I made a short Colab Notebook to simulate the situation on my local PC where I use conda / mamba and can't get any GPU working for tensorflow. I know colab can do this out of the box, but that's not, what I want to do. I'm also quite new to colab and still trying to figure out, how it's used :D.
So here's my Code for colab:
# Install Miniconda
!curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
!sh Miniconda3-latest-Linux-x86_64.sh -b -f -p /usr/local
# Set channels
!conda config --add channels defaults
!conda config --add channels bioconda
!conda config --add channels conda-forge
# Install Mamba
!conda install -y mamba
next cell:
# Create Environment
!mamba create -y -n stats-gpu tensorflow-gpu cudatoolkit cudnn
I also tried:
!mamba create -n stats-gpu python=3.8 tensorflow-gpu=2.4 cudnn=8.0 cudatoolkit=11.0
next cell:
# simulate "conda activate" by setting PYTHONPATH and PATH
import sys
import os
PYTHONPATH = os.environ['PYTHONPATH']
sys.path = ['',
PYTHONPATH,
'/usr/local/envs/stats-gpu/lib/python37.zip',
'/usr/local/envs/stats-gpu/lib/python3.7',
'/usr/local/envs/stats-gpu/lib/python3.7/lib-dynload',
'/usr/local/envs/stats-gpu/lib/python3.7/site-packages']
os.environ['PATH'] = ('/usr/local/envs/stats-gpu/bin:' +
'/usr/local/condabin:' +
os.environ['PATH'])
next cell:
# Executing directly in cell will ignore python installed by conda.
# Writing Python script in .py file and executing with !python will use
# Python from conda.
filename = "tensortest.py"
with open(filename, 'w') as file:
file.write("""import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))""")
!python tensortest.py
The output is
Num GPUs Available: 0
but it should be 1. Why is that? The GPU in colab is active and works when I just use
import tensorflow as tf
print("Num GPUs Available: ", len(tf.config.list_physical_devices('GPU')))
in an empty Notebook.
Related
I am trying to reproduce the fine-tuning stage of LaBSE[https://github.com/tensorflow/models/tree/master/official/projects/labse] model.
I have cloned the tensorflow/models repository. Set the enironment path as follows.
%env PYTHONPATH='/env/python:/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models'
!echo $PYTHONPATH
output: '/env/python:/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models'
installed pre-requisites
!pip install -U tensorflow
!pip install -U "tensorflow-text==2.10.*"
!pip install tf-models-official
Then I try to run the labse training command in readme.md.
python3 /content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models/official/projects/labse/train.py \
--experiment=labse/train \
--config_file=/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models/official/projects/labse/experiments/labse_bert_base.yaml \
--config_file=/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models/official/projects/labse/experiments/labse_base.yaml \
--params_override=${PARAMS} \
--model_dir=/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models \
--mode=train_and_eval
Issue
I get the following error.
File "/content/drive/MyDrive/Colab_Notebooks/p3_sentence_similiarity/models/official/projects/labse/train.py", line 23, in
from official.projects.labse import config_labse
ModuleNotFoundError: No module named 'official.projects.labse'
The import statement python from official.projects.labse import config_labse fails
System information
I executed this on colab as well as in a GPU machine. However in both environments I get the same error.
I need to know why the import statement failed and what corrective action should be taken for this.
I'm having trouble running this line of code in Deepnote, does anyone know why?
data = ImageDataBunch.from_folder(path, train="train", valid ="test",ds_tfms=get_transforms(), size=(256,256), bs=32, num_workers=4).normalize()
The error says:
NameError: name 'ImageDataBunch' is not defined
And previously, I have imported the Fastai library. So I don't get it!
The FastAI setup in Deepnote is not that straightforward. It's best to use a custom environment where you set stuff up in a Dockerfile and everything works afterwards in the notebook. I am not sure if the ImageDataBunch or whatever you're trying to do works the same way in FastAI v1 and v2, but here are the details for v1.
This is a Dockerfile which sets up the FastAI environment via conda:
# This is Dockerfile
FROM deepnote/python:3.9
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
RUN bash ~/miniconda.sh -b -p $HOME/miniconda
ENV PATH $HOME/miniconda/bin:$PATH
ENV PYTONPATH $HOME/miniconda
RUN $HOME/miniconda/bin/conda install python=3.9 ipykernel -y
RUN $HOME/miniconda/bin/conda install -c fastai -c pytorch fastai -y
RUN $HOME/miniconda/bin/python -m ipykernel install --user --name=conda
ENV DEFAULT_KERNEL_NAME "conda"
After that, you can test the fastai imports in the notebook:
import fastai
from fastai.vision import *
print(fastai.__version__)
ImageDataBunch
And if you download and unpack this sample MNIST dataset, you should be able to load the data like you suggested:
data = ImageDataBunch.from_folder(path, train="train", valid ="test",ds_tfms=get_transforms(), size=(256,256), bs=32, num_workers=4).normalize()
Feel free to check out or clone my Deepnote project to continue working on this.
So I am trying to set up deeplab in colab.
I am running:
[1]
from google.colab import drive
drive.mount('/content/drive')
%cd /content/drive/My\ Drive/deeplab_files
[2]
%env PYTHONPATH=/content/drive/My\ Drive/deeplab_files/:/content/drive/My\ Drive/deeplab_files/slim
!echo $PYTHONPATH
[3]
!python deeplab/vis.py \
--logtostderr \
--vis_split="val" \
--model_variant="xception_65" \
--atrous_rates=6 \
--atrous_rates=12 \
--atrous_rates=18 \
--output_stride=16 \
--decoder_output_stride=4 \
--vis_crop_size=360 \
--vis_crop_size=480 \
--dataset="camvid" \
--colormap_type="pascal" \
--checkpoint_dir='/content/drive/My\ Drive/deeplab_files/deeplab/datasets/PQR/exp/train_on_trainval_set/train' \
--vis_logdir='/content/drive/My\ Drive/deeplab_files/deeplab/datasets/PQR/exp/train_on_trainval_set/vis' \
--dataset_dir='/content/drive/My\ Drive/deeplab_files/deeplab/datasets/PQR/tfrecord'
The last command, however, returns
sh: 1: export: Drive/deeplab_files/slim:/content/drive/My Drive/deeplab_files/:/content/drive/My Drive/deeplab_files/slim: bad variable name
Traceback (most recent call last):
File "deeplab/vis.py", line 28, in <module>
from deeplab import common
ModuleNotFoundError: No module named 'deeplab'
Anyone have any idea how I can set up deeplab? I have it set up on my personal machine, but it is much too slow. I uploaded the entire folder to my gdrive.
The odd thing is that I can do
from deeplab import common
from the notebook and that imports successfully
Here is a Github repo containing a Colab notebook running deeplab.
I have not tested it but the way you have uploaded your entire directory to Google Drive is not the right way to run things on Colab.
Think of Colab as a separate machine and you are mounting your Google Drive on this machine. Anything available on your Google Drive is not necessarily available to the Colab machine. You will have to add path of your Google Drive folder (say '\content\drive\My Drive\<path_to_your_folder>') to the sys.path for Colab machine using sys.path.insert(0, <path_of_your_drive_folder>) to make that path available to python environment running on the Colab machine.
Solved mt question. The linked repo that abggcv gave, unfortunately, runs into the same issue this question was citing.
You should clone the repo as normal, and run everything as normal. The only change is that before you run train.py, eval.py, or vis.py you'll need to run the following block:
%cd /root/deeplabvc/models/research/
import sys
sys.path.extend(['/root/deeplabvc/models/research/', '/root/deeplab/models/research/slim/'])
Note that /root/deeplab/ is the path to where I cloned the repo. You'll need to change this if the directory where you cloned the repo is different.
Furthermore, for some reason, you wont be able to run train.py/eval.py/vis.py successively. Even clearing the flags will give you an error about a duplicate flag. To fix this, just restart the runtime (wont lose your files).
Happy segmenting!
Deeplab import error occurs mostly when the PYTHONPATH is not setup properly. The installation instruction given does not work with COLAB environment. The Following has worked for me
%cd /content/deeplab/models/research/
!mkdir -p deeplab/datasets/pascal_voc_seg/exp/train_on_train_set/train
!mkdir -p deeplab/datasets/pascal_voc_seg/exp/train_on_train_set/eval
!mkdir -p deeplab/datasets/pascal_voc_seg/exp/train_on_train_set/vis
!echo ${PYTHONPATH}
%env PATH_TO_TRAIN_DIR=/content/deeplab/models/research/deeplab/datasets/pascal_voc_seg/exp/train_on_train_set/train
%env PATH_TO_DATASET=/content/deeplab/models/research/deeplab/datasets/pascal_voc_seg/tfrecord
%env PYTHONPATH=/content/deeplab/models/research:/content/deeplab/models/research/deeplab:/content/deeplab/models/research/slim:/env/python
!echo ${PYTHONPATH}
Here is my COLAB notebook for Training of deeplab that worked
I was wondering if I could install RAPIDS library (executing machine learning tasks entirely on GPU) in Google Colaboratory notebook?
I've done some research but I've not been able to find the way to do that...
This is now possible with the new T4 instances https://medium.com/rapids-ai/run-rapids-on-google-colab-for-free-1617ac6323a8
To enable cuGraph too, you can replace the wget command with:
!conda install -c nvidia/label/cuda10.0 -c rapidsai/label/cuda10.0 -c pytorch \
-c numba -c conda-forge -c numba -c defaults \
boost cudf=0.6 cuml=0.6 python=3.6 cugraph=0.6 -y
Dec 2019 update
New process for RAPIDS v0.11+
Because
RAPIDS v0.11 has dependencies (pyarrow) which were
not covered by the prior install script,
the notebooks-contrib repo, which contains RAPIDS demo notebooks (e.g.
colab_notebooks) and the Colab install script, now follows RAPIDS standard version-specific branch structure*
and some Colab users still enjoy v0.10,
our honorable notebooks-contrib overlord taureandyernv has updated the script which now:
If running v0.11 or higher, updates pyarrow library to 0.15.x.
Here's the code cell to run in Colab for v0.11:
# Install RAPIDS
!wget -nc https://raw.githubusercontent.com/rapidsai/notebooks-contrib/890b04ed8687da6e3a100c81f449ff6f7b559956/utils/rapids-colab.sh
!bash rapids-colab.sh
import sys, os
dist_package_index = sys.path.index("/usr/local/lib/python3.6/dist-packages")
sys.path = sys.path[:dist_package_index] + ["/usr/local/lib/python3.6/site-packages"] + sys.path[dist_package_index:]
sys.path
if os.path.exists('update_pyarrow.py'): ## This file only exists if you're using RAPIDS version 0.11 or higher
exec(open("update_pyarrow.py").read(), globals())
For a walk thru setting up Colab & implementing this script, see How to Install RAPIDS in Google Colab
-* e.g. branch-0.11 for v0.11 and branch-0.12 for v0.12 with default set to the current version
Looks like various subparts are not yet pip-installable so the only way to get them on colab would be to build them on colab, which might be more effort than you're interested in investing in this :)
https://github.com/rapidsai/cudf/issues/285 is the issue to watch for rapidsai/cudf (presumably the other rapidsai/ libs will follow suit).
Latest solution;
!wget -nc https://github.com/rapidsai/notebooks-extended/raw/master/utils/rapids-colab.sh
!bash rapids-colab.sh
import sys, os
sys.path.append('/usr/local/lib/python3.6/site-packages/')
os.environ['NUMBAPRO_NVVM'] = '/usr/local/cuda/nvvm/lib64/libnvvm.so'
os.environ['NUMBAPRO_LIBDEVICE'] = '/usr/local/cuda/nvvm/libdevice/'
was pushed a few days ago, see issues #104 or #110, or the full rapids-colab.sh script for more info.
Note: instillation currently requires a Tesla T4 instance, checking for this can be done with;
# check gpu type
!nvidia-smi
import pynvml
pynvml.nvmlInit()
handle = pynvml.nvmlDeviceGetHandleByIndex(0)
device_name = pynvml.nvmlDeviceGetName(handle)
# your dolphin is broken, please reset & try again
if device_name != b'Tesla T4':
raise Exception("""Unfortunately this instance does not have a T4 GPU.
Please make sure you've configured Colab to request a GPU instance type.
Sometimes Colab allocates a Tesla K80 instead of a T4. Resetting the instance.
If you get a K80 GPU, try Runtime -> Reset all runtimes...""")
# got a T4, good to go
else:
print('Woo! You got the right kind of GPU!')
With old Jupyter notebooks, I could create interactive plots via:
import matplotlib.pyplot as plt
%matplotlib notebook
x = [1,2,3]
y = [4,5,6]
plt.figure()
plt.plot(x,y)
However, in JupyterLab, this gives an error:
JavaScript output is disabled in JupyterLab
I have also tried the magic (with jupyter-matplotlib installed):
%matplotlib ipympl
But that just returns:
FigureCanvasNbAgg()
Inline plots work, but they are not interactive plots:
%matplotlib inline
JupyterLab 3.0+
Install jupyterlab and ipympl.
For pip users:
pip install --upgrade jupyterlab ipympl
For conda users:
conda update -c conda-forge jupyterlab ipympl
Restart JupyterLab.
Decorate the cell containing plotting code with the header:
%matplotlib widget
# plotting code goes here
JupyterLab 2.0
Install nodejs, e.g. conda install -c conda-forge nodejs.
Install ipympl, e.g. conda install -c conda-forge ipympl.
[Optional, but recommended.] Update JupyterLab, e.g.
conda update -c conda-forge jupyterlab==2.2.9==py_0.
[Optional, but recommended.] For a local user installation, run:
export JUPYTERLAB_DIR="$HOME/.local/share/jupyter/lab".
Install extensions:
jupyter labextension install #jupyter-widgets/jupyterlab-manager
jupyter labextension install jupyter-matplotlib
Enable widgets: jupyter nbextension enable --py widgetsnbextension.
Restart JupyterLab.
Decorate with %matplotlib widget.
To enable the jupyter-matplotlib backend, use the matplotlib Jupyter magic:
%matplotlib widget
import matplotlib.pyplot as plt
plt.figure()
x = [1,2,3]
y = [4,5,6]
plt.plot(x,y)
More info here jupyter-matplotlib on GitHub
As per Georgy's suggestion, this was caused by Node.js not being installed.
Steps for JupyterLab 3.*
I had previously used Mateen's answer several times, but when I tried them with JupyterLab 3.0.7 I found that jupyter labextension install #jupyter-widgets/jupyterlab-manager returned an error and I had broken widgets.
After a lot of headaches and googling I thought I would post the solution for anyone else who finds themselves here.
The steps are now simplified, and I was able to get back to working interactive plots with the following:
pip install jupyterlab
pip install ipympl
Decorate with %matplotlib widget
Step 2 will automatically take care of the rest of the dependencies, including the replacements for (the now depreciated?) #jupyter-widgets/jupyterlab-manager
Hope this saves someone else some time!
Summary
In a complex setup, where jupyter-lab process and the Jupyter/IPython kernel process are running in different Python virtual environments, pay attention to Jupyter-related Python package and Jupyter extension (e.g. ipympl, jupyter-matplotlib) versions and their compatibility between the environments.
And even in single Python virtual environment make sure you comply with the ipympl compatibility table.
Example
A couple of examples how to run JupyterLab.
Simple(st)
The simplest cross-platform way to run JupyterLab, I guess, is running it from a Docker container. You can build and run JupyterLab 3 container like this.
docker run --name jupyter -it -p 8888:8888 \
# This line on a Linux- and non-user-namespaced Docker will "share"
# the directory between Docker host and container, and run from the user.
-u 1000 -v $HOME/Documents/notebooks:/tmp/notebooks \
-e HOME=/tmp/jupyter python:3.8 bash -c "
mkdir /tmp/jupyter; \
pip install --user 'jupyterlab < 4' 'ipympl < 0.8' pandas matplotlib; \
/tmp/jupyter/.local/bin/jupyter lab --ip=0.0.0.0 --port 8888 \
--no-browser --notebook-dir /tmp/notebooks;
"
When it finishes (and it'll take a while), the bottommost lines in the terminal should be something like.
To access the server, open this file in a browser:
...
http://127.0.0.1:8888/lab?token=abcdef...
You can just click on that link and JupyterLab should open in your browser. Once you shut down the JupyterLab instance the container will stop. You can restart it with docker start -ai jupyter.
Complex
This GitHub Gist illustrates the idea how to build a Python virtual environment with JupyterLab 2 and also building all required extensions with Nodejs in the container, without installing Nodejs on host system. With JupyterLab 3 and pre-build extensions this approach gets less relevant.
Context
I was scratching my head today while debugging the %matplotlib widget not working in JupyterLab 2. I have separate pre-built JupyterLab venv (as described above) which powers local JupyterLab as Chromium "app mode" (i.e. c.LabApp.browser = 'chromium-browser --app=%s' in the config), and a few IPython kernels from simple Python venvs with specific dependencies (rarely change) and an application exposing itself as an IPython kernel. The issue with the interactive "widget" mode manifested in different ways.
For instance, having
in JupyterLab "host" venv: jupyter-matplotlib v0.7.4 extension and ipympl==0.6.3
in the kernel venv: ipympl==0.7.0 and matplotlib==3.4.2
In the browser console I had these errors:
Error: Module jupyter-matplotlib, semver range ^0.9.0 is not registered as a widget module
Error: Could not create a model.
Could not instantiate widget
In the JupyterLab UI:
%matplotlib widget succeeds on restart
Charts stuck in "Loading widget..."
Nothing on re-run of the cell with chart output
On previous attempts %matplotlib widget could raise something like KeyError: '97acd0c8fb504a2288834b349003b4ae'
On downgrade of ipympl==0.6.3 in the kernel venv in the browser console:
Could not instantiate widget
Exception opening new comm
Error: Could not create a model.
Module jupyter-matplotlib, semver range ^0.8.3 is not registered as a widget module
Once I made the packages/extensions according to ipympl compatibility table:
in JupyterLab "host" venv: jupyter-matplotlib v0.8.3 extension, ipympl==0.6.3
in the kernel venv: ipympl==0.6.3, matplotlib==3.3.4
It more or less works as expected. Well, there are verious minor glitches like except I put %matplotlib widget per cell with chart, say on restart, the first chart "accumulates" all the contents of all the charts in the notebook. With %matplotlib widget per cell, only one chart is "active" at a time. And on restart only last widget is rendered (but manual re-run of a cell remediates).
This solution works in jupyterlab
import numpy as np
import matplotlib.pyplot as plt
from IPython.display import clear_output
n = 10
a = np.zeros((n, n))
plt.figure()
for i in range(n):
plt.imshow(a)
plt.show()
a[i, i] = 1
clear_output(wait=True)