conference command: TimeoutError: [Errno 60] Operation timed out

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202007121748 (2020-07-12 17:48:02 UTC)
Description
conference command gives traceback.

Also it did not show an error dialog making it unlikely that someone would report this as a bug.

Log:
UCSF ChimeraX version: 1.1.dev202007121748 (2020-07-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/presentations/remdesivir-ar-may2020/data/rdv.pdb
> format pdb

> conference start cxconference.rbvi.ucsf.edu:443/remdesivir

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 263, in execute  
cmd.run(cmd_text)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/meeting/conference.py", line 98, in conference  
conference.connect(action, location, name, **kw)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/meeting/conference.py", line 249, in connect  
self._mux_node.start(callback=self._setup_cb)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/meeting/mux.py", line 431, in start  
self.setup_connection(make_node_socket(self._hostname, self._port))  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/meeting/mux.py", line 89, in make_node_socket  
s = get_ctx_node().wrap_socket(s, server_hostname=hostname)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 423, in wrap_socket  
session=session  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 870, in _create  
self.do_handshake()  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 1139, in do_handshake  
self._sslobj.do_handshake()  
TimeoutError: [Errno 60] Operation timed out  
  
TimeoutError: [Errno 60] Operation timed out  
  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 1139, in do_handshake  
self._sslobj.do_handshake()  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 240, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata  
h.request('POST', url, body=body, headers=headers)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 938, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 707, in create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File "/Users/goddard/Desktop/ChimeraX July 13
2020.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 752, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 9 days 10:02

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9

[goddard@…]

Actually the conference error did show an error dialog.  Also the log shows a traceback from trying to report the bug with no internet connection.  That can be ignored.   That was not the problem with the conference command.  Have reproduced the same conference command error.

[Tom Goddard]

Same timeout error running conference from a machine on the UCSF network (descartes.cgl.ucsf.edu). Original report was trying it from home (not on VPN).

[Tom Goddard]

After using "conference host" on descartes.cgl.ucsf.edu and then trying to connect to it from home I get a connect failure. The originally reported failure gets to ssl handshake suggesting it does get through any firewall and tries to connect.

conference start descartes.cgl.ucsf.edu:50762/remdesivir
Traceback (most recent call last):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 263, in execute

cmd.run(cmd_text)

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2805, in run

result = ci.function(session, kw_args)

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/meeting/conference.py", line 98, in conference

conference.connect(action, location, name, kw)

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/meeting/conference.py", line 249, in connect

self._mux_node.start(callback=self._setup_cb)

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/meeting/mux.py", line 431, in start

self.setup_connection(make_node_socket(self._hostname, self._port))

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/meeting/mux.py", line 87, in make_node_socket

s = socket.create_connection((hostname, port))

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 728, in create_connection

raise err

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 716, in create_connection

sock.connect(sa)

TimeoutError: [Errno 60] Operation timed out

TimeoutError: [Errno 60] Operation timed out

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)

See log for complete Python traceback.

[Tom Goddard]

Scooter reports the hub server (on crick) is getting connection requests but the log shows the same handshake failures.

Begin forwarded message:

From: Scooter Morris
Subject: Re: ChimeraX conference server not working
Date: July 14, 2020 at 9:58:22 AM PDT
To: Tom Goddard

It's certainly running, but I'm seeing lots of errors in the log:

INFO:root:hub connection:: from ('192.35.168.96', 28558)
INFO:root:run terminated: None/None
INFO:root:hub connection:: from ('83.97.20.31', 40696)
INFO:root:run terminated: None/None
ERROR:root:hub accept() failed
Traceback (most recent call last):

File "/usr/local/bin/cxconference", line 674, in run

ns, addr = self._socket.accept()

File "/usr/lib64/python3.6/ssl.py", line 1081, in accept

server_side=True)

File "/usr/lib64/python3.6/ssl.py", line 365, in wrap_socket

_context=self, _session=session)

File "/usr/lib64/python3.6/ssl.py", line 773, in init

self.do_handshake()

File "/usr/lib64/python3.6/ssl.py", line 1033, in do_handshake

self._sslobj.do_handshake()

File "/usr/lib64/python3.6/ssl.py", line 645, in do_handshake

self._sslobj.do_handshake()

ssl.SSLError: [SSL: HTTP_REQUEST] http request (_ssl.c:877)
ERROR:root:hub accept() failed
Traceback (most recent call last):

File "/usr/local/bin/cxconference", line 674, in run

ns, addr = self._socket.accept()

File "/usr/lib64/python3.6/ssl.py", line 1081, in accept

server_side=True)

File "/usr/lib64/python3.6/ssl.py", line 365, in wrap_socket

_context=self, _session=session)

File "/usr/lib64/python3.6/ssl.py", line 773, in init

self.do_handshake()

File "/usr/lib64/python3.6/ssl.py", line 1033, in do_handshake

self._sslobj.do_handshake()

File "/usr/lib64/python3.6/ssl.py", line 645, in do_handshake

self._sslobj.do_handshake()

ssl.SSLEOFError: EOF occurred in violation of protocol (_ssl.c:877)

Unfortunately, I don't know anything about the cxconference stuff, but it does look like you are at least connecting, which means that it isn't a firewall issue. Doesn't help much, but at least it rules out some possibilities.

-- scooter

[Tom Goddard]

More info from Scooter:

If you do a "sudo pcs status" you'll see that cxconference is running on crick, but the code is in /usr/local/bin.

[Tom Goddard]

Starting a conference using the descartes hub works if I am on the RBVI VPN from home. If I start the conference from one ChimeraX at home then join it from another ChimeraX from home it copies the session. Pointer synchronization does not work. The joining ChimeraX shows its own pointer, but the starting one never shows any pointer.

[Tom Goddard]

Tested starting conference on cxconference.rbvi.ucsf.edu from Windows -- fails in the same way as Mac, as expected.

[Tom Goddard]

Simpler testing setup is to start hub (conference host) on a machine at home on my local network and connect to it with same or other machines on my local network. Tried this with Mac laptop as hub, starting session on windows desktop and joining on windows laptop. Session sync worked and command sync (surface command) worked, but pointer synchronization did not work. No VR was used.

In previous tests months ago at UCSF VR conference did not work. Possibly the issue that causes pointer sync not to work is also the cause of VR conferences not working.