trixi-framework / trixi-framework/Trixi.jl

HDF5 issue with parallel execution on clusters

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Dominant language
Julia
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Description

Hello,

I am trying to run Mach3 step test problem on a cluster using MPI. The program raises an error related to HDF5 when the mesh file or solution file is being written in the "out" folder. Sometime when I change the number of cores the simulation runs and solution files are written just fine but after some time into the simulation the HDF5 error will be raised again. Here is a sample of the error that I get:

ERROR: ERROR: LoadError: LoadError: HDF5.API.H5Error: Error getting attribute name
libhdf5 Stacktrace:
[1] H5Aget_name: Invalid arguments to routine/Inappropriate type
not an attribute
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/HDF5/wWr4z/src/api/HDF5.API.H5Error: Error getting attribute name
libhdf5 Stacktrace:error.jl:18 [inlined]
[2]
[1] h5a_get_name(H5Aget_name: Invalid arguments to routine/Inappropriate typeattr_id::
not an attribute

The operating system on the cluster is Red Hat. I am using openmpi_4.0.0_gcc version and the file system is GPFS.

Contributor guide

Open the contributing guide

Research direction

Start by reproducing the Mach3 step test with MPI on a cluster using the reported OpenMPI, GPFS, and Red Hat environment. Inspect the HDF5 writes for mesh and solution files in the out folder while varying core counts. Done means the simulation writes these files reliably without the H5Aget_name error during execution.

Written by the indexing model from the issue text.

Assessment

Tech stack
julia
Domain
distributed-systems
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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