I have a Dockerfile that installs Julia and some dependencies, then call a script.
The 1st line of the script is "using JSServe" which should be installed.
# Runs ubuntu commands
FROM ubuntu
# Install wget and other
RUN apt-get update && \
apt-get install -y wget && \
apt-get install -y tar
# Downloads and install julia
ENV JULIA_NAME "julia-1.9.0-beta2-linux-x86_64.tar.gz"
RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/${JULIA_NAME} && \
tar -xvzf ${JULIA_NAME} && \
mv julia-1.9.0-beta2 /opt/ && \
ln -s /opt/julia-1.9.0-beta2/bin/julia /usr/local/bin/julia && \
rm ${JULIA_NAME}
# Copy files
COPY Project.toml ./Project.toml
COPY JSServe_app.jl ./JSServe_app.jl
# Install deps
RUN julia --project -e "import Pkg; Pkg.instantiate(); Pkg.precompile()"
# Run apps
CMD julia --project -e 'include("JSServe_app.jl")'
This works perfectly locally.
But on a remote server (Heroku), I get the following error:
Starting process with command `/bin/sh -c julia\ -e\ \'include\(\"JSServe_app.jl\"\)\'`
ERROR: LoadError: ArgumentError: Package JSServe not found in current path.
I don't understand why... JSServe should be installed - Docker build does work locally.
All files can be seen on GitHub https://github.com/AlexisRenchon/app-wglmakie-fig
I tried to install the dependencies in my Docker image, it worked locally, but not on the Heroku remote server.
EDIT:
looks like the problem is packages installed are removed somehow...
2023-01-31T14:38:11.444805+00:00 heroku[web.1]: Starting process with command `/bin/sh -c julia\ --project\=.\ -e\ \"import\ Pkg\;\ Pkg.status\(\)\"`
2023-01-31T14:38:13.572537+00:00 app[web.1]: Installing known registries into `~/.julia`
2023-01-31T14:38:17.410042+00:00 heroku[web.1]: Process exited with status 0
2023-01-31T14:38:17.466348+00:00 heroku[web.1]: State changed from starting to crashed
2023-01-31T14:38:17.176302+00:00 app[web.1]: Status `~/Project.toml`
2023-01-31T14:38:17.212226+00:00 app[web.1]: → [824d6782] JSServe v2.1.0
2023-01-31T14:38:17.212346+00:00 app[web.1]: → [276b4fcb] WGLMakie v0.8.6
2023-01-31T14:38:17.212445+00:00 app[web.1]: Info Packages marked with → are not downloaded, use `instantiate` to download
I think you're missing the --project=., notice the =.
Ok I got it to work:
# Runs ubuntu commands
FROM ubuntu
# Install wget and other
RUN apt-get update && \
apt-get install -y wget && \
apt-get install -y tar
# Downloads and install julia
ENV JULIA_NAME "julia-1.9.0-beta2-linux-x86_64.tar.gz"
RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/${JULIA_NAME} && \
tar -xvzf ${JULIA_NAME} && \
mv julia-1.9.0-beta2 /opt/ && \
ln -s /opt/julia-1.9.0-beta2/bin/julia /usr/local/bin/julia && \
rm ${JULIA_NAME}
ENV mainpath ./
RUN mkdir -p ${mainpath}
USER ${NB_USER}
ENV USER_HOME_DIR /home/${NB_USER}
ENV JULIA_PROJECT ${USER_HOME_DIR}
ENV JULIA_DEPOT_PATH ${USER_HOME_DIR}/.julia
# Copy files
COPY Project.toml ${mainpath}/Project.toml
COPY JSServe_app.jl ${mainpath}/JSServe_app.jl
# Install deps
RUN julia --project=${mainpath} -e "import Pkg; Pkg.instantiate(); Pkg.precompile()"
# Run apps
CMD julia --project=${mainpath} -e 'include("JSServe_app.jl")'
Related
I have the following Dockerfile:
FROM --platform=linux/x86_64 nvidia/cuda:11.7.0-devel-ubuntu20.04
COPY app ./app
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get -y upgrade && apt-get install -y apt-utils
RUN apt-get install -y \
net-tools iputils-ping \
build-essential cmake git \
curl wget vim \
zip p7zip-full p7zip-rar \
imagemagick ffmpeg \
libomp5
# RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
COPY Miniconda3-latest-Linux-x86_64.sh .
RUN chmod guo+x Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3
RUN export PATH=~/miniconda3/bin:$PATH
RUN conda --version
RUN conda update -n base conda
RUN conda create -y --name servier python=3.6
RUN conda activate servier
RUN conda install -c conda-forge rdkit
CMD ["bash"]
When I run: docker image build -t image_test_cuda2 . it breaks in the RUN conda --version.
The error is RUN conda --version: ... /bin/sh: 1: conda: not found. The problem is that RUN export PATH=~/miniconda3/bin:$PATH is not working. It is not creating conda link in the PATH.
If I build the image until RUN bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/miniconda3 and manually I get access to the container using docker exec -it <id> /bin/bash and then from the #/ manually I run the same command #/export PATH=~/miniconda3/bin:$PATH it works good. If I manually run the next command inside the container RUN conda update -n base conda it works good.
The conclusion is that it seems that the command RUN export PATH=~/miniconda3/bin:$PATH is not working in Dockerfile - docker image build. How to solve this issue?
I have RStudio in docker, and am trying to save a plotly image using orca. I installed orca following Docker and Plotly.
I build and start successfully, and to check if I can save an image I run:
library(plotly)
library(processx)
fig <- plot_ly(z = ~volcano) %>% add_surface()
orca(fig,"t.png")
Whereupon I receive the following error:
Error in `processx::run("orca", "-h")`:
! System command 'orca' failed
---
Exit status: 127
Stderr: <empty>
---
Type .Last.error to see the more details.
Warning message:
'orca' is deprecated.
Use 'kaleido' instead.
See help("Deprecated")
> .Last.error
<system_command_status_error/rlib_error_3_0/rlib_error/error>
Error in `processx::run("orca", "-h")`:
! System command 'orca' failed
---
Exit status: 127
Stderr: <empty>
---
Backtrace:
1. plotly::orca(fig, "t.png")
2. plotly:::orca_available()
3. plotly:::correct_orca()
4. processx::run("orca", "-h")
5. processx:::throw(new_process_error(res, call = sys.call(), echo = echo, …
>
Is there another way to install orca, or save a plotly image in RStudio running in docker?
My full dockerfile:
FROM rocker/verse
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends build-essential libpq-dev python3.9 python3-pip python3-setuptools python3-dev
RUN pip3 install --upgrade pip
ADD . ./home/rstudio
ADD requirements.txt .
ADD install_packages.r .
# Miniconda and dependencies
RUN cd /tmp/ && \
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 && \
/root/miniconda3/condabin/conda install -y python=3.7
ENV PATH=$PATH:/root/miniconda3/bin
#RUN npm install phantomjs-prebuilt --phantomjs_cdnurl=http://cnpmjs.org/downloads
# installing python libraries
RUN pip3 install -r requirements.txt
# installing r libraries
RUN Rscript install_packages.r
RUN if ! [[ "16.04 18.04 20.04 21.04 21.10" == *"$(lsb_release -rs)"* ]]; \
then \
echo "Ubuntu $(lsb_release -rs) is not currently supported."; \
exit; \
fi
RUN sudo su
RUN apt-get update && apt-get install -y gnupg2
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/$(lsb_release -rs)/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN exit
RUN sudo apt-get update
RUN sudo ACCEPT_EULA=Y apt-get install -y msodbcsql17
RUN chmod -R 777 /home/rstudio
# Download orca AppImage, extract it, and make it executable under xvfb
RUN apt-get install --yes xvfb libgconf-2-4
RUN wget https://github.com/plotly/orca/releases/download/v1.1.1/orca-1.1.1-x86_64.AppImage -P /home
RUN chmod 777 /home/orca-1.1.1-x86_64.AppImage
# To avoid the need for FUSE, extract the AppImage into a directory (name squashfs-root by default)
RUN cd /home && /home/orca-1.1.1-x86_64.AppImage --appimage-extract
RUN printf '#!/bin/bash \nxvfb-run --auto-servernum --server-args "-screen 0 640x480x24" /home/squashfs-root/app/orca "$#"' > /usr/bin/orca
RUN chmod 777 /usr/bin/orca
RUN chmod -R 777 /home/squashfs-root/
I am using Poetry to install a python project using Poetry in a Docker container. Below you can find my Docker file, which used to work fine until recently when I switched to a new version of Poetry (1.2.1) and the new recommended Poetry installer:
# pull official base image
FROM ubuntu:20.04
ENV PATH = "${PATH}:/home/poetry/bin"
ENV APP_HOME=/home/app/web
RUN apt-get -y update && \
apt upgrade -y && \
apt-get install -y \
python3-pip \
curl \
netcat \
gunicorn && \
rm -fr /var/lib/apt/lists
# alias python2 to python3
RUN ln -s /usr/bin/python3 /usr/bin/python
# Install Poetry
RUN mkdir -p /home/poetry && \
curl -sSL https://install.python-poetry.org | POETRY_HOME=/home/poetry python -
# Cleanup
RUN apt-get remove -y curl && \
apt-get clean
RUN pip install --upgrade pip && \
pip install cryptography && \
pip install psycopg2-binary
# create directory for the app user
# create the app user
# create the appropriate directories
RUN adduser --system --group app && \
mkdir -p $APP_HOME/static-incdtim && \
mkdir -p $APP_HOME/mediafiles
# copy project
COPY . $APP_HOME
WORKDIR $APP_HOME
# Install Python packages
RUN poetry config virtualenvs.create false
RUN poetry install --only main
# copy entrypoint-prod.sh
COPY ./entrypoint.incdtim.prod.sh $APP_HOME/entrypoint.sh
RUN chmod a+x $APP_HOME/entrypoint.sh
# chown all the files to the app user
RUN chown -R app:app $APP_HOME
# change to the app user
USER app
# run entrypoint.prod.sh
ENTRYPOINT ["/home/app/web/entrypoint.sh"]
The poetry install works fine, I attached to a running container and run it myself and found that it works without problems. However, when I open a Python console and try to import a module (django) which is installed by the Poetry project, the module is not found. Please note that I am installing my project in the system environment (poetry config virtualenvs.create false). I verified, and there is only one version of python installed in the docker container. The specific error I get when trying to import a python module installed by Poetry is: ModuleNotFoundError: No module named xxxx
Although this is not an answer, it is too long to fit within the comment section. It is rather a piece of advice:
declare your ENV at the top of the Dockerfile to make it easier to read.
merge the multiple RUN commands together to avoid creating useless intermediate layers. In the particular case of apt-get install, this will also prevent you from installing a package which dates back from the first "apt-get update". Indeed, since the command line has not changed Docker will not re-execute the command and thus not refresh the package list..
avoid making a copy of all the files in "." when you previously copy some specific files to specific places..
Here, you Dockerfile could rather look like:
# pull official base image
FROM ubuntu:20.04
ENV PATH = "${PATH}:/home/poetry/bin"
ENV HOME=/home/app
ENV APP_HOME=/home/app/web
RUN apt-get -y update && \
apt upgrade -y && \
apt-get install -y \
python3-pip \
curl \
netcat \
gunicorn && \
rm -fr /var/lib/apt/lists
# alias python2 to python3
RUN ln -s /usr/bin/python3 /usr/bin/python
# Install Poetry
RUN mkdir -p /home/poetry && \
curl -sSL https://install.python-poetry.org | POETRY_HOME=/home/poetry python -
# Cleanup
RUN apt-get remove -y \
curl && \
apt-get clean
RUN pip install --upgrade pip && \
pip install cryptography && \
pip install psycopg2-binary
# create directory for the app user
# create the app user
# create the appropriate directories
RUN mkdir -p /home/app && \
adduser --system --group app && \
mkdir -p $APP_HOME/static-incdtim && \
mkdir -p $APP_HOME/mediafiles
WORKDIR $APP_HOME
# copy project
COPY . $APP_HOME
# Install Python packages
RUN poetry config virtualenvs.create false && \
poetry install --only main
# copy entrypoint-prod.sh
RUN cp $APP_HOME/entrypoint.incdtim.prod.sh $APP_HOME/entrypoint.sh && \
chmod a+x $APP_HOME/entrypoint.sh && \
chown -R app:app $APP_HOME
# change to the app user
USER app
# run entrypoint.prod.sh
ENTRYPOINT ["/home/app/web/entrypoint.sh"]
UPDATE:
Let's get back to your question. Having your program running okay when you "run it yourself" does not mean all the dependencies are met. Indeed, this can mean that your module has not been imported yet (and thus has not triggered the ModuleNotFoundError exception yet).
In order to validate this theory, you can either:
create a simple application which imports the failing module and then quits. If the import succeeds then there is something weird indeed.
list the installed modules with poetry show --latest. If the package is listed, then there is something weird indeed.
If none of the above indicates the module is installed, that just means the module is not installed and you should update your Dockerfile to install it.
NOTE: I do not know much about poetry, but you may want to have a list external dependencies to be met for your application. In the case of pip3, the list is expressed as a file named requirement.txt and can be installed with pip3 install -r requirement.txt.
It turns out this is known a bug in Poetry: https://github.com/python-poetry/poetry/issues/6459
I have a project running with meteor and node.js in my local. The meteor version is 2.4, node.js version is 8.9.4, I have meteor/release file to make meteor version be 2.2 so that meteor and node can work together.
(base) xxx$ meteor --version
Meteor 2.4
(base) xxx$ node -v
v8.9.4
It seems fine so I deploy this project to docker container to server. The Dockerfile first line I wrote
# node version dependent on meteor version
FROM node:8.9.4
After successfully deployed, the docker logs shows error siad.
Waiting for mongodb server to start - sleeping
warn: --minUptime not set. Defaulting to: 1000ms
warn: --spinSleepTime not set. Your script will exit if it does not stay up for at least 1000ms
info: Forever processing file: /app/bundle/main.js
error: undefined
data: /app/bundle/main.js:34 - Meteor requires Node v12.0.0 or later.
data: /app/bundle/main.js:34 - error: Forever detected script exited with code: 1
I check inside docker, the node version is 8.9.4
(base) [xxx]$ docker exec -it -u root tblbuilder_meteor_1 /bin/bash -c 'node --version'
v8.9.4
So I assume it is meteor version. But first I dont know how to check meteor version inside the docker. And second why this happens? I am sure the release file is updated to push project folder.
With some great man help, I kinda understand it. In local I use meteor 2.2, in docker file I use node.js 8.9.4 work with meteor2.2. So the thing I left is to modify DOCKERFILE, change it from node 8.9.4 to node 12. Below is my Dockerfile file, I try to change it to node 12.22.2, but it keep give me error, I spent one day to solve them. Currently, I stack at install r-base part.
Is there some guide for change node 8 to node 12.
# node version dependent on meteor version
FROM node:8.9.4
# I am going to use 12.22.2
#FROM node:12.22.2
# (even if copied as root you still need to change)
# https://github.com/moby/moby/issues/6119
COPY ./compose/meteor/entrypoint.sh /entrypoint.sh
COPY ./compose/meteor/run_app.sh /run_app.sh
COPY ./compose/meteor/r-cran.pgp /r-cran.pgp
COPY ./settings/settings.json /app/settings.json
COPY ./requirements.txt /requirements.txt
COPY ./r_requirements.sh /r_requirements.sh
# set locale to utf8: https://github.com/docker-library/docs/pull/703/files
# added [check-valid-until=no] & Acquire::Check-Valid-Until "false"; https://unix.stackexchange.com/questions/508724/failed-to-fetch-jessie-backports-repository
# Needs work to bring it up-to-date
RUN \
echo "deb [check-valid-until=no] http://archive.debian.org/debian jessie-backports main" > /etc/apt/sources.list.d/jessie-backports.list && \
sed -i '/deb http:\/\/deb.debian.org\/debian jessie-updates main/d' /etc/apt/sources.list && \
apt-get -o Acquire::Check-Valid-Until=false update && \
\
sh -c 'echo "deb [check-valid-until=no] http://cran.rstudio.com/bin/linux/debian jessie-cran35/" >> /etc/apt/sources.list' && \
apt-key add /r-cran.pgp && \
\
apt-get -o Acquire::Check-Valid-Until=false update && \
apt-get -o Acquire::Check-Valid-Until=false install -y locales && \
\
localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 && \
export LC_ALL=en_US.UTF-8 && \
export LANG=en_US.UTF-8 && \
export LANGUAGE=en_US.UTF-8
ENV LANG en_US.utf8
ENV LC_ALL en_US.UTF-8
# add rstudio debian install for R (requires version >3.3)
# https://cran.r-project.org/bin/linux/debian/
# install R from apt-get
# install python 3.6 from source :/
RUN apt install -y --force-yes r-base-core r-recommended r-base-html r-base-core
RUN apt-get install -y --force-yes wget bsdtar r-base r-base-dev && \
apt-get clean && \
\
wget https://www.python.org/ftp/python/3.6.5/Python-3.6.5.tgz && \
tar zxf Python-3.6.5.tgz && \
cd ./Python-3.6.5 && \
./configure && \
make && \
make altinstall && \
cd .. && \
rm Python-3.6.5.tgz && \
rm -rf ./Python-3.6.5
# create paths and users
# change executable permissions
RUN npm install forever -g && \
\
mkdir -p /app/production && \
mkdir -p /app/logs && \
mkdir -p /app/crons && \
\
groupadd -r app && \
useradd -m -d /home/app -g app app && \
\
chmod +x /entrypoint.sh && \
chmod +x /run_app.sh && \
chmod +x /r_requirements.sh && \
chmod +x /requirements.txt && \
\
chown -R app:app /app && \
chown app:app /entrypoint.sh && \
chown app:app /run_app.sh && \
chown app:app /r_requirements.sh &&\
chown app:app /requirements.txt
USER app
# 1) install R packages
# 2) install python packages
RUN export "R_LIBS=/home/app/R_libs" && \
mkdir /home/app/R_libs && \
bash /r_requirements.sh && \
\
/usr/local/bin/pip3.6 install --user -r /requirements.txt
USER root
COPY ./compose/meteor/src/src.tar.gz /app/src.tar.gz
COPY ./src/private /app/src/private
RUN chown -R app:app /app
USER app
RUN cd /app && \
bsdtar -xzvf src.tar.gz && \
npm install --prefix /app/bundle/programs/server --production
ENTRYPOINT ["/entrypoint.sh"]
There are many wrong understanding in your tests:
Your Meteor version is 2.2, because is the version inside your project;
To you see the Node version of this Meteor project, see this answers that many guys send to you in Meteor Docker Node.js version is not match
Usually, we build the Meteor, that mean transform it in a NodeJS package build, then, inside of the Docker you don't need Meteor.
We need see your Dockerfile and understand what process you do to build do Docker image.
I'm trying to learn Synatxnet. I have it running through Docker. But I really dont know much about either program Synatxnet or Docker. On the Github Sytaxnet page it says
The SyntaxNet models are configured via a combination of run-time
flags (which are easy to change) and a text format TaskSpec protocol
buffer. The spec file used in the demo is in
syntaxnet/models/parsey_mcparseface/context.pbtxt.
How exactly do I find the spec file to edit it?
I compiled SyntaxNet in a Docker container using these Instructions.
FROM java:8
ENV SYNTAXNETDIR=/opt/tensorflow PATH=$PATH:/root/bin
RUN mkdir -p $SYNTAXNETDIR \
&& cd $SYNTAXNETDIR \
&& apt-get update \
&& apt-get install git zlib1g-dev file swig python2.7 python-dev python-pip -y \
&& pip install --upgrade pip \
&& pip install -U protobuf==3.0.0b2 \
&& pip install asciitree \
&& pip install numpy \
&& wget https://github.com/bazelbuild/bazel/releases/download/0.2.2b/bazel-0.2.2b-installer-linux-x86_64.sh \
&& chmod +x bazel-0.2.2b-installer-linux-x86_64.sh \
&& ./bazel-0.2.2b-installer-linux-x86_64.sh --user \
&& git clone --recursive https://github.com/tensorflow/models.git \
&& cd $SYNTAXNETDIR/models/syntaxnet/tensorflow \
&& echo "\n\n\n" | ./configure \
&& apt-get autoremove -y \
&& apt-get clean
RUN cd $SYNTAXNETDIR/models/syntaxnet \
&& bazel test --genrule_strategy=standalone syntaxnet/... util/utf8/...
WORKDIR $SYNTAXNETDIR/models/syntaxnet
CMD [ "sh", "-c", "echo 'Bob brought the pizza to Alice.' | syntaxnet/demo.sh" ]
# COMMANDS to build and run
# ===============================
# mkdir build && cp Dockerfile build/ && cd build
# docker build -t syntaxnet .
# docker run syntaxnet
First, comment out the command line in the dockerfile, then create and cd into an empty directory on your host machine. You can then create a container from the image, mounting a directory in the container to your hard-drive:
docker run -it --rm -v /pwd:/tmp bash
You'll now have a bash session in the container. Copy the spec file into /tmp from /opt/tensorflow/syntaxnet/models/parsey_mcparseface/context.pbtxt (I'm guessing that's where it is given the info you've provided above -- I can't get your dockerfile to build an image so I can't confirm it; you can always run find . -name context.pbtxt from root to find it), and exit the container (ctrl-d or exit).
You now have the file on your host's hd ready to edit, but you really want it in a running container. If the directory it comes from contains only that file, then you can simply mount your host directory at that path in the container. If it contains other things, then you can use a, so called, bootstrap script to move the file from your mounted directory (in the example above, that's tmp) to its home location. Alternatively, you may be able to tell the software where to find the spec file with a flag, but that will take more research.