I have the same Read timeout issue. My log file shows this:
2017-05-19 06:31:40,618:DEBUG:acme.client:Sending GET request to https://acme-v01.api.letsencrypt.org/directory.
2017-05-19 06:31:40,620:INFO:requests.packages.urllib3.connectionpool:Starting new HTTPS connection (1): acme-v01.api.letsencrypt.org
2017-05-19 06:32:25,700:WARNING:certbot.renewal:Attempting to renew cert from /etc/letsencrypt/renewal/donasec.cz.conf produced an unexpected error: HTTPSConnectionPool(host='acme-v01.api.letsencrypt.org', port=443): Read timed out. (read timeout=45). Skipping.
2017-05-19 06:32:25,701:DEBUG:certbot.renewal:Traceback was:
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/certbot/renewal.py", line 418, in handle_renewal_request
main.renew_cert(lineage_config, plugins, renewal_candidate)
File "/usr/lib/python2.7/site-packages/certbot/main.py", line 648, in renew_cert
le_client = _init_le_client(config, auth, installer)
File "/usr/lib/python2.7/site-packages/certbot/main.py", line 399, in _init_le_client
return client.Client(config, acc, authenticator, installer, acme=acme)
File "/usr/lib/python2.7/site-packages/certbot/client.py", line 202, in __init__
acme = acme_from_config_key(config, self.account.key)
File "/usr/lib/python2.7/site-packages/certbot/client.py", line 42, in acme_from_config_key
return acme_client.Client(config.server, key=key, net=net)
File "/usr/lib/python2.7/site-packages/acme/client.py", line 69, in __init__
self.net.get(directory).json())
File "/usr/lib/python2.7/site-packages/acme/client.py", line 658, in get
self._send_request('GET', url, **kwargs), content_type=content_type)
File "/usr/lib/python2.7/site-packages/acme/client.py", line 631, in _send_request
response = self.session.request(method, url, *args, **kwargs)
File "/usr/lib/python2.7/site-packages/requests/sessions.py", line 464, in request
resp = self.send(prep, **send_kwargs)
File "/usr/lib/python2.7/site-packages/requests/sessions.py", line 576, in send
r = adapter.send(request, **kwargs)
File "/usr/lib/python2.7/site-packages/requests/adapters.py", line 433, in send
raise ReadTimeout(e, request=request)
ReadTimeout: HTTPSConnectionPool(host='acme-v01.api.letsencrypt.org', port=443): Read timed out. (read timeout=45)
2017-05-19 06:32:25,701:DEBUG:certbot.main:Exiting abnormally:
Traceback (most recent call last):
File "/bin/certbot", line 9, in <module>
load_entry_point('certbot==0.12.0', 'console_scripts', 'certbot')()
File "/usr/lib/python2.7/site-packages/certbot/main.py", line 896, in main
return config.func(config, plugins)
File "/usr/lib/python2.7/site-packages/certbot/main.py", line 702, in renew
renewal.handle_renewal_request(config)
File "/usr/lib/python2.7/site-packages/certbot/renewal.py", line 435, in handle_renewal_request
len(renew_failures), len(parse_failures)))
Error: 1 renew failure(s), 0 parse failure(s)
I can telnet acme-v01.api.letsencrypt.org on 443