Hi Andrew, Since it’s going to be hard to replicate this, could you provide more information by attaching a debugger and show the trace of where the hang is?
Thanks, Mohamad From: Hdf-forum <[email protected]> on behalf of Andrew Ho <[email protected]> Reply-To: hdf-forum <[email protected]> Date: Friday, June 10, 2016 at 10:06 PM To: hdf-forum <[email protected]> Subject: [Hdf-forum] Parallel HDF5 file locking error I'm having some issues with file locking on a parallel filesystem which I believe is related the problem here: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2011-February/004254.html I tried the suggestion of disabling romio_ds_read and romio_ds_write, but this doesn't fix the problem. I've also tried setting H5Pset_seive_buf_size to 0 to disable data striding in HDF5 itself, but that doesn't work, either. Here's a short snippet of the relevant code: hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS); MPI_Info info; MPI_Info_create(&info); MPI_Info_set(info, "romio_ds_read", "disable"); MPI_Info_set(info, "romio_ds_write", "disable"); H5Pset_sieve_buf_size(fapl_id, 0); H5Pset_fapl_mpio(fapl_id, comm, info); hid_t f_id = H5Fcreate("test_file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); It's on this last line that the program hangs, and eventually MPI_ABORT gets called. Note that I get the same problem regardless of if I try to create a new file, or if I try to open an existing file: hid_t f_id = H5Fopen("test_file.h5", H5F_ACC_RDWR, fapl_id); Other relevant information: 1. Filesystem is NFS v3 with noac off (can't change) 2. Tested with HDF 5.8.13 and 5.8.14 3. Tested with OpenMPI 1.6.5 and 1.10.2 What am I missing? I saw that there's an option to disable filesystem atomicity, but this requires that the file already be opened, and I can't even get that far. I also know that my code does work on different computers with different filesystems and/or mount options.
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