Opened 5 years ago

Closed 5 years ago

#3563 closed defect (fixed)

Timeout launching Modeller job

Reported by: tonyelin@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Web Services Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I input 5 structures into my work file. After revealing their sequence alignment, I initiated the modeller comparative function. 

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Some installed bundles are out of date. Please update the following bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/CMGC_DYRK1A_5A4E_T.pdb"

CMGC_DYRK1A_5A4E_T.pdb title:  
DYRK1A In complex with methoxy benzothiazole fragment [more info...]  
  
Chain information for CMGC_DYRK1A_5A4E_T.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in CMGC_DYRK1A_5A4E_T.pdb #1  
---  
7QQ — (7QQ)  
PTR — (PTR)  
  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/CMGC_MAPK14_3K3I_T.pdb"

CMGC_MAPK14_3K3I_T.pdb title:  
P38Α bound to novel DGF-out compound PF-00215955 [more info...]  
  
Chain information for CMGC_MAPK14_3K3I_T.pdb #2  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in CMGC_MAPK14_3K3I_T.pdb #2  
---  
I46 — (I46)  
JZJ — (JZJ)  
  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/CMGC_MAPK14_4EHV_T.pdb"

CMGC_MAPK14_4EHV_T.pdb title:  
Human P38 map kinase In complex with Np-F10 and RL87 [more info...]  
  
Chain information for CMGC_MAPK14_4EHV_T.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in CMGC_MAPK14_4EHV_T.pdb #3  
---  
0SJ — (0SJ)  
IRG — (IRG)  
  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/CMGC_MAPK14_5N67_T.pdb"

CMGC_MAPK14_5N67_T.pdb title:  
Crystal structure of P38Α In complex with lipid pocket ligand 9L [more
info...]  
  
Chain information for CMGC_MAPK14_5N67_T.pdb #4  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in CMGC_MAPK14_5N67_T.pdb #4  
---  
8ON — (8ON)  
  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/CMGC_MAPK14_5O8U_T.pdb"

CMGC_MAPK14_5O8U_T.pdb title:  
Covalent inhibitor 4B bound to the lipid pocket of P38Α mutant S252C [more
info...]  
  
Chain information for CMGC_MAPK14_5O8U_T.pdb #5  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in CMGC_MAPK14_5O8U_T.pdb #5  
---  
9O5 — (9O5)  
  

> open "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Templates/3K3I_Ligand.sdf"

> save "/Users/tonylin/TMU/DYRK1A/Allosteric DYRK1A/Modeling
> Structures/Chimera/Modeling_ChimeraX.cxs"

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #2/A

Alignment identifier is 2.A  

> sequence chain #3/A

Alignment identifier is 3.A  

> sequence chain #4/A

Alignment identifier is 4.A  

> sequence chain #5/A

Alignment identifier is 5.A  

> ui tool show "Modeller Comparative"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #2/A

Alignment identifier is 2.A  

> ui tool show "Modeller Comparative"

> modeller comparative 1.A:1 multichain true numModels 5 fast false
> hetPreserve true hydrogens true waterPreserve false

> view clip false

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 728, in create_connection  
raise err  
File
"/Applications/ChimeraX-1.0.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  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 115, in __init__  
self.wsdl = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 150, in open  
d = self.fn(url, self.options)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/wsdl.py", line 136, in __init__  
d = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 74, in open  
d = self.download(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 92, in download  
fp = self.options.transport.open(Request(url))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 62, in open  
return HttpTransport.open(self, request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 67, in open  
return self.u2open(u2request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1347, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 60] Operation timed out>  
  
Exception in thread 1:  
urllib.error.URLError:  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 604, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 409, in on_finish  
err = self.get_file("stderr.txt")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> delete atoms #6

> delete bonds #6

> show #!1 models

> show #!2 models

> ui tool show "Show Sequence Viewer"

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1.A  

> sequence chain #2/A

Alignment identifier is 2.A  

> ui tool show "Modeller Comparative"

> modeller comparative 1.A:1,2.A:1 multichain true numModels 5 fast false
> hetPreserve true hydrogens true waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 728, in create_connection  
raise err  
File
"/Applications/ChimeraX-1.0.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  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 115, in __init__  
self.wsdl = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 150, in open  
d = self.fn(url, self.options)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/wsdl.py", line 136, in __init__  
d = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 74, in open  
d = self.download(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 92, in download  
fp = self.options.transport.open(Request(url))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 62, in open  
return HttpTransport.open(self, request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 67, in open  
return self.u2open(u2request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1347, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 60] Operation timed out>  
  
Exception in thread 2:  
urllib.error.URLError:  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 604, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 409, in on_finish  
err = self.get_file("stderr.txt")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> ui tool show "Modeller Comparative"

> modeller comparative 1.A:1,2.A:1 multichain true numModels 5 fast false
> hetPreserve true hydrogens true waterPreserve false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Applications/ChimeraX-1.0.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
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 728, in create_connection  
raise err  
File
"/Applications/ChimeraX-1.0.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  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/tasks.py", line 283, in run  
self.launch(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/client.py", line 115, in __init__  
self.wsdl = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 150, in open  
d = self.fn(url, self.options)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/wsdl.py", line 136, in __init__  
d = reader.open(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 74, in open  
d = self.download(url)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/reader.py", line 92, in download  
fp = self.options.transport.open(Request(url))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/https.py", line 62, in open  
return HttpTransport.open(self, request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 67, in open  
return self.u2open(u2request)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/suds/transport/http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1347, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [Errno 60] Operation timed out>  
  
Exception in thread 3:  
urllib.error.URLError:  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Modeller job ID None finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 604, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/modeller/comparative.py", line 409, in on_finish  
err = self.get_file("stderr.txt")  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,1
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 162.0.0.0.0
      SMC Version (system): 2.16f68

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G73)
      Kernel Version: Darwin 19.6.0
      Time since boot: 3 days 7:42

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        BenQ EW2755ZH:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: A7H00623SL0 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (5)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Web Services
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Timeout launching Modeller job

comment:2 by Eric Pettersen, 5 years ago

Status: accepted → feedback

Hi Tony,

In a web browser, can you reach ​http://webservices.rbvi.ucsf.edu/opal2/ or does it hang/time out? If it hangs, you need to have your sys admin fix your network settings so that you can reach that site. If it doesn't hang, does your Modeller job still hang? If it does, do you use an HTTP proxy to reach web sites? If so, you need to go to the Web Access section of ChimeraX's preferences and fill in your web proxy info (and click Save).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 5 years ago

Hi Tony,

This is a problem with our web services -- they are currently unreachable from outside UCSF. I was fooled into thinking it was a problem with your machine because I checked from within UCSF and it worked fine. I will let you know when we get things working again.

--Eric

in reply to:  4 ; comment:4 by tonyelin@…, 5 years ago 

I understand. Thank you for the update.

On Sat, Aug 1, 2020 at 12:09 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:5 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: feedback → closed

The web services are up now.

--Eric

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