Skip to content

Commit d9cdc8d

Browse files
gjbexgjbex
authored
Merge pull request #21 from gjbex/development
Development
2 parents 59175af + 6a9783e commit d9cdc8d

File tree

7 files changed

+206
-0
lines changed

7 files changed

+206
-0
lines changed

‎.gitignore

+1
Original file line numberDiff line numberDiff line change
@@ -6,3 +6,4 @@
66

77
# direnv config file
88
.envrc
9+
/~$containers_for_hpc.pptx

‎containers_for_hpc.pptx

56.4 KB
Binary file not shown.

‎examples/apptainer_build.slurm

+25
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
#!/usr/bin/env -S bash -l
2+
#SBATCH --account=lpt2_sysadmin
3+
#SBATCH --nodes=1
4+
#SBATCH --ntasks=1
5+
#SBATCH --cpus-per-task=8
6+
#SBATCH --time=03:00:00
7+
#SBATCH --mem=20G
8+
#SBATCH --cluster=wice
9+
#SBATCH [email protected]
10+
#SBATCH --mail-type=END,FAIL
11+
12+
if [ -z $RECIPE ]
13+
then
14+
(>&2 echo "RECIPE not set")
15+
exit 1
16+
fi
17+
18+
IMAGE=$(basename "${RECIPE%.*}.sif")
19+
20+
export APPTAINER_TMPDIR=$VSC_SCRATCH/singularity_tmp
21+
mkdir -p $APPTAINER_TMPDIR
22+
export APPTAINER_CACHEDIR=$VSC_SCRATCH/singularity_cache
23+
mkdir -p $APPTAINER_CACHEDIR
24+
25+
apptainer build --fakeroot $IMAGE $RECIPE

‎examples/persistent_overlays/.gitignore

+2
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
overlay_dir/
2+
r_container.sif

‎examples/persistent_overlays/README.md

+26
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,26 @@
1+
# Persisntent overlays
2+
3+
Persistent overlays allow to overlay a writable filesystem while building or running a container.
4+
5+
6+
## What is it?
7+
8+
1. `r_container.py`: hpccm recipe file to build a container with R installed.
9+
1. `r_container.recipe`: Singularity recipe file to build a container with R installed.
10+
11+
## How to use it?
12+
13+
Create thé overlay directory:
14+
```bash
15+
$ mkdir overlay_dir/
16+
```
17+
18+
Create the image:
19+
```bash
20+
$ apptainer build r_container.sif r_container.recipe
21+
```
22+
23+
Use the overlay:
24+
```bash
25+
$ apptainer exec --overlay overlay_dir/ r_container.sif /bin/bash
26+
```

‎examples/persistent_overlays/r_container.py

+46
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
1+
'''Recipe to create either a docker container or Singularity image
2+
for computations using R.
3+
4+
Usage:
5+
$ hpccm --recipe r_container.py --format docker
6+
$ hpccm --recipe r_container.py --format singularity
7+
'''
8+
9+
# Choose a base image
10+
Stage0.baseimage('ubuntu:22.04')
11+
12+
# Install utilities
13+
Stage0 += apt_get(ospackages=['gist', 'wget', 'rclone', ])
14+
15+
# Install tools to install R
16+
Stage0 += apt_get(ospackages=['software-properties-common', 'apt-transport-https', 'dirmngr', 'gnupg'])
17+
18+
# Add signature key for CRAN
19+
Stage0 += shell(commands=['wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc'])
20+
21+
# Add CRAN repository
22+
Stage0 += shell(commands=['add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"'])
23+
24+
# Install build tools
25+
Stage0 += apt_get(ospackages=['build-essential', 'make'])
26+
Stage0 += cmake(eula=True)
27+
28+
# Install GNU compilers (upstream)
29+
compilers = gnu()
30+
Stage0 += compilers
31+
32+
# Install libraries required to build R
33+
Stage0 += apt_get(ospackages=['openssl', 'libxml2-dev', 'libcurl4-openssl-dev', 'libz-dev', 'libssl-dev',
34+
'libjpeg-dev', ])
35+
# Install BLAS and Lapack
36+
Stage0 += apt_get(ospackages=['libopenblas-dev', 'liblapack-dev'])
37+
38+
# Install R
39+
Stage0 += apt_get(ospackages=['r-base', ])
40+
41+
# installing libraries required by R packages, e.g., GDAL library
42+
Stage0 += apt_get(ospackages=['libgdal-dev', 'libudunits2-dev'])
43+
44+
# Set environment variables
45+
Stage0 += environment(variables={'LC_ALL': 'C.UTF-8'})
46+
Stage0 += environment(variables={'TZ': 'Europe/Brussels'})

‎examples/persistent_overlays/r_container.recipe

+106
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,106 @@
1+
BootStrap: docker
2+
From: ubuntu:22.04
3+
%post
4+
. /.singularity.d/env/10-docker*.sh
5+
6+
%post
7+
apt-get update -y
8+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
9+
gist \
10+
rclone \
11+
wget
12+
rm -rf /var/lib/apt/lists/*
13+
14+
%post
15+
apt-get update -y
16+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
17+
apt-transport-https \
18+
dirmngr \
19+
gnupg \
20+
software-properties-common
21+
rm -rf /var/lib/apt/lists/*
22+
23+
%post
24+
cd /
25+
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
26+
27+
%post
28+
cd /
29+
add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
30+
31+
%post
32+
apt-get update -y
33+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
34+
build-essential \
35+
make
36+
rm -rf /var/lib/apt/lists/*
37+
38+
# CMake version 3.25.1
39+
%post
40+
apt-get update -y
41+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
42+
make \
43+
wget
44+
rm -rf /var/lib/apt/lists/*
45+
%post
46+
cd /
47+
mkdir -p /var/tmp && wget -q -nc --no-check-certificate -P /var/tmp https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.sh
48+
mkdir -p /usr/local
49+
/bin/sh /var/tmp/cmake-3.25.1-linux-x86_64.sh --prefix=/usr/local --skip-license
50+
rm -rf /var/tmp/cmake-3.25.1-linux-x86_64.sh
51+
%environment
52+
export PATH=/usr/local/bin:$PATH
53+
%post
54+
export PATH=/usr/local/bin:$PATH
55+
56+
# GNU compiler
57+
%post
58+
apt-get update -y
59+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
60+
g++ \
61+
gcc \
62+
gfortran
63+
rm -rf /var/lib/apt/lists/*
64+
65+
%post
66+
apt-get update -y
67+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
68+
libcurl4-openssl-dev \
69+
libjpeg-dev \
70+
libssl-dev \
71+
libxml2-dev \
72+
libz-dev \
73+
openssl
74+
rm -rf /var/lib/apt/lists/*
75+
76+
%post
77+
apt-get update -y
78+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
79+
liblapack-dev \
80+
libopenblas-dev
81+
rm -rf /var/lib/apt/lists/*
82+
83+
%post
84+
apt-get update -y
85+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
86+
r-base
87+
rm -rf /var/lib/apt/lists/*
88+
89+
%post
90+
apt-get update -y
91+
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
92+
libgdal-dev \
93+
libudunits2-dev
94+
rm -rf /var/lib/apt/lists/*
95+
96+
%environment
97+
export LC_ALL=C.UTF-8
98+
%post
99+
export LC_ALL=C.UTF-8
100+
101+
%environment
102+
export TZ=Europe/Brussels
103+
%post
104+
export TZ=Europe/Brussels
105+
106+

0 commit comments

Comments
 (0)