takluyver
commented
4 years ago It looks like your indexamajig is using an older version of HDF5 (it says Error detected in HDF5 (1.8.12)). You need to build it with HDF5 1.10 or above to read the virtual datasets.
If you've compiled indexamajig yourself, hopefully you can work out how to build it with a newer HDF5. If you're using a version someone has provided on Maxwell, you could either ask them to ensure it's built with a newer HDF5, or switch to the version we provide, which is available with:
module load exfel exfel_crystfel/0.8.0 
Calpas
Dear experts, I run (1) but I when I run (2), I got this error message (3). I already run on these files successfully 2 months ago. Do you see why it can't open the file? Regards
(1) /gpfs/exfel/sw/software/hdf5-virtualise/make_cxi.py /gpfs/exfel/d/proc/SPB/201801/p002120/r0096 -o r96.cxi # OK
/gpfs/exfel/sw/software/hdf5-virtualise/access_check.py r96.cxi # OK
(2) indexamajig -i r96.lst -o r96.stream -j 15 -g agipd_vds_2120_v2_120mm.geom ...
(3) ... Indexing parameters: Check unit cell parameters: on (axis combinations) Check peak alignment: on Refine indexing solutions: on Multi-lattice indexing ("delete and retry"): off Retry indexing: on HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
000: ../../src/H5F.c line 1585 in H5Fopen(): unable to open file
001: ../../src/H5F.c line 1376 in H5F_open(): unable to read superblock
002: ../../src/H5Fsuper.c line 353 in H5F_super_read(): unable to load superblock
003: ../../src/H5AC.c line 1329 in H5AC_protect(): H5C_protect() failed.
004: ../../src/H5C.c line 3574 in H5C_protect(): can't load entry
005: ../../src/H5C.c line 7954 in H5C_load_entry(): unable to load entry
006: ../../src/H5Fsuper_cache.c line 169 in H5F_sblock_load(): bad superblock version number
Couldn't open file: r96.cxi Failed to open r96.cxi