I want to build a container from my conda environment following this post. However, I get the following error: '/bin/sh: 1: cannot create ~/.bashrc: Directory nonexistent'. I am using a vagrant VM to build my image and would be grateful for any help.
Editing the .bashrc, aside from failing, will not be helpful as the shell loaded by singularity is explicitly --norc. You want to use the $SINGULARITY_ENVIRONMENT variable in %post to have the values available.
Something along these lines:
%post
# You may need to install some pre-reqs your host system has installed outside of conda, e.g.
# apt update && apt install -y build-essential make zlib
ENV_NAME=$(head -1 environment.yml | cut -d' ' -f2)
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate $ENV_NAME" >> $SINGULARITY_ENVIRONMENT
. /opt/conda/etc/profile.d/conda.sh
conda env create -f environment.yml -p /opt/conda/envs/$ENV_NAME
I listed a few libraries that you probably have installed in your current machine that might not be installed in the slim docker image. You can install them via apt or conda, depending on your preference. If it does happen though, it'll be specific to your environment.yml and host OS, so you'll have to iterate through until the build succeeds.
Related
I would like to build a singularity container for an application shipped via AppImage. To do so, I build the following def file:
Bootstrap: docker
From: debian:bullseye-slim
%post
apt-get update -y
apt-get install -y wget unzip fuse libglu1 libglib2.0-dev libharfbuzz-dev libsm6 dbus
cd /opt
wget https://www.ill.eu/fileadmin/user_upload/ILL/3_Users/Instruments/Instruments_list/00_-_DIFFRACTION/D3/Mag2Pol/Mag2Pol_v5.0.2.AppImage
chmod u+x Mag2Pol_v5.0.2.AppImage
%runscript
exec /opt/Mag2Pol_v5.0.2.AppImage
I build the container using singularity build -f test.sif test.def command. The build runs OK but when running the sif file using ./test.sif I get an /.singularity.d/runscript: 3: exec: /opt/Mag2Pol_v5.0.2.AppImage: Permission denied error. Looking inside the container using a singularity shell command shows that the /opt/Mag2Pol_v5.0.2.AppImage executable belongs to root. I guess that it is the source of the problem but I do not know how to solve it. Would you have any idea ?
I wrote a small test project for Singularity Compose, consisting of a small server application, with the following YAML file:
version: "1.0"
instances:
server:
build:
context: ./server
recipe: server.recipe
ports:
- 9999:9999
When I call singularity-compose build, it successfully builds server.sif. Calling singularity-compose up also seemingly works without error, and calling singularity-compose ps results in something that looks just fine:
+ singularity-compose ps
INSTANCES NAME PID IMAGE
1 server 4176911 server.sif
However, the server application does not work, calling my test client results in it saying that there is no answer from the server.
But if I run server.sif directly without compose, everything works just fine.
Also, I tripple checked, my test application listens to port 9999, thus should be reachable from the outside.
What did I do wrong?
Edit:
I also checked whether there actually is any process listening at port 9999 by calling sudo lsof -i -P -n | grep LISTEN, this is not the case. Only when I manually start server.sif without compose it shows me the process listening.
Edit:
I went into the Singularity Compose shell and tried to start the Server application directly in there, just as a test, and it resulted in Permission denied. Not sure if that means anything.
Edit:
I now gave the application execution rights within the shell and called in there, this works. Am now trying to add execution rights in the recipe. If that works, it would be kind of strange, as the executable was build right there, and thus should already have execution rights.
Edit:
I added chmod +x in my recipe both after building Server and before executing it. Doesn't work either.
Also checked whether any bridges exist using brctl show, this is not the case.
Edit: My recipe, adjusted by the input of tsnowlan in his answer below:
Bootstrap: docker
From: ubuntu:20.04
%files
connection.cpp
connection.h
main.cpp
server.cpp
server.h
server.pro
%post
# get some basics
apt update
apt-get install -y wget
apt-get install -y software-properties-common
# get C++ compiler
apt-get install -y g++
apt-get install -y build-essential
apt-get install -y build-essential cmake
# get Qt
apt-get install -y qt5-default
# compile
qmake
make
ls
%runscript
/Server
%startscript
/Server
Again, note that the application works just fine both when compiled and startet normally and when started within a Singularity image (but without Singularity Compose).
The ls at the end of the %post block is used to verify that the Server application was build successfully.
Please share the server.recipe, as it is difficult to identify should be/is happening without it.
Without having that, my guess is that you have a %runscript in your definition file, but no %startscript. When the image is executed directly or via singularity run image.sif, the contents of %runscript determine what happens. To emulate the docker-compose style, the singularity images are started as persistent instances. In this case, the %startscript block determines what runs. If it is empty, it will just start up and sit there doing nothing. This would explain why when run by hand it works but not when using compose.
First of all, I would like to say that I'm new to Docker and all that is around it.
I have been wanting to make a container where I have Apache, php and Firebird installed. So far, so good ; everything seems to work and I can get my default page when I type in my Internet search bar my ip address and :8080. I do so by first starting my container like this :
docker run -p 8080:80 -d apps
Where "apps" is the name of my container.
I have achieved this with my Dockerfile, which looks like this (it might be a bit messy, still learning the good practices !) :
# Download of base image - ubuntu 20.04
FROM ubuntu:20.04
# Updating/upgrading
RUN apt-get update -y && apt-get upgrade -y
# Installing apache2, php and firebird with modules
RUN DEBIAN_FRONTEND="noninteractive" apt-get install apache2 php libapache2-mod-php -y && \
apt-get install php-curl php-gd php-intl php-json php-mbstring php-xml php-zip -y && \
DEBIAN_FRONTEND="noninteractive" apt-get install firebird3.0-server -y && apt-get install firebird->
# Start up apache in foreground by default
CMD /usr/sbin/apache2 -D FOREGROUND
ENTRYPOINT service apache2 restart && /bin/bash
# Expose apache
EXPOSE 80
Now, my idea was to export this container to another computer and try the same thing. I have followed a few tutorials and got to import my container on the new machine. My problem here is that somehow, the command I previously used doesn't work ; it shows me this error :
docker: Error response from daemon: No command specified.
See 'docker run --help'.
Which is odd, because it works just fine on the other machine. I also did this command, WHICH WORKS :
docker run -i -t -p 8080:80 apps /bin/bash
This one works alright, but I don't want to have to access the bash everytime I want my Apache page to load. I would want my container to run without me having to get in my container, if that makes sense.
In my opinion, it probably comes from the fact that I only loaded the container, and not the image used to build it (maybe a bad practice? Couldn't find anything about it on google).
Here is my setup just in case ---
On the first machine (which is the one where I created the image and the container) :
Ubuntu 20.04 LTS
Apache/2.4.41
Docker 19.03.8
On the other machine which I'm trying to make my container work :
Ubuntu 18.04 LTS
Apache/2.4.29
Docker 19.03.6
Thank you for your patience and time !
apps is your docker image, if you want to give name for your container you can specify --name in the run command ie,
docker run --name container_name -p 8080:80 -d apps
You can use sudo docker save -o apps.tar apps to create a tar file of the image
then change the root permission of the tar file sudo chmod 777 apps.tar
Copy this tar file to the other system you want to try, then
sudo docker load --input apps.tar
This will load the image, then you can use the previous command to start the container
docker run -p 8080:80 -d apps
Where "apps" is the name of my container. <- This statement is incorrect and perhaps the misunderstood concept that leads you to the problem.
apps is the name of the image, not the name of the container. On the host on which you can run the container, you must have built that image from the Dockerfile that you shared using the command:
docker build -t apps .
Copy the Dockerfile on the host where you cannot run the container, built the image in-there as well and try again running the container.
I just created a docker container and tried to install SQL Relay inside it.
I've checked the prerequisites here and followed the installation documents here.
However, at the end of make install of sqlrelay, I saw an error like this:
update-rc.d: /etc/init.d/sqlrelay: file does not exist
update-rc.d: /etc/init.d/sqlrcachemanager: file does not exist
make[1]: *** [install] Error 1
make[1]: Leaving directory `/sqlrelay-0.66.0/init'
make: *** [install-init] Error 2
What might be wrong with my installation?
Here's the docker file I used to start my installation:
FROM ubuntu:trusty
RUN apt-get update && \
apt-get install libxml2-dev libpcre3 libpcre3-dev libmysqld-dev -y
RUN apt-get install mysql-server libmysqlclient-dev -y
# sql relay prerequisites
RUN apt-get install g++ make perl php5-dev python-dev ruby-dev \
tcl-dev openjdk-7-jdk erlang-dev nodejs-dev node-gyp mono-devel \
libmariadbclient-dev libpq-dev firebird-dev libfbclient2 libsqlite3-dev \
unixodbc-dev freetds-dev mdbtools-dev -y
COPY rudiments-0.56.0.tar.gz /
COPY sqlrelay-0.66.0.tar.gz /
EXPOSE 80
Here are the outputs of ./configure, make, and make install inside sqlrelay-0.66.0 folder:
configure_log
make_log
make_install_log
If you need more information of my installation process, just let me know. I can provide it.
I think you should use ADD instead of COPY in your lines such as
COPY rudiments-0.56.0.tar.gz /
Your COPY just copies the .tar.gz, but does not unpack them
as with ADD
If the <src> parameter of ADD is an archive in a recognised compression format, it will be unpacked
This is extracted from
What is the difference between the `COPY` and `ADD` commands in a Dockerfile?
I have recently hit the same issue. The issue I found was that the init Makefile was incorrectly detecting the use of systemctl on Ubuntu Trusty and putting the scripts there. Later on the script would try to find the scripts in init.d and fail.
The solution is to edit the Makefile: sqlrelay-X.X.X/init/Makefile
Replace:
install:
if ( test -d "/lib/systemd/system" ); \
With:
install:
if ( test -d "/lib/systemd/system_x" ); \
Make a similar change to the uninstall option later in the script and it will now correctly install on Ubuntu.
I have tried in all ways to get wkhtmltopdf installed on our web server but unfortunately it is not getting installed. I cannot access user/bin folder as stated in a tutorial on installation.
On the server in public_html folder there is a sub folder _vti_bin, I copied the file wkhtmltopdf-i386 from wkhtmltopdf-0.9.1-static-i386, but I am not able to execute it.
How to install wkhtmltopdf on (shared hosting) web server and get it working?
I've managed to successfully install wkhtmltopdf-amd64 on my shared hosting account without root access.
Here's what i did:
Downloaded the relevant static binary v0.10.0 from here: http://code.google.com/p/wkhtmltopdf/downloads/list
EDIT: The above has moved to here
via ssh on my shared host typed the following:
$ wget {relavant url to binary from link above}
$ tar -xvf {filename of above wget'd file}
you'll then have the binary on your host and will be able to run it regardless of if its in the /usr/bin/ folder or not. (or at least i was able to)
To test:
$ ./wkhtmltopdf-amd64 http://www.example.com example.pdf
Note remember that if you're in the folder in which the executable is, you should probably preface it with ./ just to be sure.
Worked for me anyway
If you have sudo access...
Ubuntu 14.04 / 15.04 / 18.04:
sudo apt-get install wkhtmltopdf
# or
sudo apt install wkhtmltopdf
Others
Look at the other answers.
If its ubuntu then go ahead with this, already tested.:--
first, installing dependencies
sudo aptitude install openssl build-essential xorg libssl-dev
for 64bits OS
wget http://wkhtmltopdf.googlecode.com/files/wkhtmltopdf-0.9.9-static-amd64.tar.bz2
tar xvjf wkhtmltopdf-0.9.9-static-amd64.tar.bz2
mv wkhtmltopdf-amd64 /usr/local/bin/wkhtmltopdf
chmod +x /usr/local/bin/wkhtmltopdf
for 32bits OS
wget http://wkhtmltopdf.googlecode.com/files/wkhtmltopdf-0.9.9-static-i386.tar.bz2
tar xvjf wkhtmltopdf-0.9.9-static-i386.tar.bz2
mv wkhtmltopdf-i386 /usr/local/bin/wkhtmltopdf
chmod +x /usr/local/bin/wkhtmltopdf
Debian 8 Jessie
This works
sudo apt-get install wkhtmltopdf
Chances are that without full access to this server (due to being a hosted account) you are going to have problems. I would go so far as to say that I think it is a fruitless endeavor--they have to lock servers down in hosted environments for good reason.
Call your hosting company and make the request to them to install it, but don't expect a good response--they typically won't install very custom items for single users unless there is a really good reason (bug fixes for example).
Lastly, depending on how familiar you are with server administration and what you are paying for server hosting now consider something like http://www.slicehost.com. $20 a month will get you a low grade web server (256 ram) and you can install anything you want. However, if you are running multiple sites or have heavy load the cost will go up as you need larger servers.
GL!
Latest update for CentOS:
sudo yum install -y libpng libjpeg openssl icu libX11 libXext libXrender xorg-x11-fonts-Type1 xorg-x11-fonts-75dpi
wget https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
tar -xvf wkhtmltox-0.12.4_linux-generic-amd64.tar
sudo mv wkhtmltox/bin/* /usr/local/bin/
check installation success: wkhtmltopdf -V
rm -rf wkhtmltox
rm -f wkhtmltox-0.12.4_linux-generic-amd64.tar
Place the wkhtmltopdf executable on the server and chmod it +x.
Create an executable shell script wrap.sh containing:
#!/bin/sh
export HOME="$PWD"
export LD_LIBRARY_PATH="$PWD/lib/"
exec $# 2>/dev/null
#exec $# 2>&1 # debug mode
Download needed shared objects for that architecture and place them an a folder named "lib":
lib/libfontconfig.so.1
lib/libfontconfig.so.1.3.0
lib/libfreetype.so.6
lib/libfreetype.so.6.3.18
lib/libX11.so.6 lib/libX11.so.6.2.0
lib/libXau.so.6 lib/libXau.so.6.0.0
lib/libxcb.so.1 lib/libxcb.so.1.0.0
lib/libxcb-xlib.so.0
lib/libxcb-xlib.so.0.0.0
lib/libXdmcp.so.6
lib/libXdmcp.so.6.0.0
lib/libXext.so.6 lib/libXext.so.6.4.0
(some of them are symlinks)
… and you're ready to go:
./wrap.sh ./wkhtmltopdf-amd64 --page-size A4 --disable-internal-links --disable-external-links "http://www.example.site/" out.pdf
If you experience font problems like squares for all the characters, define TrueType fonts explicitly:
#font-face {
font-family:Trebuchet MS;
font-style:normal;
font-weight:normal;
src:url("http://www.yourserver.tld/fonts/Trebuchet_MS.ttf");
format(TrueType);
}
List of stable versions wkhtmltopdf: http://wkhtmltopdf.org/downloads.html
Installing wkhtmltopdf on Debian 8.2 (jessie) x64:
sudo apt-get install xfonts-75dpi
sudo apt-get install xfonts-base
sudo wget http://download.gna.org/wkhtmltopdf/0.12/0.12.2.1/wkhtmltox-0.12.2.1_linux-jessie-amd64.deb
sudo dpkg -i wkhtmltox-0.12.2.1_linux-jessie-amd64.deb
Shared hosting no ssh or shell access?
Here is how i did it;
Visit https://wkhtmltopdf.org/downloads.html and download the appropriate stable release for Linux. For my case I chose 32-bit
which is wkhtmltox-0.12.4_linux-generic-i386.tar.xz
Unzip to a folder on your local drive.
Upload the folder to public_html (or whichever location fits your need) using an FTP program just like any other file(s)
Change the binary paths in snappy.php file to point the appropriate files in the folder you just uploaded.
Bingo! there you have it. You should be able to generate PDF files.
A few things have changed since the top answers were added. They used to work out for me, but not quite anymore, so I have been hacking around for a bit and came up with the following solution for Ubuntu 16.04. For Ubuntu 14.04, see the comment at the bottom of the answer. Apologies if this doesn't work for shared hosting, but it seems like this is the goto answer for wkhtmltopdf installation instructions in general.
# Install dependencies
apt-get install libfontconfig \
zlib1g \
libfreetype6 \
libxrender1 \
libxext6 \
libx11-6
# TEMPORARY FIX! SEE: https://github.com/wkhtmltopdf/wkhtmltopdf/issues/3001
apt-get install libssl1.0.0=1.0.2g-1ubuntu4.8
apt-get install libssl-dev=1.0.2g-1ubuntu4.8
# Download, extract and move binary in place
curl -L -o wkhtmltopdf.tar.xz https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
tar -xf wkhtmltopdf.tar.xz
mv wkhtmltox/bin/wkhtmltopdf /usr/local/bin/wkhtmltopdf
chmod +x /usr/local/bin/wkhtmltopdf
Test it out:
wkhtmltopdf http://www.google.com google.pdf
You should now have a file named google.pdf in the current working directory.
This approach downloads the binary from the website, meaning that you can use the latest version instead of relying on package managers to be updated.
Note that as of today, my solution includes a temporary fix to this bug. I realize that the solution is really not great, but hopefully it can be removed soon. Be sure to check the status of the linked GitHub issue to see if the fix is still necessary when you read this answer!
For Ubuntu 14.04, you will need to downgrade to a different version of libssl. You can find the versions here. Anyways, be sure to consider the implications of downgrading libssl before doing so on any production server.
I hope this helps someone!
After trying, below command work for me
cd ~
yum install -y xorg-x11-fonts-75dpi xorg-x11-fonts-Type1 openssl git-core fontconfig
wget https://downloads.wkhtmltopdf.org/0.12/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
tar xvf wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
mv wkhtmltox/bin/wkhtmlto* /usr/bin
Version 12.5 of wkhtmltopdf only lists DEB files on their download page now. Being a mac user and not knowing much linux or what DEB files were I couldn't use the solutions posted.
This page helped me get past the knew twist of downloading a DEB file: http://www.g-loaded.eu/2008/01/28/how-to-extract-rpm-or-deb-packages/
Basically what I did was:
Downloaded from https://wkhtmltopdf.org/downloads.html
Unzipped the DEB file.
Unzipped data.tar.xz
Uploaded the binary in the unzipped 'usr' folder from step 3 (usr/local/bin/wkhtmltopdf)
Then I found out that the 'exec' function was disabled on my host. So make sure you can specifically run 'exec' if you're using PHP to run this. "Can I run the wkhtmltopdf binary" isn't specific enough. My fault.