unable to open file "h3_cells_id_res0-4.h5"

[cq-eng]

Hello, when I ran python3 StarPerf.py, I encountered the following error:

Traceback (most recent call last):
  File "/home/chenqing/StarPerf_Simulator-release-v2.0/StarPerf.py", line 74, in <module>
    standalone_module_test_cases.standalone_module_test_cases()
  File "/home/chenqing/StarPerf_Simulator-release-v2.0/samples/standalone_module/standalone_module_test_cases.py", line 37, in standalone_module_test_cases
    satellite_redundancy.satellite_redundancy(1, "OneWeb", 1000,
  File "/home/chenqing/StarPerf_Simulator-release-v2.0/src/standalone_module/satellite_redundancy.py", line 115, in satellite_redundancy
    with h5py.File('data/h3_cells_id_res0-4.h5', 'r') as file:
  File "/usr/local/lib/python3.10/dist-packages/h5py/_hl/files.py", line 564, in __init__
    fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
  File "/usr/local/lib/python3.10/dist-packages/h5py/_hl/files.py", line 238, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 56, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 57, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 102, in h5py.h5f.open
OSError: Unable to synchronously open file (file signature not found)

The error suggests that the file h3_cells_id_res0-4.h5 is corrupted (not missing), as the signature cannot be read. Could you please verify the integrity of this file or provide a valid version?

Thanks for your help!

[root-hbx]

Hi @cq-eng

I conducted tests on my device and did not encounter this issue. Everything works well, and the H5 file opens correctly.

Here are some approaches for trouble shooting :))

Check the integrity of this .h5 file

(1) File Integrity Check

Inspect the beginning of the file to check for corruption:

```bash
❯ hexdump -C ./data/h3_cells_id_res0-4.h5 | head -5
00000000  89 48 44 46 0d 0a 1a 0a  00 00 00 00 00 08 08 00  |.HDF............|
00000010  04 00 10 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000020  ff ff ff ff ff ff ff ff  20 b0 f6 00 00 00 00 00  |........ .......|
00000030  ff ff ff ff ff ff ff ff  00 00 00 00 00 00 00 00  |................|
00000040  60 00 00 00 00 00 00 00  01 00 00 00 00 00 00 00  |`...............|
```

(2) Visual Inspection

Perform a visual inspection using HDFView.

Attached with my results:

Take a deeper look

(1) Ensure u have permissions:

ls -la ./data/h3_cells_id_res0-4.h5
chmod 644 ./data/h3_cells_id_res0-4.h5

(2) Ensure u have a correct h5py version:

❯ python3 -c "import h5py; print('h5py version:', h5py.version.version); print('HDF5 version:', h5py.version.hdf5_version)"
h5py version: 3.10.0
HDF5 version: 1.12.2

[pamystri]

Hi

I am facing the same error, @root-hbx which linux OS version are you running?
thanks

[root-hbx]

Hi @pamystri

In fact, this issue is not related to the system version. The real problem lies in the fact that your current h3_cells_id_res0-4.h5 file is tracked by Git LFS.

As such, what you have is essentially a pointer rather than the actual file.

To be more specific, I believe your h3_cells_id_res0-4.h5 now looks like this:

(starperf) server@server-PowerEdge-R750:~/bxhu/StarPerf-Sim$ ls -la data/h3_cells_id_res0-4.h5 
-rw-rw-r-- 1 starlink starlink 133 jun  8 11:16 data/h3_cells_id_res0-4.h5

!!! Problem here !!!

Only 133 (file size), it's a pointer, not the file itself. The actual file is stored on GitLFS !!!

Hence, you need to fetch the file using Git LFS, after which the program should run properly.

TL; DR

For a newly initialized repository, the recommended steps are as follows:

0. git clone:

git clone https://github.com/SpaceNetLab/StarPerf_Simulator.git

1. Fetch the specific file using Git LFS:

sudo apt update && sudo apt install git-lfs
git lfs install
git lfs pull

After this, the h3_cells_id_res0-4.h5 file should look like:

(starperf) server@server-PowerEdge-R750:~/bxhu/StarPerf-Sim$ ls -la data/h3_cells_id_res0-4.h5
-rw-rw-r-- 1 server server 16166944 Jul 11 22:10 data/h3_cells_id_res0-4.h5

Now the size is 16166944 ✅

2. Execute the global initialization script:

(starperf) server@server-PowerEdge-R750:~/bxhu/StarPerf-Sim$ python StarPerf.py

Now it's ready to go :))

[root-hbx]

Besides, given that this project is currently under highly-intensive development, there is a potential nit in the current version that is worth noting:

Current StartPerf.py:

if __name__ == '__main__':
    import samples.standalone_module.standalone_module_test_cases as standalone_module_test_cases

    standalone_module_test_cases.standalone_module_test_cases()

LTS Version

if __name__ == '__main__':
    main()

CC' @yunanhou2023