CERTIFICATE_VERIFY_FAILED

[weigua...@computeontario.ca]

Hi,

I am a user support at Compute Canada. Recently, I've helped a user compile Cactus after lots of trouble-shootings. Now I can run it on our login node which has network connection to the outsider. But our compute nodes don't have internet connection. As a result, Cactus failed to run on a compute node. The error message (I copy/past part of it) is

......

  File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/urllib2.py", line 1241, in https_open
    context=self._context)
  File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib/python2.7/urllib2.py", line 1198, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>

Can you tell me why it needs to verify certificate and what workaround can you suggest? Thanks.

Best,

Weigaung

[Joel Armstrong]

Hi Weiguang,

Do you have more of the error message? Unfortunately that part of the traceback only refers to Python standard library code. There are two things that I can immediately think of that would access the internet:

a) if Docker support is enabled (by default, a Docker image is downloaded containing our dependencies). If that's the case, you can disable this and use your locally compiled binaries by adding the --binariesMode local option.

b) if the input sequence file refers to HTTP(s) urls

I think what might be happening is the latter, that the example we suggest running ("evolverMammals.txt") downloads its sequences from the Internet. But those files can be downloaded beforehand and the config file modified to reflect that. That is, after downloading the listed files in evolverMammals.txt, edit the file to refer only to local paths, like this:

((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974):0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303):0.032898);

simCow_chr6 /local/path/to/simCow.chr6
simDog_chr6 /local/path/to/simDog.chr6
simHuman_chr6 /local/path/to/simHuman.chr6
simMouse_chr6 /local/path/to/simMouse.chr6
simRat_chr6 /local/path/to/simRat.chr6

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