IOR HDF5 backend no longer works

[shanedsnyder]

Building against current main, a very simple IOR command using the HDF5 backend bombs:

shane@shane-x1-carbon ~/software/ior/build (main) $ ./src/ior -a HDF5
IOR-4.1.0+dev: MPI Coordinated Test of Parallel I/O
Began               : Tue Feb 28 14:31:54 2023
Command line        : ./src/ior -a HDF5
Machine             : Linux shane-x1-carbon
TestID              : 0
StartTime           : Tue Feb 28 14:31:54 2023https://github.com/hpc/ior/issues
Path                : testFile
FS                  : 218.2 GiB   Used FS: 51.1%   Inodes: 13.9 Mi   Used Inodes: 6.5%

Options: 
api                 : HDF5
apiVersion          : 1.12.0 (Parallel)
test filename       : testFile
access              : single-shared-file
type                : independent
segments            : 1
ordering in a file  : sequential
ordering inter file : no tasks offsets
nodes               : 1
tasks               : 1
clients per node    : 1
memoryBuffer        : CPU
dataAccess          : CPU
GPUDirect           : 0
repetitions         : 1
xfersize            : 262144 bytes
blocksize           : 1 MiB
aggregate filesize  : 1 MiB

Results: 

access    bw(MiB/s)  IOPS       Latency(s)  block(KiB) xfer(KiB)  open(s)    wr/rd(s)   close(s)   total(s)   iter
------    ---------  ----       ----------  ---------- ---------  --------   --------   --------   --------   ----
write     73.26      671.46     0.001489    1024.00    256.00     0.006890   0.005957   0.000803   0.013650   0   
read      206.91     3850       0.000260    1024.00    256.00     0.003502   0.001039   0.000292   0.004833   0   
HDF5-DIAG: Error detected in HDF5 (1.12.0) MPI-process 0:
  #000: ../../src/H5F.c line 941 in H5Fdelete(): unable to delete the file
    major: File accessibility
    minor: Unable to delete file
  #001: ../../src/H5VLcallback.c line 3755 in H5VL_file_specific(): file specific failed
    major: Virtual Object Layer
    minor: Can't operate on object
  #002: ../../src/H5VLcallback.c line 3684 in H5VL__file_specific(): file specific failed
    major: Virtual Object Layer
    minor: Can't operate on object
  #003: ../../src/H5VLnative_file.c line 408 in H5VL__native_file_specific(): H5Fdelete() is currently not supported in the native VOL connector
    major: File accessibility
    minor: Feature is unsupported
** error **
ERROR in ../../src/aiori-HDF5.c (line 533): cannot delete file.
** exiting **

Just looking at commit history, maybe this is related to recent work to make HDF5 backend work with VOLs (#441)?

[JulianKunkel]

Mhh, I see in the AIORI code, various checks for HAVE_H5PGET_VOL_ID that cause for instance this output. However:

I downloaded the latest version 1.14 from the webpage, then compiled HDF5 with:
$ configure --prefix=./install --enable-parallel --enable-direct-vfd --enable-mirror-vfd

Configure IOR:
$ configure --with-aio --with-hdf5 --with-ncmpi LDFLAGS=-L./install/lib/ CFLAGS=-I./install/include

ldd showed that it was correctly linked to libhdf5.so.310

api                 : HDF5
apiVersion          : 1.14.0 (Parallel)
test filename       : testFile
access              : single-shared-file
type                : independent
segments            : 1
ordering in a file  : sequential
ordering inter file : no tasks offsets
nodes               : 1
tasks               : 1
clients per node    : 1
repetitions         : 1
xfersize            : 262144 bytes
blocksize           : 1 MiB
aggregate filesize  : 1 MiB

Results: 

access    bw(MiB/s)  IOPS       Latency(s)  block(KiB) xfer(KiB)  open(s)    wr/rd(s)   close(s)   total(s)   iter
------    ---------  ----       ----------  ---------- ---------  --------   --------   --------   --------   ----
write     339.10     2437.49    0.000410    1024.00    256.00     0.000973   0.001641   0.000335   0.002949   0   
read      968.21     13563      0.000074    1024.00    256.00     0.000643   0.000295   0.000095   0.001033   0   

Can you give some details what exactly you did?

Maybe you can try with 1.14 as well?

[shanedsnyder]

I did try with 1.14.0 and confirmed things work fine.

If you try to build against older HDF5 versions (I tried 1.12.0), you get the errors I mention initially. So, appears HDF5 backend is somehow tied to newer HDF5 (VOL) APIs?

[JulianKunkel]

It worked for me with a 1.10.0 as well.
Maybe one revision of 1.12. doesn't work. I would tend to close this issue here.

[carns]

I think that 1.12 is still fairly common in the wild. It would be safer to either fix it or have it fail at configure time if it's really not compatible.