslanpour]

Do you get the same error?