I installed deepchem following the instruction on their website. I dint get any error during the installation but when I import deepchem from jupyternotebbok, the kernel will be dead:
The kernel appears to have died. It will restart automatically.
If I import deepchem from terminal, I get
Segmentation fault: 11
Any help is appreciated.
Sorry for the very slow answer on here! DeepChem's latest versions should work on Mac. Can you try installing DeepChem 2.3 and seeing if you're still having issues?
Related
Platform: Precision 5820, 32G, rtx4000; Win 10 Pro, Arcgis Pro 2.6 concurrent license;
Issue:
I installed the deep learning tools following the guidelines provided here:
deeplearninginstallation
tersorflow was not found after installation so I manually installed the 2.1.0 version. I now have arcgis 1.8.2, pro 2.6, fastai 1.0.60, python 3.6.12, pytorch 1.4.0, tensorflow-gpu 2.1.0; environment check in arcgis pro python seemed fine.
However, after I select toolbox-image analyst-deeplearning-traindeeplearningmodel, the program seems to go into a hang, with most buttons disabled/unresponsive, this would continue until I force terminate the program. I also ran into "tool not licensed" twice, which was gone after I restarted the program; and a "name 'CallBackHandler' is not defined" once, which was also gone after I restarted.
I tried runing the command from the arcgis pro python prompt:
TrainDeepLearningModel(r"**", r"**", 40, "RETINANET", 16, "# #", None, "RESNET50", None, 10, "STOP_TRAINING", "FREEZE_MODEL")
executing the command would also send the program into a hang similar to the previous one. Monitor shows that ram and GPU usage haven't changed much, so I left the program running for an hour before forcibly terminating it.
I'd greatly appreciate it if anyone can tell me what the issues are here. I'll post any other env parameters if anyone requires. Cheers.
I got the tool up and running now by running conda install -c pytorch -c fastai fastai=1.0.54 pytorch=1.1.0 torchvision scikit-image and removing all the conflicting specifications in the cloned arcgispro-py3 env that I had. Now I still don't understand what went wrong. Presumably one or more packages in the env was conflicting. But seeing as I'm not a python expert, I couldn't identify the exact issue.
Before this I tried the versions stated here deeplearning install guide, but wasn't able to get pass tensorflow-gpu because python kept checking conflications. Now I actually don't have tensorflow-gpu in the env. I have tensorflow 2.1.0, keras-applications 1.0.8/base 2.3.1/preprocesing 1.1.0 (no keras-gpu), scikit-image 0.17.2, pillow 6.2.1, fastai 1.0.54, pytorch 1.1.0, libtiff 4.0.10. Some are different from what the guideline provided.
Thing is when I ran the process, CPU usage was up and GPU wasn't despite the fact that I specified GPU as the processing core. But I have much more pressing things to do right now like getting the analysis finished. So I'll probably tweek the env around a little after I'm done with this bit and see what happens. Meanwhile, anyone's input is still welcome.
After updating my 2019 Macbook Pro yesterday to MacOS Mojave 10.14.6, a tkinter application that I have packaged with pyinstaller now crashes my computer. The screen turns black for a second, and then restarts to the login screen. When I run the program through the command line (unpackaged), it runs just fine.
The error code that appears several times in terminal is: CGSTrackingRegionSetIsEnabled returned CG error 268435459.
The research I've done has led me to these links:
This unanswered StackOverflow question
This semi-related SuperUser question
This question on the Japanese Q&A site teratail
The unanswered StackOverflow question is slightly different than my own problem, as it seems that that user cannot create a Tk() window at all, whereas I can create a Tk() window (including the Python IDLE), but it breaks when I package it with pyinstaller.
The SuperUser question is unanswered, but as one of the answers suggest I have uninstalled and reinstalled pyinstaller to no avail.
The question on teratail was answered, and says that the problem was fixed by uninstalling "Anaconda", but I don't know what Anaconda is or how to uninstall it.
I suspect that this is a problem with the MacOS update, and that there is nothing I can do to fix it and I'll have to wait for a patch.
Why is this happening? How can I fix it?
This problem has troubled me for a long time. My macOS version is 10.14.6 (Mojave). Running tkinter will crash the system, but I don’t want to update macOS version to 10.15 (Catalina) for this problem.
I got a solution by updating the python version.
My own test results, python versions 3.8.2 and 3.8.3 can fix the problem, but python versions 3.8.1, 3.7.x, 3.6.x will cause the crash.
I can confirm that this happens with Python 3.7.x. Moving to 3.8.3 fixes the problem.
Workaround: boot in Safe Mode..
(Other apps are experiencing this.)
The macOS Window Server is crashing..
The Console.app contains the crash report in the "System Reports" node.
Process: WindowServer
Thread 0 (main thread) crashes in CGXBeginSurfaceLayerUpdate
I had the same problem with Mac OSX 10.14.6 completely crashing with no error messages and logging me out or rebooting. It was fixed by removing Anaconda and using the python.org ver 3.7.4. A good link for removing Anaconda is here. How to uninstall Anaconda completely from macOS
The new MacOS Catalina (Version 10.15) update seems to fix the problem for me. By specifying the tcl version and making sure the right tcl is used, I was able to successfully bundle and run my python script with tkinter. Yay!
I have been trying to get Keras working on my laptop running El Capitan but when I attempt to import it I get the following message
Using TensorFlow backend.
Illegal instruction: 4
I've looked for solutions, and have tried updating theano, installing mxnet-mkl, and running an older version of numpy (1.13) to avoid a FutureWarning error. None of these has seemed to fix the issue, though. I feel like I must be missing something somewhere.
Try installing an older version of TensorFlow (1.5 seems to work). AVX2 instructions are now enabled by default in latest TF pip wheels, meaning if your processor doesn't support these instructions, then you will get an illegal instruction error.
Another solution is to install TensorFlow from source, which should detect your processor and configure it accordingly.
The iPython 2 console and notebook as well as the iPython 3 console work fine on my system.
But running ipython3 notebook gives an ImportError saying No module named 'IPython.frontend.html' and this traceback.
I think it may have something to do with Ubuntu RR package problems, but I'm not sure.
10x.
Ubuntu split the notebook functionality away form the main ipython3 package into ipython3-notebook in Raring.
Now installing ipython3 should install ipython3-notebook for you automatically as it recommends it; but when I had this problem, Raring critically depended on a package of python3 too high for python3-zmq which was depended on by ipython3-notebook causing ipython3-notebook' to not be installed (which I did not notice). Whew...
This might be due to the fact that the package layout has been change and IPython.frontend.html is now IPython.html do you have dev version installed by any chance ?
I had this problem and fixed it by upgrading ipython (using --upgrade)
I'm running Canopy 64-bit on a mac. After installing scikit-learn (using the package manager), I tried to import svm, and got the following error.
ImportError: dlopen(/Users/johnsaccount/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sklearn/svm/liblinear.so, 2): Library not loaded: /System#rpath/libBLAS.dylib
Referenced from: /Users/johnsaccount/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/sklearn/svm/liblinear.so
Reason: image not found
Any ideas on what might be the problem?
Jsen,
My apologies for this error, it was my mistake when building that egg. The update should now be available and fix that error (the fixed version is 0.13.1-3, both 0.13.1-1 and 0.13.1-2 are broken on os x).
Thanks for the report and sorry for the inconvenience.
I can reproduce this, apparently due to a build error on OSX (it works ok on Windows). We'll let you know when it is fixed.