I am trying to make the image for the Singularity using the following file(which is Singularity.recepie):
Bootstrap: docker
From: ubuntu:18.04
%post
apt-get -y update
apt-get install -y python3-pip
%files
QC.py /
%runscript
python3 /QC.py
I build the image using the following command:
sudo singularity build ubuntu.simg Singularity.recepie
and run the image using this command:
./ubuntu.simg
when I run the image it works but I do not see the result files in the directory that I am working at. do you know how I can the results and copy them to my current directory?
By default, your current working directory is mounted into the image and used as the working directory. If no files are being created and they should be, then you need to look at where your script is trying to write to. Also check the singularity error/warnings output for additional info.
If you're using an older version of Singularity (implied by .simg instead of .sif extension), you may also be running on a kernel that does not support overlayfs, which can cause issues attempting to mount to a non-existing folder. If this is the case, singularity will give a warning but continue on and possibly fail in a hard to detect manner. More info on mounting with overlay here.
Related
I need to install Cuda, CuDNN, and NCCL in a singularity container to build the MXNET Library for GPU Support. Currently, I have this minimal Definition File:
Bootstrap: library
From: ubuntu:20.04
%environment
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
... some other stuff
%post
... some other installation stuff
apt-get install linux-headers-$(uname -r)
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget https://developer.download.nvidia.com/compute/cuda/11.2.0/local_installers/cuda-repo-ubuntu2004-11-2-local_11.2.0-460.27.04-1_amd64.deb
dpkg -i cuda-repo-ubuntu2004-11-2-local_11.2.0-460.27.04-1_amd64.deb
apt-key add /var/cuda-repo-ubuntu2004-11-2-local/7fa2af80.pub
apt-get update
apt-get -y install cuda
export PATH=/usr/local/cuda-11.2/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/usr/local/cuda-11.2/lib64\
${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
/usr/bin/nvidia-persistenced --verbose
... clone and build mxnet
Installing Cuda is not a problem. However, in order to install CudNN, one first needs to log into an NVIDIA Account. Similarly, to install NCCL, one needs to complete a survey.
I obviously cannot do that per command line. But I can download these files beforehand. How can I access these files in %post?
You can use the %files section of the definition file. All files added there are available in %post and, if not moved, are included in the final image.
#tsnowlan gave a correct answer.
For the others wondering, how to get Cuda, CuDNN, and NCCL easily into an singularity container:
There are Docker images from NVidia, that already come with these tools:
https://hub.docker.com/r/nvidia/cuda/tags
One can easily use these images as a base image for the docker container:
https://docs.sylabs.io/guides/3.0/user-guide/build_a_container.html
I am trying to install Inkscape 1.2beta on Linux Ubuntu 20.04. The website currently only offers an AppImage and a source tarball. Since I would like to access the newest features of Inkscape via the command line, I need to build and install the source tarball.
INSTALL.md states that I need all submodules and dependencies before install.
How do I find these dependencies to successfully build and install Inkscape?
This list should satisfy all required dependencies on Linux Ubuntu:
apt install
cmake
imagemagick
libdouble-conversion-dev
libgdl-3-dev
libagg-dev
libpotrace-dev
libboost-all-dev
libsoup2.4-dev
libgc-dev
libwpg-dev
poppler-utils
libpoppler-dev
libpoppler-glib-dev
libpoppler-private-dev
libvisio-dev libvisio-tools
libcdr-dev
libgtkmm-3.0-dev
libgspell-1-dev
libxslt-dev libxslt1-dev
libreadline6-dev
lib2geom-dev
lib2geom-dev is needed to solve error "<ieeefp.h> not found".
For building Inkscape:
Download source tarball for Inkscape v1.2 from inkscape.org and extract
cd <extracted inkscape directory>
mkdir build && cd build
cmake ..
make
make install
If you still get an error during cmake .., please comment below with the names of the missing modules in the error message.
The details on how to build Inkscape (and the dependencies) could be found in the repository itself, or Inkscape website (For completness, the steps are copied from the website here):
To obtain the latest source code, use the following command (downloads into a subdirectory of your current working directory called "inkscape" by default):
git clone --recurse-submodules https://gitlab.com/inkscape/inkscape.git
To update this code later, change into the download folder and use:
git pull --recurse-submodules && git submodule update
By default, git will download every branch and every commit. If you are on a slow machine, have limited disk space, or limited internet bandwidth, you can use shallow clone and single branch clone options to limit the amount of data it will download:
git clone --depth=1 --single-branch --recurse-submodules --shallow-submodule https://gitlab.com/inkscape/inkscape.git
Building Inkscape on Linux
Open a terminal at the root of the folder into which you downloaded the source code in the previous step.
Install build dependencies
Download and run the script to install everything required for compiling Inkscape (check script to see if your distribution is supported):
wget -v https://gitlab.com/inkscape/inkscape-ci-docker/-/raw/master/install_dependencies.sh -O install_dependencies.sh
bash install_dependencies.sh --recommended
Compile
To compile with CMake, do the following:
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/install_dir -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache
make -j8
make install
Notes:
Using ccache is optional but speeds up compilation.
The optional -j8 argument to make tells it to run 8 jobs in parallel. Feel free to adjust this to the number of hardware threads (physical cores) available on your computer.
The recommended -DCMAKE_INSTALL_PREFIX argument allows to specify a custom isolated installation location (in the example above install_dir/ inside the build folder). It avoids installation into system locations (where it could conflict with other versions of Inkscape) and allows running multiple versions of Inkscape in parallel. It will still use all the files (including the preferences.xml) that reside in the ~/.config/inkscape directory.
Run
Run it from the build directory:
install_dir/bin/inkscape
I have downloaded the Image Magic from the following Link:
http://www.imagemagick.org/download/linux/CentOS/i386/ImageMagick-6.9.1-3.i386.rpm
Extracted the rpm file using rpm2cpio ImageMagick-6.9.1-3.i386.rpm | cpio -idmv
Running below command to create the thumbnail for the first page of PDF
convert source.pdf[0] output.jpg
But I am getting error:
convert: No match.
Anyone has any idea why it is not working? What I am doing wrong?
Instead of installing ImageMagick, you have extracted it instead. What you would want to do is install it.
You could run yum install ImageMagick to install it, which will take care of all the necessary dependencies as well. Or, if you wanted to install using the rpm, you should run rpm -i ImageMagick-6.9.1-3.i386.rpm. I would suggest going through the yum route instead, however.
Note: The above answer is based upon the assumption that you are using CentOS or RedHat or a similar distribution. If you are using Ubuntu or a similar distribution, you would need to use apt-get install imagemagick.
I've installed CMake 2.8.11.2 package from CMake's website for Mac 64-bit. We recently upgraded a project from Qt 4 to Qt 5 and the CMake upgrade is mandatory for CMake to use Qt 5. However, when I type cmake . I get the following error:
CMake Error: Could not find CMAKE_ROOT !!!
CMake has most likely not been installed correctly.
Modules directory not found in
/Applications/CMake 2.8-11.app/Contents/bin
CMake Error: Error executing cmake::LoadCache(). Aborting.
I can confirm, there is no modules directory in the bin folder. I really don't know how to resolve this error, or how to get the modules needed.
Do hash -r to clear the cache, then do cmake --version.
It should work.
I had the same problem after upgrading on Ubuntu.
Removing cmake and the cmake-data package before performing the update solved it for me.
sudo apt-get remove cmake cmake-data
Now perform the update via
sudo -E add-apt-repository -y ppa:george-edison55/cmake-3.x
sudo -E apt-get update
sudo apt-get install cmake
This worked for me :
cd cmake-3.4.3
./bootstrap --prefix=/usr
make
sudo make install
Additionally, you may encounter the same error when running CMake from Cygwin. This may be caused by a PATH variable listing /bin before /usr/bin: in this case CMake is launched as /bin/cmake instead of /usr/bin/cmake, and trying to load modules from //share/cmake-X.Y.Z (which is a UNC path on Windows) instead of /usr/share/cmake-X.Y.Z.
Explicitly export'ing a correct CMAKE_ROOT isn't helpful, and cmake keeps displaying the same misleading message.
The issue can be solved by setting PATH to /usr/bin:/bin:/everything/else in your .bash_profile.
I was able to fix this error on Linux (for other who may be searching for answer on Linux) while trying to upgrade cmake 2.8.11 to 2.8.12 by exporting the CMAKE_ROOT environment variable like so:
export CMAKE_ROOT=/path_to_install/cmake-2.8.12.2-Linux-i386/share/cmake-2.8
The share directory should be on the same level as your bin directory.
I got the same error message upgrading cmake-3.5.1 to cmake-3.7.1 on Ubuntu 16.04.01 LTS. I just updated the repositories with
sudo apt-get update
Then
cmake --version
brought up the correct and upgraded cmake version and the error messages was gone.
In my opinion/case this is a developer "problem". I suspect this occurs mostly to new developers so I go a bit deeper to put it in the right perspective:
To "not mess with" the original system files used for daily work and separate the new compiled and volatile programs in a separate location it is common to not just change but add/mount a complete folder structure similar to the original OS folder structure in a special "development" location.
So more or less a mirrored folder structure of the original one but connected/linked to the original resources.
There for we need to add an environment variable to our user bash profile where we tell the system: "link our development folders to the following direction/dir."
On Arch Linux this is done in a file in ~/.bashrc - that is linked/forwarded in/by the ~/.bash_profile ("~" stands for /home/your user name/) and MacOS/Unix will be similar.
To do that there are 2 ways:
you can open the .bashrc file and add your environment path to the bottom of it
or
you can use "export" to put the environment variables to the right place in your user bash file.
for kde development e.g. you need to add a path at the end of the ~/.bashrc file like so:
# Adding the kdesrc-build directory to the path
export PATH="$HOME/kde/src/kdesrc-build:$PATH"
what basically tells the system: the development is done in the /home/user name/kde/src folder - there are your files. You can choose where you want to locate your development environment.
If you execute cmake it "thinks" your files are in the original OS folder and the "Could not find CMAKE_ROOT" - message will disappear because it finds all your files since properly linked from your development folder structure to your system folder structure.
So basically to solve the problem you could just execute cmake in the right system folder - it just could mess up your system if the program or make files are not proper done so it is pulled to the home folder development folder structure. And you just have to tell that cmake, so it can find all needed files to compile your stuff, including the CMAKE_ROOT.
Another problem could be that cmake isn't properly installed.
On Arch Linux systems that can be made sure by using the "sudo pacman -Syu cmake" command and it copies the files in the right direction and sets the right user variables to get it executed and reinstall cmake if necessary.
Btw, if you are on other systems like Debian make sure to use a Debian apt repository, it can differ from the Ubuntu repository, especially if you compile for the chosen system.
I tried to write a general "beginners in mind" overview to get em a fundamental picture. Executing cmake in the right folder solved that exact problem for me that was asked for.
(Actual that flags works for the actual cmake version from the official arch repository:
1:
cd /home/ivanovic/kde/src/program_name
than:
2:
cmake -S/home/ivanovic/kde/src/program_name -B/home/ivanovic/kde/build/program_name -DCMAKE_INSTALL_PREFIX=/home/ivanovic/kde/usr -DCMAKE_BUILD_TYPE=Debug
Pay attention that between -S and /home/... is no space, same at -B and /home/...
This worked fine for my kde system software builds.
)
If anyone gets the following error:
Modules directory not found in
/usr/share/cmake-3.20
cmake version 3.20.2
Solution which worked for me:
sudo cp -r /share/cmake-3.20 /usr/share/
The above command copies the cmake-3.20 directory from /share to /usr/share
This also happened to me on a fresh install of Ubuntu 21.04 and was fixed by installing it from "snap":
sudo snap install cmake --classic
(and then making sure that /snap/bin is in $PATH)
tl;dr: check the permission of folder /usr/local/share/cmake-x.xx.
I had a similar problem with the cmake that I build from source code. I compile the code with the following command.
./configure
make
sudo make install
and the binary files were placed into /usr/local/bin as expected. But I will encounter the same problem when executing cmake without sudo privilege. This is because the normal user don't have reading permission with folder /usr/local/share/cmake-3.xx.
The error went away when I give myself the permission to read/execute, with the command.
sudo chmod 755 /usr/local/share/cmake-3.xx
(xx will be the specific version that you installed.)
After downloading emscripten via
git clone git://github.com/kripken/emscripten.git
and running
./emcc
a .emscripten file is created in my user root.
==============================================================================
Welcome to Emscripten!
This is the first time any of the Emscripten tools has been run.
A settings file has been copied to ~/.emscripten, at absolute path: /Users/calvin/.emscripten
Please edit that file and change the paths to fit your system. Specifically,
make sure LLVM_ROOT and NODE_JS are correct.
This command will now exit. When you are done editing those paths, re-run it.
==============================================================================
I have llvm installed and nodejs installed via macports. So where should I change LLVM_ROOT and NODE_JS to point to?
running emsdk activate latest (after having run emsdk install latest, which takes a while) gets all of my aliases and such working, I've added it to my bash profile
Are the LLVM / Node.js commands accessible on your path? E.g. does running node or clang work?
If so, you can detect the paths you need from there. For LLVM_ROOT, you want the directory containing the LLVM binaries:
$ dirname `which llvm-config`
/usr/local/bin
For NODE_JS, you want the path to the node binary itself:
$ which node
/usr/local/bin/node
If this fails (because they are not on your path already), then try looking in /opt/local/bin. That's seems like the right place from the MacPorts docs (I don't use MacPorts myself).