[FLASH-USERS] HDF5 IO problem

[t_schlegel at t-online.de]

Hello,
 
I have installed the modules:
GCC/7.2.0 5)
OpenMPI/3.0.0-GCC-7.2.0
FLASH/4.5-OpenMPI-3.0.0-GCC-7.2.0
hypre/2.11.2-OpenMPI-3.0.0-GCC-7.2.0
HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 for parallel output
either HDF5/1.10.2-GCC-7.2.0 for serial one
parallel_netcdf/1.9.0-OpenMPI-3.0.0-GCC-7.2.0       on our cluster.
 
The Sedov example with serial HDF5 works as expected, 
but using the HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0 module instead of serial 
IO
 
(./setup Sedov -auto +parallelio, putting the right path for 
HDF5/1.10.1-OpenMPI-3.0.0-GCC-7.2.0
in Makefile.h)
 
the job will be aborted at first write of a ckeckpoint file.
Part of the error output:
HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 3:
#000: H5Ddeprec.c line 187 in H5Dopen1(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 251 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
flash4: io_h5_attribute.c:49: io_h5_attribute_create: Assertion `dsetID >= 
0' failed.
Program received signal SIGABRT: Process abort signal.
 
A similar situation I observed with the more complex example LaserSlab:
 
HDF5-DIAG: Error detected in HDF5 (1.10.1) MPI-process 4:
#000: H5Dio.c line 269 in H5Dwrite(): can't prepare for writing data
major: Dataset
minor: Write failed
#001: H5Dio.c line 345 in H5D__pre_write(): can't write data
major: Dataset
minor: Write failed
#002: H5Dio.c line 791 in H5D__write(): can't write data
major: Dataset
minor: Write failed
#003: H5Dmpio.c line 527 in H5D__contig_collective_write(): couldn't finish 
shared collective MPI-IO
major: Low-level I/O
minor: Write failed
#004: H5Dmpio.c line 1398 in H5D__inter_collective_io(): couldn't finish 
collective MPI-IO
major: Low-level I/O
minor: Can't get value
#005: H5Dmpio.c line 1442 in H5D__final_collective_io(): optimized write 
failed
major: Dataset
minor: Write failed
#006: H5Dmpio.c line 295 in H5D__mpio_select_write(): can't finish 
collective parallel write
major: Low-level I/O
minor: Write failed
#007: H5Fio.c line 195 in H5F_block_write(): write through page buffer 
failed
major: Low-level I/O
minor: Write failed
#008: H5PB.c line 1041 in H5PB_write(): write through metadata accumulator 
failed
major: Page Buffering
minor: Write failed
#009: H5Faccum.c line 834 in H5F__accum_write(): file write failed
major: Low-level I/O
minor: Write failed
#010: H5FDint.c line 308 in H5FD_write(): driver write request failed
major: Virtual File Layer
minor: Write failed
#011: H5FDmpio.c line 1864 in H5FD_mpio_write(): file write failed
major: Low-level I/O
minor: Write failed
flash4: io_h5_xfer_mesh_dataset.c:210: io_h5_xfer_mesh_dataset: Assertion 
`err >= 0' failed.
Program received signal SIGABRT: Process abort signal.
 
How can I overcome these problems?
Thanks in advancce,
Theo

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