¶ Server Install
We run Ubuntu 20.04
¶ At install time
- partitions table:
Output of df -h:
root@centuri-engineering:/home/guillaume# df -h
Filesystem Size Used Avail Use% Mounted on
udev 16G 0 16G 0% /dev
tmpfs 3.2G 9.6M 3.1G 1% /run
/dev/sda2 127G 6.1G 115G 6% /
tmpfs 16G 8.0K 16G 1% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 16G 0 16G 0% /sys/fs/cgroup
/dev/sda1 511M 13M 499M 3% /boot/efi
/dev/sda5 309G 2.1G 291G 1% /home
/dev/md0 7.3T 659G 6.3T 10% /mnt/md0
tmpfs 3.2G 0 3.2G 0% /run/user/1000
Here is /etc/fstab:
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point> <type> <options> <dump> <pass>
# / was on /dev/sda2 during installation
UUID=b8306de5-7b14-4aa5-b327-e8f4a08de658 / ext4 errors=remount-ro 0 1
# /boot/efi was on /dev/sda1 during installation
UUID=74D2-21A6 /boot/efi vfat umask=0077 0 1
# /home was on /dev/sda5 during installation
UUID=970e738e-0331-4d42-bf09-1d698ad1de1c /home ext4 defaults 0 2
# swap was on /dev/sda4 during installation
UUID=f602a833-f03d-4450-ab14-a33c3823094b none swap sw 0 0
# Added manualy
/dev/md0 /mnt/md0 ext4 defaults,nofail,discard 0 0
¶ first boot
TIL when running su, the root shell keeps the user's environement. So
for example, /usr/sbin/ is not in $PATH. So better use su -s
Update fstab to permanentely mount de RAID 1 disk:
# as root
echo '/dev/md0 /mnt/md0 ext4 defaults,nofail,discard 0 0' | tee -a /etc/fstab
¶ Some basic installs
apt install \
emacs-nox \
git rsync \
postgresql-11 \
postgresql-server-dev-11 \
apt-transport-https \ # https://docs.docker.com/engine/install/debian/
ca-certificates \
curl \
gnupg-agent \
software-properties-common \
nvidia-detect # see https://wiki.debian.org/fr/NvidiaGraphicsDrivers
python3-venv
# as root
# add caddy repository
echo "deb [trusted=yes] https://apt.fury.io/caddy/ /" \
| sudo tee -a /etc/apt/sources.list.d/caddy-fury.list
# add docker repositories
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add -
apt-key fingerprint 0EBFCD88 # see docker website for a check
add-apt-repository \
"deb [arch=amd64] https://download.docker.com/linux/ubuntu \
$(lsb_release -cs) \
stable"
apt update
apt install caddy libnss3-tools \
docker-ce docker-ce-cli containerd.io
usermod -aG docker guillaume
- Install miniconda in user space (as user):
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
chmod +x Miniforge3-Linux-x86_64.sh
./Miniforge3-Linux-x86_64.sh
After you log out & in again, install docker-compose (via pip, in user
space)
pip install docker-compose
- Install mkcert for self certification (outdated)
# as root
wget https://github.com/FiloSottile/mkcert/releases/download/v1.4.1/mkcert-v1.4.1-linux-amd64
mv mkcert-v1.4.1-linux-amd64 /usr/local/bin/mkcert
chmod +x /usr/local/bin/mkcert
mkcert -install
mkcert localhost centuri-engineering.luminy.univ-amu.fr 139.124.81.38 127.0.0.1 ::1
mv localhost+4-key.pem key.pem
mv localhost+4.pem cert.pem
mv *.pem /etc/caddy
cd /etc/caddy && caddy reload
¶ Reverse-proxy docker containers with Caddy
The basic idea is a container serves it's app at a local port (say 4080) and we reverse-route all the requests from a given subdomain (with ports 80 and 443) to this port. Caddy takes care of automated https with LetsEncrypt.
Here is a sample of the /etc/caddy/Caddyfile doing this:
wiki.centuri-engineering.univ-amu.fr {
reverse-proxy 127.0.0.1:4080
}
This certainly is the thinest server configuration possible 
¶ omero, docker and postgresql
-
Warning This is an example of installation at some point in time, it certainly will not work as is!
-
Get docker compose files
pip install docker-compose git clone git@github.com:centuri-engineering/omero-at-centuri.git -
Restore DB
cd omero-at-centuri/docker # Pull only the database up docker-compose up -d database docker-compose exec database psql -U omero -d omero -f /backups/omero.sql -
Start all
cd omero-at-centuri/docker docker-compose up -d docker-compose exec database psql -U omero -d omero -f /backups/omero.sql -
Dump DB
docker-compose exec database pg_dump omero -U omero > backups/omero.sql
- Fix windows path issue:
This reference was usefull
Relevant command line:
UPDATE pixels SET path = regexp_replace(path,'\\','/','g');
¶ restoring an old DB, root password update
https://davidamick.wordpress.com/2014/07/19/docker-postgresql-workflow/
Looks easier to go through docker-compose exec commands - so:
COMMAND="psql -U omero -d omero -f /backups/omero.dump.sql"
docker-compose exec database $COMMAND
Note that old passwords are conserved in the db, so we might need to
reset the root omero user password. This is done on the omeroserver
machine through:
# Log on the server
docker-compose exec omeroserver bash
export PATH=$PATH:/opt/omero/server/OMERO.server/bin
omero db password
This prints a SQL cmmand with the hashed password. In the database
server then:
docker-compose exec database psql -U omero
# we have to remove the extra quotes for some reason
omero=# UPDATE password SET hash = 'mFkbWqddcdsqsdHffffdd4==' WHERE experimenter_id = 0;
¶ omero-py
conda create -n pyomero python=3.8
conda install -c conda-forge \
jupyter\
notebook\
jupyterlab\
ipywidgets\
scikit-image\
matplotlib
pandas
# dependences to install zeroc-ice
sudo apt install libbz2-dev libssl-dev
pip install omero-py
¶ Data transfer tool
https://github.com/imcf/auto-tx