Re: [ease-dev] numpy in EASE

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Re: [ease-dev] numpy in EASE

From: <Christian.Pontesegger@xxxxxxxxxxxx>
Date: Mon, 25 Jun 2018 12:36:39 +0000
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Thread-topic: [ease-dev] numpy in EASE

Hi,

sorry, no idea. I was hoping that Jonah & Martin hang around to jump in as they are the python experts in EASE. At least with our anaconda setup I was able reproduce the hangup on help(“modules”). As a non-python guy I am lost here. What I get is all kinds of errors (see below). I know we are using the single-threaded API from py4j. As I see some threading involved below, this might be the root cause – just guessing.

Christian

Importing numpy...

numpy imported.

Please wait a moment while I gather a list of all available modules...

C:\PROGRAM FILES\ANACONDA3\lib\site-packages\IPython\kernel\__init__.py:13: ShimWarning: The `IPython.kernel` package has been deprecated. You should import from ipykernel or jupyter_client instead.

"You should import from ipykernel or jupyter_client instead.", ShimWarning)

C:\PROGRAM FILES\ANACONDA3\lib\site-packages\flask\exthook.py:71: ExtDeprecationWarning: Importing flask.ext.cors is deprecated, use flask_cors instead.

.format(x=modname), ExtDeprecationWarning

C:\PROGRAM FILES\ANACONDA3\lib\site-packages\matplotlib\cbook.py:137: MatplotlibDeprecationWarning: The matplotlib.delaunay module was deprecated in version 1.4. Use matplotlib.tri.Triangulation instead.

warnings.warn(message, mplDeprecation, stacklevel=1)

C:\PROGRAM FILES\ANACONDA3\lib\site-packages\nltk\twitter\__init__.py:20: UserWarning: The twython library has not been installed. Some functionality from the twitter package will not be available.

warnings.warn("The twython library has not been installed. "

C:\PROGRAM FILES\ANACONDA3\lib\pkgutil.py:86: FutureWarning: The pandas.rpy module is deprecated and will be removed in a future version. We refer to external packages like rpy2.

See here for a guide on how to port your code to rpy2: http://pandas.pydata.org/pandas-docs/stable/r_interface.html

__import__(name)

C:\PROGRAM FILES\ANACONDA3\lib\site-packages\skimage\filter\__init__.py:6: skimage_deprecation: The `skimage.filter` module has been renamed to `skimage.filters`. This placeholder module will be removed in v0.13.

warn(skimage_deprecation('The `skimage.filter` module has been renamed '

Fatal Python error: Segmentation fault

Thread 0x00002324 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 429 in _handle_results

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00002d80 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 376 in _handle_tasks

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00001ce0 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 367 in _handle_workers

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00002528 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 108 in worker

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00001abc (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 108 in worker

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00003218 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 108 in worker

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00000fe0 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\queue.py", line 164 in get

File "C:\PROGRAM FILES\ANACONDA3\lib\multiprocessing\pool.py", line 108 in worker

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x000019dc (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\socket.py", line 575 in readinto

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 449 in wait_for_commands

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 378 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x000031cc (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\socket.py", line 575 in readinto

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 449 in wait_for_commands

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 378 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Current thread 0x00000248 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\qtawesome\iconic_font.py", line 200 in load_font

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\qtawesome\iconic_font.py", line 168 in __init__

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\qtawesome\__init__.py", line 36 in _instance

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\qtawesome\__init__.py", line 153 in load_font

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\spyder\utils\icon_manager.py", line 257 in icon

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\spyder\plugins\runconfig.py", line 445 in RunConfigPage

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\spyder\plugins\runconfig.py", line 440 in <module>

File "<frozen importlib._bootstrap>", line 222 in _call_with_frames_removed

File "<frozen importlib._bootstrap_external>", line 665 in exec_module

File "<frozen importlib._bootstrap>", line 673 in _load_unlocked

File "<frozen importlib._bootstrap>", line 958 in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 969 in _find_and_load

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\spyder_profiler\profiler.py", line 22 in <module>

File "<frozen importlib._bootstrap>", line 222 in _call_with_frames_removed

File "<frozen importlib._bootstrap_external>", line 665 in exec_module

File "<frozen importlib._bootstrap>", line 673 in _load_unlocked

File "<frozen importlib._bootstrap>", line 958 in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 969 in _find_and_load

File "C:\PROGRAM FILES\ANACONDA3\lib\site-packages\spyder_profiler\__init__.py", line 6 in <module>

File "<frozen importlib._bootstrap>", line 222 in _call_with_frames_removed

File "<frozen importlib._bootstrap_external>", line 665 in exec_module

File "<frozen importlib._bootstrap>", line 673 in _load_unlocked

File "<frozen importlib._bootstrap>", line 958 in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 969 in _find_and_load

File "C:\PROGRAM FILES\ANACONDA3\lib\pkgutil.py", line 86 in walk_packages

File "C:\PROGRAM FILES\ANACONDA3\lib\pydoc.py", line 2066 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\pydoc.py", line 2037 in listmodules

File "C:\PROGRAM FILES\ANACONDA3\lib\pydoc.py", line 1886 in help

File "C:\PROGRAM FILES\ANACONDA3\lib\pydoc.py", line 1845 in __call__

File "C:\PROGRAM FILES\ANACONDA3\lib\_sitebuiltins.py", line 103 in __call__

File "<console>", line 1 in <module>

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\..\..\..\..\..\git\org.eclipse.ease.core\plugins\org.eclipse.ease.lang.python.py4j\pysrc\ease_py4j_main.py", line 161 in runcode

File "C:\PROGRAM FILES\ANACONDA3\lib\code.py", line 75 in runsource

File "C:\PROGRAM FILES\ANACONDA3\lib\code.py", line 250 in push

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 490 in _call_proxy

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 457 in wait_for_commands

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\clientserver.py", line 378 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00002e70 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x000016e8 (most recent call first):

File "C:\Userdata\Development\sysbox-oxygen\ws\.metadata\.plugins\org.eclipse.pde.core\.bundle_pool\plugins\py4j-python_0.10.4.bnd-2odeag\src\py4j\java_gateway.py", line 2062 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 862 in run

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 914 in _bootstrap_inner

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 882 in _bootstrap

Thread 0x00003008 (most recent call first):

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 293 in wait

File "C:\PROGRAM FILES\ANACONDA3\lib\threading.py", line 549 in wait

py4j.Py4JException: Error while sending a command.

at py4j.CallbackClient.sendCommand(CallbackClient.java:357)

at py4j.CallbackClient.sendCommand(CallbackClient.java:316)

at py4j.reflection.PythonProxyHandler.invoke(PythonProxyHandler.java:103)

at com.sun.proxy.$Proxy21.executeInteractive(Unknown Source)

at org.eclipse.ease.lang.python.py4j.internal.Py4jScriptEngine.internalExecute(Py4jScriptEngine.java:233)

at org.eclipse.ease.lang.python.py4j.internal.Py4jScriptEngine.execute(Py4jScriptEngine.java:226)

at org.eclipse.ease.AbstractScriptEngine.inject(AbstractScriptEngine.java:227)

at org.eclipse.ease.AbstractScriptEngine.run(AbstractScriptEngine.java:289)

at org.eclipse.core.internal.jobs.Worker.run(Worker.java:56)

Caused by: py4j.Py4JNetworkException: Error while sending a command: c

executeInteractive

shelp("modules")

at py4j.ClientServerConnection.sendCommand(ClientServerConnection.java:223)

at py4j.CallbackClient.sendCommand(CallbackClient.java:344)

... 8 more

Caused by: java.net.SocketException: Connection reset

at java.net.SocketInputStream.read(SocketInputStream.java:210)

at java.net.SocketInputStream.read(SocketInputStream.java:141)

at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)

at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)

at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)

at java.io.InputStreamReader.read(InputStreamReader.java:184)

at java.io.BufferedReader.fill(BufferedReader.java:161)

at java.io.BufferedReader.readLine(BufferedReader.java:324)

at java.io.BufferedReader.readLine(BufferedReader.java:389)

at py4j.ClientServerConnection.readBlockingResponse(ClientServerConnection.java:275)

at py4j.ClientServerConnection.sendCommand(ClientServerConnection.java:199)

... 9 more

From: ease-dev-bounces@xxxxxxxxxxx <ease-dev-bounces@xxxxxxxxxxx> On Behalf Of LOPEZ BETANCUR David
Sent: Montag, 25. Juni 2018 13:50
To: ease developer discussions <ease-dev@xxxxxxxxxxx>
Subject: Re: [ease-dev] numpy in EASE

Hello Christian,

Thanks for your reply.

Previously we had the 2.7 version running on windows 10, jdk 9.0, but we updated to python 3.6.5, ran the ```help(“modules”)``` command and it returned with the expected list of modules. We proceeded to install *numpy* via _pip install_. Then we re-ran help(“modules”) and it hang as before. We uninstalled numpy, ran help(“modules”), and it gave us the list again. So it seems there’s something blocking with at least one package installed along with numpy.

We also trying just importing numpy in our script and it got stuck. Our script only has these 3 lines:

print("Importing numpy...")

import numpy as np

print("numpy imported.")

We switched to the Anaconda python distribution and configured py4j to use it, ran the script and it can indeed import numpy, yet the help(“modules”) still hangs.

Do you have any idea of why the standard distribution (at least in windows) of python isn’t working with EASE and numpy?

Cheers,

Sébastien,

David.

De : ease-dev-bounces@xxxxxxxxxxx <ease-dev-bounces@xxxxxxxxxxx> De la part de Christian Pontesegger
Envoyé : mercredi 20 juin 2018 17:00
À : ease-dev@xxxxxxxxxxx
Objet : Re: [ease-dev] numpy in EASE

Hi David,

tried both commands on my linux system without any problems using EASE-nightly.

On windows we encountered some problems depending on the installed python version with some other commands. My local python version is 3.5.5
Which version are you using?

Christian

On 19.06.2018 16:01, LOPEZ BETANCUR David wrote:

Hello EASE-devs,

We are trying to use numpy with py4j, but our script is hanging at the line ```import numpy as np```.

Furthermore, when we run ```help("modules")``` it also hangs. Tracking the source of the problem, we found it's getting stuck in the *py4j.ClientServerConnection.readBlockingResponse* call. We are not sure why is this happening.

Has anybody ran ```help("modules")``` within EASE ?

Cheers,

Sébastien.
David.
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References:
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  - From: LOPEZ BETANCUR David
- Re: [ease-dev] numpy in EASE
  - From: Christian Pontesegger
- Re: [ease-dev] numpy in EASE
  - From: LOPEZ BETANCUR David

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