File locking when using hdf5, collective mode

[cbartz]

Hello,
when i am using the hdf5 api, collective mode, the underlying system
tries to do file locking (ADIOI_Set_lock).
After doing some investigation, I think I have found the reason:

In aiori-HDF5.c, the line 295

memDataSpaceDims[0] = (hsize_t) param->transferSize;

invokes strided io in the romio ADIO layer (ad_write_str). The line should be

memDataSpaceDims[0] = (hsize_t) param->transferSize / sizeof(IOR_size_t);

After changing this line of code, the configuration works without file locking.

[roblatham00]

I'm happy you are looking at the HDF5 driver. It doesn't get a lot of (any?) attention.

How are you observing that ADIOI_Set_lock is getting called?

[cbartz]

My program crashed and I got the following error output:

"File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type
F_WRLCK/1,whence 0) with return value FFFFFFFF and errno 26.

• If the file system is NFS, you need to use NFS version 3, ensure that
  the lockd daemon is running on all the machines, and mount the directory
  with the 'noac' option (no attribute caching).
• If the file system is LUSTRE, ensure that the directory is mounted with
  the 'flock' option.

ADIOI_Set_lock:: Function not implemented"