Getrandom runtime error

[j0hnn0]

I get:
RuntimeError: getrandom
with pod5. I've tried many versions, on many different python3 versions, still no success.
O/S CentOS Linux release 7.3.1611 3.10.0-514.el7.x86_64.
Updating O/S not an option. This is a whole cluster environment, with custom compiled kernel.

Any ideas please?

Tx!

[0x55555555]

Hi @j0hnn0 ,

What are you running when this occurs? Is there a call stack?

Thanks,

• George

[j0hnn0]

Hi I'm running pod5 merge: export POD5_DEBUG=1 pod5 merge *.pod5 merged.pod5 Traceback (most recent call last): File "/apps/python-3.11.3/bin/pod5", line 8, in <module> sys.exit(main()) ^^^^^^ File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/tools/main.py", line 56, in main return run_tool(parser) ^^^^^^^^^^^^^^^^ File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/tools/parsers.py", line 41, in run_tool raise exc File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/tools/parsers.py", line 38, in run_tool return tool_func(**kwargs) ^^^^^^^^^^^^^^^^^^^ File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/tools/parsers.py", line 409, in run return merge_pod5(**kwargs) ^^^^^^^^^^^^^^^^^^^^ File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/tools/pod5_merge.py", line 67, in merge_pod5 with p5.Writer(output.absolute()) as writer: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/apps/python-3.11.3/lib/python3.11/site-packages/pod5/writer.py", line 86, in __init__ self._writer: Optional[p5b.FileWriter] = p5b.create_file( ^^^^^^^^^^^^^^^^ RuntimeError: getrandom This error occurs with all versions of pod5, and all the python3 versions I tried. Regards Johann Swart Systems Administrator Centre for Bioinformatics and Computational Biology Faculty of Natural Sciences University of Pretoria ***@***.*** http://www.bi.up.ac.za Tel. +27-12-420-5824 Fax. +27-12-420-5800 Rm 3-5, FABI Square

…

On Fri, Jul 28, 2023 at 9:26 AM jorj1988 ***@***.***> wrote: Hi @j0hnn0 <https://github.com/j0hnn0> , What are you running when this occurs? Is there a call stack? Thanks, - George — Reply to this email directly, view it on GitHub <#63 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABH52NPFUHMXFEJPXZRBBSLXSNSRTANCNFSM6AAAAAA22WUW3I> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Johann W. Swart Phone: +2776 239 2920 Email: ***@***.***

[HalfPhoton]

Hi @j0hnn0 ,

I can see that you've tried multiple versions but we'll continue with only the most current version 0.2.4 going forward.

getrandom appears to have been added to GLIBC in version 2.25

Can you please report your GLIBC version?

Kind regards,
Rich

[j0hnn0]

Hi ldd --version ldd (GNU libc) 2.17 Regards Johann Swart Systems Administrator Centre for Bioinformatics and Computational Biology Faculty of Natural Sciences University of Pretoria ***@***.*** http://www.bi.up.ac.za Tel. +27-12-420-5824 Fax. +27-12-420-5800 Rm 3-5, FABI Square

…

On Fri, Jul 28, 2023 at 10:55 AM Richard Harris ***@***.***> wrote: Hi @j0hnn0 <https://github.com/j0hnn0> , I can see that you've tried multiple versions but we'll continue with only the most current version 0.2.4 going forward. getrandom appears to have been added in version <https://abi-laboratory.pro/?view=changelog&l=glibc&v=2.25> 2.25 Can you please report your GLIBC version? Kind regards, Rich — Reply to this email directly, view it on GitHub <#63 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABH52NNWPV5NPS66HJH2IVTXSN46XANCNFSM6AAAAAA22WUW3I> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Johann W. Swart Phone: +2776 239 2920 Email: ***@***.***

[HalfPhoton]

@j0hnn0 ,

Can you build the wheel and install locally? Here are the instructions.

These instructions should create a wheel in: build/c++/pod5_format_pybind/wheel_* which can be used to update the pod5 venv with:

(pod5) $ pip install -U build/c++/pod5_format_pybind/wheel_*/lib_pod5-*.whl

[HalfPhoton]

@j0hnn0 , was your issue resolved?

Best regards,
Rich