Dear all,
I am encountering an issue with HDF5/XDMF output using
DataOut::write_hdf5_parallel() on large meshes. Up to a resolution of
256×256×256, everything works correctly, but at *512×512×512* the program
aborts with the following HDF5 error:
```
#014 HDF5-DIAG: Error ... unable to set chunk sizes
major: Dataset
minor: Bad value
#015 HDF5-DIAG: ... chunk size must be < 4GB
```
I have attached the error log as well.
>From inspecting the source in data_out_base.cc, HDF5 uses chunked layout,
with chunk dimensions set internally in deal.II. At 512³, the computed
chunk size exceeds the HDF5 hard limit of 4 GB per chunk, which leads to
the failure.
Is there a recommended way for users to avoid this error when writing large
output files?
I would really appreciate any suggestions.
Thank you.
Best Regards,
JRK
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HDF5-DIAG: Error detected in HDF5 (1.14.5) MPI-process 0:
#000:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5D.c
line 186 in H5Dcreate2(): unable to synchronously create dataset
major: Dataset
minor: Unable to create file
#001:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5D.c
line 135 in H5D__create_api_common(): unable to create dataset
major: Dataset
minor: Unable to create file
#002:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5VLcallback.c
line 1865 in H5VL_dataset_create(): dataset create failed
major: Virtual Object Layer
minor: Unable to create file
#003:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5VLcallback.c
line 1830 in H5VL__dataset_create(): dataset create failed
major: Virtual Object Layer
minor: Unable to create file
#004:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5VLnative_dataset.c
line 282 in H5VL__native_dataset_create(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#005:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Dint.c
line 351 in H5D__create_named(): unable to create and link to dataset
major: Dataset
minor: Unable to initialize object
#006:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Lint.c
line 492 in H5L_link_object(): unable to create new link to object
major: Links
minor: Unable to initialize object
#007:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Lint.c
line 732 in H5L__create_real(): can't insert link
major: Links
minor: Unable to insert object
#008:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Gtraverse.c
line 824 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#009:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Gtraverse.c
line 596 in H5G__traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#010:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Lint.c
line 537 in H5L__link_cb(): unable to create object
major: Links
minor: Unable to initialize object
#011:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Oint.c
line 2346 in H5O_obj_create(): unable to open object
major: Object header
minor: Can't open object
#012:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Doh.c
line 273 in H5O__dset_create(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#013:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Dint.c
line 1304 in H5D__create(): unable to construct layout information
major: Dataset
minor: Unable to initialize object
#014:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Dchunk.c
line 835 in H5D__chunk_construct(): unable to set chunk sizes
major: Dataset
minor: Bad value
#015:
/tmp/root/spack-stage/spack-stage-hdf5-1.14.5-26nmxvbzekiovzoy56uibsnolivaxi3e/spack-src/src/H5Dchunk.c
line 798 in H5D__chunk_set_sizes(): chunk size must be < 4GB
major: Dataset
minor: Unable to initialize object
----------------------------------------------------
Exception on processing:
--------------------------------------------------------
An error occurred in line <8330> of file
</tmp/root/spack-stage/spack-stage-dealii-9.6.2-pz5z6ke2736dynce3mxjd6346tifhuyk/spack-src/source/base/data_out_base.cc>
in function
void dealii::{anonymous}::do_write_hdf5(const
std::vector<dealii::DataOutBase::Patch<dim, spacedim> >&, const
dealii::DataOutBase::DataOutFilter&, const dealii::DataOutBase::Hdf5Flags&,
bool, const string&, const string&, MPI_Comm) [with int dim = 3; int spacedim =
3; std::string = std::__cxx11::basic_string<char>; MPI_Comm =
ompi_communicator_t*]
The violated condition was:
cell_dataset >= 0
Additional information:
An input/output error has occurred. There are a number of reasons why
this may be happening, both for reading and writing operations.
If this happens during an operation that tries to read data: First,
you may be trying to read from a file that doesn't exist or that is
not readable given its file permissions. Second, deal.II uses this
error at times if it tries to read information from a file but where
the information in the file does not correspond to the expected
format. An example would be a truncated file, or a mesh file that
contains not only sections that describe the vertices and cells, but
also sections for additional data that deal.II does not understand.
If this happens during an operation that tries to write data: you may
be trying to write to a file to which file or directory permissions do
not allow you to write. A typical example is where you specify an
output file in a directory that does not exist.
Stacktrace:
-----------
#0
/apps/spack/opt/spack/linux-rocky8-zen2/gcc-11.2.0/dealii-9.6.2-pz5z6ke2736dynce3mxjd6346tifhuyk/lib/libdeal_II.so.9.6.2:
#1
/apps/spack/opt/spack/linux-rocky8-zen2/gcc-11.2.0/dealii-9.6.2-pz5z6ke2736dynce3mxjd6346tifhuyk/lib/libdeal_II.so.9.6.2:
void dealii::DataOutBase::write_hdf5_parallel<3,
3>(std::vector<dealii::DataOutBase::Patch<3, 3>,
std::allocator<dealii::DataOutBase::Patch<3, 3> > > const&,
dealii::DataOutBase::DataOutFilter const&, dealii::DataOutBase::Hdf5Flags
const&, bool, std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, ompi_communicator_t*)
#2
/apps/spack/opt/spack/linux-rocky8-zen2/gcc-11.2.0/dealii-9.6.2-pz5z6ke2736dynce3mxjd6346tifhuyk/lib/libdeal_II.so.9.6.2:
dealii::DataOutInterface<3,
3>::write_hdf5_parallel(dealii::DataOutBase::DataOutFilter const&, bool,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&, std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, ompi_communicator_t*) const
#3 ./build/main: CGSEM<3>::output_results_xdmf()
#4 ./build/main: CGSEM<3>::output_results()
#5 ./build/main: CGSEM<3>::run()
#6 ./build/main: main
--------------------------------------------------------
Aborting!
----------------------------------------------------
