Difference between revisions of "Singularity Summary and Tips"
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1: Singularity image container is a binary file. | 1: Singularity image container is a binary file. | ||
2: The size of image container is small. | 2: The size of image container is small. | ||
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<span style="color:blue">Disadvantage</span> | <span style="color:blue">Disadvantage</span> | ||
1: Hard to be expanded (size is fixed). | 1: Hard to be expanded (size is fixed). | ||
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==Sandbox== | ==Sandbox== | ||
sudo singularity build --sandbox ./3DSlicer.ssb ../singularity_3DSlicer.recipe | sudo singularity build --sandbox ./3DSlicer.ssb ../singularity_3DSlicer.recipe | ||
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<span style="color:blue">Advantage</span> | <span style="color:blue">Advantage</span> | ||
1: It is very easy to be expanded (no size limitation). | 1: It is very easy to be expanded (no size limitation). | ||
2: You can install any additional packages and libraries after the container been created. | 2: You can install any additional packages and libraries after the container been created. | ||
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<span style="color:blue">Disadvantage</span> | <span style="color:blue">Disadvantage</span> | ||
1: Singularity sandbox container is a folder. | 1: Singularity sandbox container is a folder. | ||
Revision as of 17:15, 15 November 2019
Contents
How to create singularity recipe file
Three important sections should be defined in recipe file.
1: BootStrap: in this section you can figure out use which method (library, docker, debootstrap/yum) to get which OS (ubuntu, centos, redhat) with which version (trusty, xenial) from where (singularity hub, docker hub, ubuntu/centos official website) and install which libraries (bash vim less) by default.
Example 1 BootStrap: debootstrap OSVersion: xenial MirrorURL: http://us.archive.ubuntu.com/ubuntu/ Include: bash vim less man-db apt-utils tzdata --------- Example 2 BootStrap: docker From: ubuntu:xenial
2: %environment: in this section, you can figure out the language and location of OS. inaddition, you an export some paths into environment variables inside singularity container.
%environment
LC_ALL=C
LD_LIBRARY_PATH=/usr/local/lib64:/usr/local/lib:/usr/lib64:/usr/lib:/lib64:/lib:/usr/local/cuda/extras/CUPTI/lib64
TZ='America/New_York'
export LC_ALL LD_LIBRARY_PATH TZ
3: %post: in this section, you can figure out all customized script that be used to install the specific libraries, software and packages.
%post
#Get 3DSlicer
wget -P /home/software/3DSlicer https://download.slicer.org/bitstream/1023242
tar -xvf /home/software/3DSlicer/1023242 -C /home/software/3DSlicer
#For 3DSlicer
apt-get install -y libfontconfig1 \
libxrender1 \
libgl1-mesa-dev \
libglu1-mesa \
libglu1-mesa-dev \
libxtst6 \
libegl1-mesa-dev
4: Example
(1)The singularity recipe file for 3DSlicer: https://github.com/lxwgcool/singularity/blob/master/singularity_3DSlicer.recipe (2)The singularity recipe file for tensorflow with ubuntu xenial, python 3.6.7 and cuda 9.0: https://github.com/lxwgcool/singularity/blob/master/Singularity.tensorflow-gpu-1.12.0
How to create singularity container
1: There are two types of container, including "image" and "sandbox".
2: Any singularity container should be created by using "sudo".
Now, we use the recipe file of 3D Slicer as an example: https://github.com/lxwgcool/singularity/blob/master/singularity_3DSlicer.recipe
Image
sudo singularity build ./3DSlicer.ssb ../singularity_3DSlicer.recipe Advantage 1: Singularity image container is a binary file. 2: The size of image container is small. Disadvantage 1: Hard to be expanded (size is fixed). 2: You are not allowed to install new packages and libraries once the image been created.
Sandbox
sudo singularity build --sandbox ./3DSlicer.ssb ../singularity_3DSlicer.recipe Advantage 1: It is very easy to be expanded (no size limitation). 2: You can install any additional packages and libraries after the container been created. Disadvantage 1: Singularity sandbox container is a folder. 2: The size of sandbox container is around 3 times larger than image container.
