I'm trying to build a docker image that uses nvidia hardware decoding in gstreamer and have encountered a strange problem with making the image.
The build process does not find the nvidia cuda related stuff while running docker build (or nvidia-docker build), but when I spin up the failed image as a container and do those very same steps from within the container everything works. I even saved the container as image which gave me a persistent image that works as intended.
Has anyone experienced similar problem and can shed some light on it?
Dockerfile:
FROM nvcr.io/nvidia/deepstream:3.0-18.11 AS base
ENV DEBIAN_FRONTEND noninteractive
#install some dependencies. NOTE - not removing apt cache for the MWE
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential \
libdc1394-22 \
tmux \
vim \
libjpeg-dev \
libpng-dev \
libpng12-dev \
cuda-toolkit-10-0 \
python3-setuptools \
python3-pip ninja-build pkg-config gobject-introspection gnome-devel bison flex libgirepository1.0-dev liborc-0.4-dev
RUN pip3 install meson && ldconfig
FROM base
#pull and make gstreamer:
RUN cd /tmp && mkdir gstreamer
RUN git clone https://github.com/GStreamer/gst-build.git /tmp/gstreamer \
&& cd /tmp/gstreamer \
&& git checkout tags/1.16.0 \
&& ./setup.py -Dgtk_doc=disabled -Dgst-plugins-bad:nvdec=enabled -Dgst-plugins-bad:nvenc=enabled -Dgst-plugins-bad:iqa=disabled -Dgst-plugins-bad:bluez=disabled --reconfigure \
&& ninja -C build \
&& ninja install -C build
Testing:
build and run the container. Inside the container:
$ gst-inspect-1.0 nvdec
No such element or plugin 'nvdec'
$ cd /tmp/gstreamer
$ ./setup.py -Dgtk_doc=disabled -Dgst-plugins-bad:nvdec=enabled -Dgst-plugins-bad:nvenc=enabled -Dgst-plugins-bad:iqa=disabled -Dgst-plugins-bad:bluez=disabled --reconfigure
$ ninja -C build
$ ninja install -C build
$ gst-inspect-1.0 nvdec
Factory Details:
Rank primary (256)
[... all plugin parameters show up]
GObject
+----GInitiallyUnowned
+----GstObject
+----GstElement
+----GstVideoDecoder
+----GstNvDec
EDIT1
The image builds with no errors, only when I try to call gstreamer it is built with no acceleration. I noticed that in the build process the major difference is
meson.build:109:2: Exception: Problem encountered: The nvdec plugin was enabled explicitly, but required CUDA dependencies were not found.
which does not happen when building from within the container.
Lack of error is related, most likely, to the ninja+meson build system which looks for compatible packages, reports the exception, but doesn't throw it and continues as if nothing wrong happened
EDIT2
Answering comment:
To build it and get the error, just build the attached docker image:
sudo docker build -t gst16:latest . > build.log
This will dump all the output into the build.log file.
I don't have a docker registry that I could use for this and the docker image gets quite big by docker standards (~8 Gigs), but to produce successfully, it's fairly simple:
sudo docker run --runtime="nvidia" -ti gst16:latest /bin/bash
or
sudo nvidia-docker run -ti gst16:latest /bin/bash
which seems to work the same for me. Notice no --rm flag! From within the container:
#check if nvidia decoder plugin is there:
gst-inspect-1.0 nvdec
#fail!
#now build it from within:
cd /opt/gstreamer
./setup.py -Dgtk_doc=disabled -Dgst-plugins-bad:nvdec=enabled -Dgst-plugins-bad:nvenc=enabled -Dgst-plugins-bad:iqa=disabled -Dgst-plugins-bad:bluez=disabled --reconfigure
ninja -C build
ninja install -C build
gst-inspect-1.0 nvdec
#success reported
Now to get the image, exit the container (ctrl+d) and in the host shell:
sudo docker container ls -a to view all containers including stopped ones
from gst16:latest get the CONTAINER_ID and copy it
sudo docker commit <CONTAINER_ID> gst16:manual and after a few seconds you should have the container saved as an image. Verify with sudo docker images
run the new image with sudo docker run --runtime=`nvidia` --rm -ti gst16:manual /bin/bash
from within the container try again the gst-inspect-1.0 nvdec to verify it's working
EDIT3
$ nvidia-docker --version
Docker version 18.09.0, build 4d60db4
I think I found the solution/reason
Writing it here in case someone finds themselves in similar situation, plus I hate finding old threads with similar problem and no answer or "nevermind, I solved it" as the only follow up
Docker build does not have any ties to nvidia runtime and gstreamer requires access to the full nvidia toolchain in order to build the plugins that need it. This is to be resolved with gstreamer 1.18 but until then, there is no way to build gstreamer with nvidia codecs in docker build.
The workaround:
Build image with all dependencies.
Run a container of said image using runtime="nvidia" but don't use --rm flag
In the container, build gstreamer and install it as normally.
Verify with gst-inspect-1.0
Commit the container as new image: docker commit <container_name> <temporary_image_name>
Tag the temporary image properly.
Related
EDIT: documentation given by the informatic administration was shitty, old version of singularity, now the order of arguments is different and the problem is solved.
To make my tool more portable, and because I have to use it on a cluster, I have to put my bioinformatics tool at disposal for docker. Tool is located here. The docker hub is 007ptar007/metadbgwas, if you want to experience with it. The Dockerfile is in the repo, and to make it easier to everyone :
FROM ubuntu:latest
ENV DEBIAN_FRONTEND=noninteractive
USER root
COPY ./install_docker.sh ./
RUN chmod +x ./install_docker.sh && sh ./install_docker.sh
ENTRYPOINT ["/MetaDBGWAS/metadbgwas.sh"]
ENV PATH="/MetaDBGWAS/:${PATH}"
And the install_docker.sh script contains :
apt-get update
apt install -y libgatbcore-dev libhdf5-dev libboost-all-dev libpstreams-dev zlib1g-dev g++ cmake git r-base-core
Rscript -e "install.packages(c('ape', 'phangorn'))"
Rscript -e "install.packages('https://raw.githubusercontent.com/sgearle/bugwas/master/build/bugwas_1.0.tar.gz', repos=NULL, type='source')"
git clone --recursive https://github.com/Louis-MG/MetaDBGWAS.git
cd MetaDBGWAS
sed -i "51i#include <limits>" ./REINDEER/blight/robin_hood.h #temporary fix for REINDEER compilation
sh install.sh
The problem :
My tool parses the command line, and needs a verbose (-v, or --verbose) argument. It also needs to reject unknown arguments; anything that isn't used by the tool causes the help message to be printed in the standard output and exits. To use the tool, I need to mount volumes were the data is; using -v /path/to/files:/input option:
singularity run docker://007ptar007/metadbgwas --volumes '/path/to/data:/inputd/:/input' --files /input --strains /input/strains --threads 8 --output ~/output
But my tool sees this as a bad -v option value or the --volume as an unknown option. I can't change this on my tool. How do I solve this conflict ?
You need to put any arguments intended for singularity - such as the volume mounting - before the name of the image you want to run (e.g. the docker image you specify in your command):
singularity run -v '/path/to/data:/input' docker://007ptar007/metadbgwas --files /input --strains /input/strains --threads 8 --output ~/output
I have set up a docker image and install ubuntu on it. Can you please tell me how can I install Openmodelica inside ubuntu to that docker image?
for example, if I want to install node.js on this docker image I could use this code:
apt install nodejs
so I need some codes like that to install open Modelica on my docker image.
p.s: my docker image is an ubuntu image.
I happened to create a Docker image for OpenModelica to debug something, so I might add it here as well. We got this questions in the OpenModelica forum as well.
While the answer of #sjoelund.se will stay up to date this one is a bit more explaining.
Dockerfile
FROM ubuntu:18.04
# Export DISPLAY, so a XServer can display OMEdit
ARG DEBIAN_FRONTEND=noninteractive
ENV DISPLAY=host.docker.internal:0.0
# Install wget, gnupg, lsb-release
RUN apt-get update \
&& apt install -y wget gnupg lsb-release
# Get the OpenModelica stable version
RUN for deb in deb deb-src; do echo "$deb http://build.openmodelica.org/apt `lsb_release -cs` stable"; done | tee /etc/apt/sources.list.d/openmodelica.list
RUN wget -q http://build.openmodelica.org/apt/openmodelica.asc -O- | apt-key add -
# Install OpenModelica
RUN apt-get update \
&& apt install -y openmodelica
# Install OpenModelica libraries (like all of them)
RUN for PKG in `apt-cache search "omlib-.*" | cut -d" " -f1`; do apt-get install -y "$PKG"; done
# Add non-root user for security
RUN useradd -m -s /bin/bash openmodelicausers
USER openmodelicausers
ENV HOME /home/openmodelicausers
ENV USER openmodelicausers
WORKDIR $HOME
# Return omc version
CMD ["omc", "--version"]
Let's build and tag it:
docker build --tag openmodelica:ubuntubionic .
How to use omc from the docker image
Let's create a small helloWorld.mo Modelica model:
model helloWorld
Real x(start=1.0, fixed=true);
equations
der(x) = 2.5*x;
end helloWorld;
and a MOS script which will simulate it, called runHelloWorld.mos
loadFile("helloWorld.mo"); getErrorString();
simulate(helloWorld); getErrorString();
Now we can make our files accessible to the docker container with the -v flag and run our small example with:
docker run \
--rm \
-v $(pwd):/home/openmodelicausers \
openmodelica:ubuntubionic \
omc runHelloWorld.mos
Note that -v needs an absolute path. I added --rm to clean up.
Using OMEdit with a GUI
I'm using Windows + Docker with WSL2. So in order to get OMEdit running I need to have a XServer installed on my Windows host system. They are not trivial to set up, but I'm using VcXsrv and so far it is working for me. On Linux this is of course much simpler.
I'm using this config to start XLaunch:
<?xml version="1.0" encoding="UTF-8"?>
<XLaunch WindowMode="MultiWindow" ClientMode="NoClient" LocalClient="False" Display="-1" LocalProgram="xcalc" RemoteProgram="xterm" RemotePassword="" PrivateKey="" RemoteHost="" RemoteUser="" XDMCPHost="" XDMCPBroadcast="False" XDMCPIndirect="False" Clipboard="True" ClipboardPrimary="True" ExtraParams="" Wgl="True" DisableAC="True" XDMCPTerminate="False"/>
But when the XServer is running you can use OMEdit in nearly the same fashion you would from a Linux OS, just mount some directory with your files and that's it:
docker run \
--rm \
-v $(pwd):/home/openmodelicausers \
openmodelica:ubuntubionic \
OMEdit
You could get some inspiration from the Dockerfiles that are used to generate the OpenModelica docker images. For example: https://github.com/OpenModelica/OpenModelicaDockerImages/tree/v1.16.2
I have a problem to use the docker rstudio-image rocker/rstudio proposed
on https://www.rocker-project.org/ (docker containers for R). Since I am a beginner with both docker and RStudio, I suspect the problem comes from me and does not deserve a bug report:
I open a proper terminal with 'Docker Quickstart Terminal'
where I run the image with docker run -d -p 8787:8787 -e DISABLE_AUTH=true -v <...>:/home/rstudio/<...> --name rstudio rocker/rstudio
in my browser I then get a nice RStudio instance at the address http://192.168.99.100:8787
but in this instance I can't install several packages such as xml2. I get the message:
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
* deb: libxml2-dev (Debian, Ubuntu, etc)
* rpm: libxml2-devel (Fedora, CentOS, RHEL)
* csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/usr/local/lib/R/site-library/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
I don't know whether xml2 is on the image but the file libxml-2.0.pc does exist on my laptop in the directory /opt/local/lib/pkgconfig and pkg-config is in /opt/local/bin. So I tried linking these pkg paths when running
the image (to see what happen when I play with the image environment
in RStudio), adding options -v
/opt/local/lib/pkgconfig:/home/rstudio/lib/pkgconfig -v
/opt/local/bin:/home/rstudio/bin to the run command. But it doesn't work: for some reason
I don't see the content of lib/pkgconfig in RStudio...
Also the RStudio instance does not accept root/sudo commands so I can't
use tools such as apt-get in the RStudio terminal
so, what's the trick ?
Libraries on your laptop (the host for docker) are not available for docker containers. You should create a custom image with required libraries, create a Dockerfile like this:
FROM rocker/rstudio
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libxml2-dev # add any additional libraries you need
CMD ["/init"]
Above I added the libxml2-dev but you can add as many libraries as you need.
Then build your image using this command (you need to execute below command in directory there you created Dockerfile):
docker build -t my_rstudio:0.1 .
Then you can start your container:
docker run -d -p 8787:8787 -e DISABLE_AUTH=true --name rstudio my_rstudio:0.1
(you can add any additional arguments like -v to above).
I want to isolate a testing environment in docker, I did that on CentOS 6 How to let syslog workable in docker?
In CentOS 7, the syslog-ng's configuration is different, when I run
/usr/sbin/syslog-ng -F -p /var/run/syslogd.pid
It appears the following error message, but there is no proc/kmsg in config files.
syslog-ng: Error setting capabilities, capability management disabled; error='Operation not permitted'
Error opening file for reading; filename='/proc/kmsg', error='Operation not permitted (1)'
The Dockerfile
FROM centos
RUN yum update --exclude=systemd -y \
&& yum install -y yum-plugin-ovl \
&& yum install -y epel-release
RUN yum install -y syslog-ng syslog-ng-libdbi
The test process:
docker build -t t1 .
docker run --rm -i -t t1 /bin/bash
In container, run following commands
# check config, no keyword like proc/kmsg
cd /etc/syslog-ng
grep -r -E 'proc|kmsg'
/usr/sbin/syslog-ng -F -p /var/run/syslogd.pid
Change /etc/syslog-ng/syslog-ng.conf from
source s_sys {
system();
internal();
};
to
source s_sys {
unix-stream("/dev/log");
internal();
};
It still show error message, but running instead of exit
syslog-ng: Error setting capabilities, capability management disabled; error='Operation not permitted'
To solve this, just run with --no-caps option
/usr/sbin/syslog-ng --no-caps -F -p /var/run/syslogd.pid
I'm configuring a bamboo build plan to build docker images. Using AWS ECS as registry. Build plan is something like this;
pull the latest tag
docker pull xxx.dkr.ecr.eu-west-1.amazonaws.com/myimage:latest
build image with latest tag
docker build -t myimage:latest .
tag the image (necessary for ECS)
docker tag -f myimage:latest xxx.dkr.ecr.eu-west-1.amazonaws.com/myimage:latest
Push the image to the registry
docker push xx.dkr.ecr.eu-west-1.amazonaws.com/myimage:latest
Because build tasks run on different and fresh build engines/servers every time, It doesn't have local cache.
When I don't change anything at Dockerfile and execute it again(at another server), I would expect docker to use local cache(comes from docker pull) and doesn't execute each line again. But it tries to build image everytime. I was also expecting that when I change something at the bottom of the file, it's going to use cache and executes only the latest line, but I'm not sure about this.
Do I know something wrong or are there any opinions on approach?
are you considering using squid proxy
?
edit : in case you dont want to go to the official website above, here is quick setup on squid proxy (debian based)
apt-get install squid-deb-proxy
and then change the squid configuration to create a larger space by open up
/etc/squid/squid.conf
and replace #cache_dir ufs /var/spool/squid with cache_dir ufs /var/spool/
squid 10000 16 256
and there you go,, a 10.000 MB worth of cache space
and then point the proxy address in dockerfile,,
here is a example of dockerfile with squid proxy
yum and apt-get based distro:
apt-get based distro
`FROM debian
RUN apt-get update -y && apt-get install net-tools
RUN echo "Acquire::http::Proxy \"http://$( \
route -n | awk '/^0.0.0.0/ {print $2}' \
):8000\";" \ > /etc/apt/apt.conf.d/30proxy
RUN echo "Acquire::http::Proxy::ppa.launchpad.net DIRECT;" >> \
/etc/apt/apt.conf.d/30proxy
CMD ["/bin/bash"]`
yum based distro
`FROM centos:centos7
RUN yum update -y && yum install -y net-tools
RUN echo "proxy=http://$(route -n | \
awk '/^0.0.0.0/ {print $2}'):3128" >> /etc/yum.conf
RUN sed -i 's/^mirrorlist/#mirrorlist/' \
/etc/yum.repos.d/CentOS-Base.repo
RUN sed -i 's/^#baseurl/baseurl/' \
/etc/yum.repos.d/CentOS-Base.repo
RUN rm -f /etc/yum/pluginconf.d/fastestmirror.conf
RUN yum update -y
CMD ["/bin/bash"]`
lets say you install squid proxy in your aws registry,,only the first build would fetch the data from the internet the rest (another server) build should be from the squid proxy cached. .
this technique based on book docker in practice technique 57 with tittle set up a package cache for faster build
i dont think there is a cache feature in docker without any third party software.. maybe there is and i just dont know it. .im not sure,,
just correct me if im wrong. .