I am running a small StarCluster and using it to run an IPython Notebook. Every time I have an error in the code I'm writing in the notebook, I get the following error message added onto the end of the notebook's output:
Traceback (most recent call last):
File "/usr/lib/python2.7/logging/__init__.py", line 872, in emit
stream.write(fs % msg)
IOError: [Errno 32] Broken pipe
Logged from file ipkernel.py, line 427
Other than that, it seems to be running OK, but I don't know why that might be happening / how I can find out more about why it's doing that
Related
I am a beginner to PyMOL and I am using it for my docking project. I have encountered errors using the Autodock/Vina plugin in PyMOL.
I was trying to carry out the set up for the grid and Error 1 occurred when I was clicking on the arrow that allows me to change the grid parameter x,y and z.
As for Error 2, it occurs when I tried to generate the receptor on the next page.
Under the log section, I also got a notice saying "Batch: prepare_receptor4.py -r C:\Users\User\Desktop\plugin-test\receptor.3ig7.pdb -o C:\Users\User\Desktop\plugin-test\receptor.3ig7.pdbqt -A checkhydrogen"
It would be appreciated if you would tell me what is missing or should be done to solve these errors.
I look forward to reading any of your replies and I thank you in advance,
Elayne
Error: 1
TypeError Exception in Tk callback
Function: <bound method Autodock.n_points_Y_changed of <pmg_tk.startup.autodock_plugin.Autodock object at 0x0000020649CD9388>> (type: <class 'method'>)
Args: ('scroll', '1', 'units')
Traceback (innermost last):
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\Pmw.py", line 1823, in __call__
return self.func(*args)
TypeError: n_points_Y_changed() takes 2 positional arguments but 4 were given
Error: 2
FileNotFoundError Exception in Tk callback
Function: <bound method Autodock.generate_receptor of <pmg_tk.startup.autodock_plugin.Autodock object at 0x0000020649CD9388>> (type: <class 'method'>)
Args: ()
Traceback (innermost last):
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\Pmw.py", line 1823, in __call__
return self.func(*args)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pmg_tk\startup\autodock_plugin.py", line 1940, in generate_receptor
result, output = getstatusoutput(command)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pmg_tk\startup\autodock_plugin.py", line 85, in getstatusoutput
p = Popen(args, stdout=PIPE, stderr=STDOUT, stdin=PIPE, env=env)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\subprocess.py", line 800, in __init__
restore_signals, start_new_session)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\subprocess.py", line 1207, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
I'm also encountering the same issue on Windows, try running a linux distro on vmware and make sure to install Pymol with support for Python 2.7 because the script is not compatible with Python3.
I have installed Java 11 and Python 3 on CentOS. Trying to run a code that worked perfectly fine on a Windows environment. Getting this exception:
ERROR:root:Exception while sending command.
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/py4j/java_gateway.py", line 1188, in
send_command
raise Py4JNetworkError("Answer from Java side is empty")
py4j.protocol.Py4JNetworkError: Answer from Java side is empty
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/py4j/java_gateway.py", line 1014, in send_command
response = connection.send_command(command)
File "/usr/lib/python3.4/site-packages/py4j/java_gateway.py", line 1193, in send_command
"Error while receiving", e, proto.ERROR_ON_RECEIVE)
py4j.protocol.Py4JNetworkError: Error while receiving
Traceback (most recent call last):
File "WordInformation.py", line 493, in
status = read_from_source("../Corpora/Bhandarkar Oriental Research Books")
File "WordInformation.py", line 473, in read_from_source
author, year)
File "WordInformation.py", line 381, in fetch_from_hwn
return read_store_properties(word, file, sentence, source, category, author,
year);
File "WordInformation.py", line 79, in read_store_properties
properties["synsets"] = get_other_props(word)
File "WordInformation.py", line 226, in get_other_props
output = gateway.jvm.Properties.getProperties(word)
File "/usr/lib/python3.4/site-packages/py4j/java_gateway.py", line 1286, in
call
answer, self.gateway_client, self.target_id, self.name)
File "/usr/lib/python3.4/site-packages/py4j/protocol.py", line 336, in
get_return_value
format(target_id, ".", name))
py4j.protocol.Py4JError: An error occurred while calling
z:in.ac.iitb.cfilt.jhwnl.examples.Properties.getProperties
Initialised the gateway as follows:
gateway = JavaGateway.launch_gateway(classpath="/home/gayatri/Code/hindiwn.jar")
Is this because of some dependency? I have set the JAVA_HOME and updated the PATH variable.
I don't have the reputation to comment, but
Answer from Java side is empty
But this error indicates that the Java code is not reachable.
Just to verify basic steps
1) Be sure that the java program is running
2) Be sure that you run the Python script after the java code is running
3) The java program is running the entire time.
If you are doing those two things, then an issue may be that the operating system may be already using a port.
You can try
Java
'GatewayServerBuilder server = new GatewayServerBuilder().javaPort(1001).build()'
'server.start()'
Python
java = JavaGateway(gateway_parameters=GatewayParameters(port=1001))
I'm trying to parse text from pdf file. while I was doing tutorial of how to PyPDF2 I got the following error. I did the search for an answer but ended up finding none. Any Help will be greatly appreciated.
Traceback (most recent call last):
File "D:/text_recognizer/main.py", line 4, in <module>
inputStream = PyPDF2.PdfFileReader(input)
File "D:\KimKanna's Class\python27\lib\site-packages\PyPDF2\pdf.py", line 1084, in __init__
self.read(stream)
File "D:\KimKanna's Class\python27\lib\site-packages\PyPDF2\pdf.py", line 1689, in read
stream.seek(-1, 2)
IOError: [Errno 22] Invalid argument
here is fullcode
import PyPDF2
with open(".\\pdf\\test_sample.pdf","rb") as input:
inputStream = PyPDF2.PdfFileReader(input)
In my case the .pdf I wanted to open is empty and not closed from previous python code in powershell(cmd prompt). So, when I tried to delete those files it says 'Close the file and try again'. (that was my "AHaa" moment)
So I stopped the py.exe from my Windows task manager and deleted those empty, not closed files. Then I run the same code with another files, It worked fine.. :)
I encounter weird behavior of an ipython cluster. The calculations finish, but many results never reach the client (and the engines just idle after finishing their first calculation).
I suspect something is wrong with zmq because 1) from time to time I see the following error:
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/asyncresult.py", line 118, in get
if not self.ready():
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/asyncresult.py", line 132, in ready
self.wait(0)
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/asyncresult.py", line 142, in wait
self._ready = self._client.wait(self.msg_ids, timeout)
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/client.py", line 1058, in wait
self.spin()
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/client.py", line 1015, in spin
self._flush_results(self._task_socket)
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/parallel/client/client.py", line 814, in _flush_results
idents,msg = self.session.recv(sock, mode=zmq.NOBLOCK)
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/zmq/session.py", line 642, in recv
idents, msg_list = self.feed_identities(msg_list, copy)
File "/data/misc/nano/python/env_stable/lib/python2.7/site-packages/IPython/zmq/session.py", line 673, in feed_identities
idx = msg_list.index(DELIM)
ValueError: '<IDS|MSG>' is not in list
Additionally IPython.zmq has two test failures:
======================================================================
ERROR: test_send (IPython.zmq.tests.test_session.TestSession)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/clusterdata/python/env_stable/lib/python2.7/site-packages/IPython/zmq/tests/test_session.py", line 76, in test_send
socket = MockSocket(zmq.Context.instance(),zmq.PAIR)
File "/clusterdata/python/env_stable/lib/python2.7/site-packages/IPython/zmq/tests/test_session.py", line 34, in __init__
self.data = []
File "/clusterdata/python/env_stable/lib/python2.7/site-packages/zmq/sugar/attrsettr.py", line 38, in __setattr__
self.__class__.__name__, upper_key)
AttributeError: MockSocket has no such option: DATA
======================================================================
ERROR: test_send (IPython.zmq.tests.test_session.TestSession)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/clusterdata/python/env_stable/lib/python2.7/site-packages/zmq/tests/__init__.py", line 108, in tearDown
raise RuntimeError("context could not terminate, open sockets likely remain in test")
RuntimeError: context could not terminate, open sockets likely remain in test
----------------------------------------------------------------------
I use pyzmq 13.0.0 (as installed by pip), and the zeromq 3.2.2, compiled by the setup of pyzmq. I use ipython 13.1 and python 2.7.3.
Any suggestions of what could this be, and if not how I could figure out more information why these errors occur?
Update: It turns out the slowdown was due to a long task queue of ipcontroller, which was then taking 100% CPU and lagging horribly. That is a separate issue, but I would still appreciate feedback on the above.
Answered by #minrk in comments. ZMQ errors were unimportant, performance was due to scheduling, and was solved by setting TaskScheduler.hwm=0.
I'm trying to use PuDB with ipython as the shell, but when I drop to shell, I get the following error:
can't set attribute
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Error in sys.exitfunc:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Version details:
PuDB 2011.3.1
IPython 0.12
Python 2.7.1
Mac OS X 10.7.3
This is a known issue, and should be fixed in IPython 0.12.1 or master. Does updating to current (0.12.1) IPython help?