hdf5_bug
Minimal example that shows a bug in the HDF5 library in Cori's burst buffer
Compiling
Just type make
. The Makefile
is configured to use the latests hdf5-parallel/1.10.1
library on Cori.
Running
- Allocate an interactive queue for the
knl
partition:salloc --qos=interactive -t 01:00:00 -C knl,quad,cache -N 1 -S 4 --bbf=bbf.conf
You can use the providedbbf.conf
file. - Go to the BB directory and run the test, where
${HDF5_BUG_DIR}
is the folder where you compiled the code:Take note at the files that give errors, .e.g.:export HDF5_USE_FILE_LOCKING=FALSE cd $DW_JOB_STRIPED ${HDF5_BUG_DIR}/test_bug.py display hdf5_bug.pdf
cat output_10000000_1.log dset_size = 10000000 num_dsets = 1 Creating file output.h5 Creating dataset dset_0001 Opening file output.h5 HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0: #000: H5F.c line 586 in H5Fopen(): unable to open file major: File accessibilty minor: Unable to open file #001: H5Fint.c line 1384 in H5F_open(): unable to read superblock major: File accessibilty minor: Read failed #002: H5Fsuper.c line 530 in H5F__super_read(): truncated file: eof = 33554432, sblock->base_addr = 0, stored_eof = 40002048 major: File accessibilty minor: File has been truncated HDF5 error: -1 1
- Repeat the test in the scratch folder. There should be no errors.