Create docker image with specified CUDA toolkits and pytorch - docker

I'm using clusters of my corporation by ICM. It provides a convenient way to configure the remote by docker:
So, I want to build a docker image of my developing environment (python packages, cuda, some utility scripts like screen and rsync, also some necessary data) to deploy on the remote machine. Here is my Dockerfile:
# syntax=docker/dockerfile:1
FROM pytorch/pytorch:1.7.1-cuda11.0-cudnn8-runtime
WORKDIR /app
RUN sudo apt-get install rsync
RUN sudo apt-get install screen
RUN conda create --prefix /data/vxxx/nn python=3.8
RUN conda init
# shotcut for activating my environment
RUN echo 'alias nn="conda activate /data/xxx/nn"' >> ~/.bashrc
RUN source ~/.bashrc
RUN nn
RUN pip3 install torchtext==0.8.1 pandas scipy scikit-learn transformers tensroboard -f https://download.pytorch.org/whl/torch_stable.html
# copy files from windows
COPY /mnt/c/test .
RUN cd /data
RUN mkdir xxx
RUN cd xxx
RUN mkdir Data
RUN mkdir Code
RUN cd Code
RUN git clone https://github.com/namespace-Pt/Document-Reduction.git
RUN git config --global user.name 'xxx'
RUN git config --global user.email 'xxx#1.com'
CMD [ "sleep", "infinity"]
I'm new to docker and I followed the official python image tutorial, I have the following questions:
what is WORKDIR, does it mean to create a new directory where all files will be stored?
why my COPY command is not working?
how to publish my image to make it usable for the cluster?

Beginner here, from what i understood.
WORKDIR Is work directory for other commands as RUN, CMD, COPY or ADD.
Don't know. I will double check directories paths.
Don't know. Normally i'am using dockerhub

Related

Copy file from dockerfile build to host - bandit

I just started learning docker. To teach myself, I managed to containerize bandit (a python code scanner) but I'm not able to see the output of the scan before the container destroys itself. How can I copy the output file from inside the container to the host, or otherwise save it?
Right now i'm just using bandit to scan itself basically :)
Dockerfile
FROM python:3-alpine
WORKDIR /
RUN pip install bandit
RUN apk update && apk upgrade
RUN apk add git
RUN git clone https://github.com/PyCQA/bandit.git ./code-to-scan
CMD [ "python -m bandit -r ./code-to-scan -o bandit.txt" ]
You can mount a volume on you host where you can share the output of bandit.
For example, you can run your container with:
docker run -v $(pwd)/output:/tmp/output -t your_awesome_container:latest
And you in your dockerfile:
...
CMD [ "python -m bandit -r ./code-to-scan -o /tmp/bandit.txt" ]
This way the bandit.txt file will be found in the output folder.
Better place the code in your image not in the root directory.
I did some adjustments to your Dockerfile.
FROM python:3-alpine
WORKDIR /usr/myapp
RUN pip install bandit
RUN apk update && apk upgrade
RUN apk add git
RUN git clone https://github.com/PyCQA/bandit.git .
CMD [ "bandit","-r",".","-o","bandit.txt" ]`
This clones git in your WORKDIR.
Note the CMD, it is an array, so just devide all commands and args as in the Dockerfile about.
I put the the Dockerfile in my D:\test directory (Windows).
docker build -t test .
docker run -v D:/test/:/usr/myapp test
It will generate you bandit.txt in the test folder.
After the code is execute the container exits, as there are nothing else to do.
you can also put --rm to remove the container once it finishs.
docker run --rm -v D:/test/:/usr/myapp test

How to use "colcon build" in a Dockerfile?

I am trying to create a docker image based on ubuntu:20.04 where I want to install ROS2, ignition gazebo and the ROS2-ign-bridge with a Dockerfile.
The installation of ROS2 and ign work without any issue but during the bridge installation I need to use colcon. Heres that part from the Dockerfile:
## install ROS2 ignition gazebo bridge
RUN export IGNITION_VERSION=edifice
RUN mkdir -p ros_ign_bridge_ws/src
RUN git clone https://github.com/osrf/ros_ign.git -b foxy ros_ign_bridge_ws/src
WORKDIR ros_ign_bridge_ws
RUN rosdep install -r --from-paths src -i -y --rosdistro foxy
RUN colcon build
RUN source ros_ign_bridge_ws/install/setup.bash
RUN echo "source ros_ign_bridge_ws/install/setup.bash" >> ~/.bashrc
It fails during the colcon build step when I use
docker build -f Dockerfiles/companion_base.Dockerfile -t companion_base .
, but when I run the image created up to that step
docker run -it c125a17c2f68 /bin/bash
and then execute colcon build inside the container it works without any issue.
So what is the difference between RUN colcon build and running colcon build inside the container ?
The issue was that when you source something in a previous docker build step, it isn't available in the next step. So what I needed to do was do the sourcing and building in the same step:
RUN /bin/bash -c "source /opt/ros/foxy/setup.bash; colcon build"

Run protoc command into docker container

I'm trying to run protoc command into a docker container.
I've tried using the gRPC image but protoc command is not found:
/bin/sh: 1: protoc: not found
So I assume I have to install manually using RUN instructions, but is there a better solution? An official precompiled image with protoc installed?
Also, I've tried to install via Dockerfile but I'm getting again protoc: not found.
This is my Dockerfile
#I'm not using "FROM grpc/node" because that image can't unzip
FROM node:12
...
# Download proto zip
ENV PROTOC_ZIP=protoc-3.14.0-linux-x86_32.zip
RUN curl -OL https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/${PROTOC_ZIP}
RUN unzip -o ${PROTOC_ZIP} -d ./proto
RUN chmod 755 -R ./proto/bin
ENV BASE=/usr/local
# Copy into path
RUN cp ./proto/bin/protoc ${BASE}/bin
RUN cp -R ./proto/include/* ${BASE}/include
RUN protoc -I=...
I've done RUN echo $PATH to ensure the folder is in path and is ok:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Also RUN ls -la /usr/local/bin to check protoc file is into the folder and it shows:
-rwxr-xr-x 1 root root 4849692 Jan 2 11:16 protoc
So the file is in /bin folder and the folder is in the path.
Have I missed something?
Also, is there a simple way to get the image with protoc installed? or the best option is generate my own image and pull from my repository?
Thanks in advance.
Edit: Solved downloading linux-x86_64 zip file instead of x86_32. I downloaded the lower architecture requirements thinking a x86_64 machine can run a x86_32 file but not in the other way. I don't know if I'm missing something about architecture requirements (It's probably) or is a bug.
Anyway in case it helps someone I found the solution and I've added an answer with the neccessary Dockerfile to run protoc and protoc-gen-grpc-web.
The easiest way to get non-default tools like this is to install them through the underlying Linux distribution's package manager.
First, look at the Docker Hub page for the node image. (For "library" images like node, construct the URL https://hub.docker.com/_/node.) You'll notice there that there are several variations named "alpine", "buster", or "stretch"; plain node:12 is the same as node:12-stretch and node:12.20.0-stretch. The "alpine" images are based on Alpine Linux; the "buster" and "stretch" ones are different versions of Debian GNU/Linux.
For Debian-based packages, you can then look up the package on https://packages.debian.org/ (type protoc into the "Search the contents of packages" form at the bottom of the page). That leads you to the protobuf-compiler package. Knowing that contains the protoc binary, you can install it in your Dockerfile with:
FROM node:12 # Debian-based
RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive \
apt-get install --no-install-recommends --assume-yes \
protobuf-compiler
# The rest of your Dockerfile as above
COPY ...
RUN protoc ...
You generally must run apt-get update and apt-get install in the same RUN command, lest a subsequent rebuild get an old version of the package cache from the Docker build cache. I generally have only a single apt-get install command if I can manage it, with the packages list alphabetically one to a line for maintainability.
If the image is Alpine-based, you can do a similar search on https://pkgs.alpinelinux.org/contents to find protoc, and similarly install it:
FROM node:12-alpine
RUN apk add --no-cache protoc
# The rest of your Dockerfile as above
Finally I solved my own issue.
The problem was the arch version: I was using linux-x86_32.zip but works using linux-x86_64.zip
Even #David Maze answer is incredible and so complete, it didn't solve my problem because using apt-get install version 3.0.0 and I wanted 3.14.0.
So, the Dockerfile I have used to run protoc into a docker container is like this:
FROM node:12
...
# Download proto zip
ENV PROTOC_ZIP=protoc-3.14.0-linux-x86_64.zip
RUN curl -OL https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/${PROTOC_ZIP}
RUN unzip -o ${PROTOC_ZIP} -d ./proto
RUN chmod 755 -R ./proto/bin
ENV BASE=/usr
# Copy into path
RUN cp ./proto/bin/protoc ${BASE}/bin/
RUN cp -R ./proto/include/* ${BASE}/include/
# Download protoc-gen-grpc-web
ENV GRPC_WEB=protoc-gen-grpc-web-1.2.1-linux-x86_64
ENV GRPC_WEB_PATH=/usr/bin/protoc-gen-grpc-web
RUN curl -OL https://github.com/grpc/grpc-web/releases/download/1.2.1/${GRPC_WEB}
# Copy into path
RUN mv ${GRPC_WEB} ${GRPC_WEB_PATH}
RUN chmod +x ${GRPC_WEB_PATH}
RUN protoc -I=...
Because this is currently the highest ranked result on Google and the above instructions above won't work, if you want to use docker/dind for e.g. gitlab, this is the way how you can get the glibc-dependency working for protoc there:
#!/bin/bash
# install gcompat, because protoc needs a real glibc or compatible layer
apk add gcompat
# install a recent protoc (use a version that fits your needs)
export PB_REL="https://github.com/protocolbuffers/protobuf/releases"
curl -LO $PB_REL/download/v3.20.0/protoc-3.20.0-linux-x86_64.zip
unzip protoc-3.20.0-linux-x86_64.zip -d $HOME/.local
export PATH="$PATH:$HOME/.local/bin"

How to Edit Docker Image?

I did a basic search in the community and could not find a suitable answer, so I am asking here. Sorry if it was asked earlier.
Basically , I am working on a certain project and we keep changing code at a regular interval . So ,we need to build docker image everytime due to that we need to install dependencies from requirement.txt from scratch which took around 10 min everytime.
How can I perform direct change to docker image and also how to configure entrypoint(in Docker File) which reflect changes in Pre-Build docker image
You don't edit an image once it's been built. You always run docker build from the start; it always runs in a clean environment.
The flip side of this is that Docker caches built images. If you had image 01234567, ran RUN pip install -r requirements.txt, and got image 2468ace0 out, then the next time you run docker build it will see the same source image and the same command, and skip doing the work and jump directly to the output images. COPY or ADD files that change invalidates the cache for future steps.
So the standard pattern is
FROM node:10 # arbitrary choice of language
WORKDIR /app
# Copy in _only_ the requirements and package lock files
COPY package.json yarn.lock ./
# Install dependencies (once)
RUN yarn install
# Copy in the rest of the application and build it
COPY src/ src/
RUN yarn build
# Standard application metadata
EXPOSE 3000
CMD ["yarn", "start"]
If you only change something in your src tree, docker build will skip up to the COPY step, since the package.json and yarn.lock files haven't changed.
In my case, I was facing the same, after minor changes, i was building the image again and again.
My old DockerFile
FROM python:3.8.0
WORKDIR /app
# Install system libraries
RUN apt-get update && \
apt-get install -y git && \
apt-get install -y gcc
# Install project dependencies
COPY ./requirements.txt .
RUN pip install --upgrade pip
RUN pip install --no-cache-dir -r requirements.txt --use-deprecated=legacy-resolver
# Don't use terminal buffering, print all to stdout / err right away
ENV PYTHONUNBUFFERED 1
COPY . .
so what I did, created a base image file first like this (Avoided the last line, did not copy my code)
FROM python:3.8.0
WORKDIR /app
# Install system libraries
RUN apt-get update && \
apt-get install -y git && \
apt-get install -y gcc
# Install project dependencies
COPY ./requirements.txt .
RUN pip install --upgrade pip
RUN pip install --no-cache-dir -r requirements.txt --use-deprecated=legacy-resolver
# Don't use terminal buffering, print all to stdout / err right away
ENV PYTHONUNBUFFERED 1
and then build this image using
docker build -t my_base_img:latest -f base_dockerfile .
then the final Dockerfile
FROM my_base_img:latest
WORKDIR /app
COPY . .
And as my from this image, I was not able to up the container, issues with my copied python code, so you can edit the image/container code, to fix the issues in the container, by this mean i avoided the task of building images again and again.
When my code got fixed, I copied the changes from container to my code base and then finally, I created the final image.
There are 4 Steps
Start the image you want to edit (e.g. docker run ...)
Modify the running image by shelling into it with docker exec -it <container-id> (you can get the container id with docker ps)
Make any modifications (install new things, make a directory or file)
In a new terminal tab/window run docker commit c7e6409a22bf my-new-image (substituting in the container id of the container you want to save)
An example
# Run an existing image
docker run -dt existing_image
# See that it's running
docker ps
# CONTAINER ID IMAGE COMMAND CREATED STATUS
# c7e6409a22bf existing-image "R" 6 minutes ago Up 6 minutes
# Shell into it
docker exec -it c7e6409a22bf bash
# Make a new directory for demonstration purposes
# (note that this is inside the existing image)
mkdir NEWDIRECTORY
# Open another terminal tab/window, and save the running container you modified
docker commit c7e6409a22bf my-new-image
# Inspect to ensure it saved correctly
docker image ls
# REPOSITORY TAG IMAGE ID CREATED SIZE
# existing-image latest a7dde5d84fe5 7 minutes ago 888MB
# my-new-image latest d57fd15d5a95 2 minutes ago 888MB

Changing RUN to CMD stops the container from working

I am trying to add Glide to my Golang project but I'm not getting my container working. I am currently using:
# create image from the official Go image
FROM golang:alpine
RUN apk add --update tzdata bash wget curl git;
# Create binary directory, install glide and fresh
RUN mkdir -p $$GOPATH/bin
RUN curl https://glide.sh/get | sh
RUN go get github.com/pilu/fresh
# define work directory
ADD . /go
WORKDIR /go/src
RUN glide update && fresh -c ../runner.conf main.go
as per #craigchilds94's post. When I run
docker build -t docker_test .
It all works. However, when I change the last line from RUN glide ... to CMD glide ... and then start the container with:
docker run -it --volume=$(PWD):/go docker_test
It gives me an error: /bin/sh: glide: not found. Ignoring the glide update and directly starting fresh results in the same: /bin/sh fresh: not found.
The end goal is to be able to mount a volume (for the live-reload) and be able to use it in docker-compose so I want to be able to build it, but I do not understand what is going wrong.
This should probably work for your purposes:
# create image from the official Go image
FROM golang:alpine
RUN apk add --update tzdata bash wget curl git;
# Create binary directory, install glide and fresh
RUN go get -u github.com/Masterminds/glide
RUN go get -u github.com/pilu/fresh
# define work directory
ADD . /go
WORKDIR /go/src
ENTRYPOINT $GOPATH/bin/fresh -c /go/src/runner.conf /go/src/main.go
As far as I know you don't need to run the glide update after you've just installed glide. You can check this Dockerfile I wrote that uses glide:
https://github.com/timogoosen/dockerfiles/blob/master/btcd/Dockerfile
and here is the REAMDE: https://github.com/timogoosen/dockerfiles/blob/master/btcd/README.md
This article gives a good overview of the difference between: CMD, RUN and entrypoint: http://goinbigdata.com/docker-run-vs-cmd-vs-entrypoint/
To quote from the article:
"RUN executes command(s) in a new layer and creates a new image. E.g., it is often used for installing software packages."
In my opinion installing packages and libraries can happen with RUN.
For starting your binary or commands I would suggest use ENTRYPOINT see:"ENTRYPOINT configures a container that will run as an executable." you could use CMD too for running:
$GOPATH/bin/fresh -c /go/src/runner.conf /go/src/main.go
something like this might work, I didn't test this part:
CMD ["$GOPATH/bin/fresh", "-c", "/go/src/runner.conf /go/src/main.go"]

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