| Author: | Markus Demleitner |
|---|---|
| Email: | gavo@ari.uni-heidelberg.de |
| Date: | 2023-02-09 |
| Copyright: | Waived under CC-0 |
Contents
These installation instructions cover the installation of the complete data center suite. Installing libraries or, say, the tapsh, is much less involved. See the respective pages at the GAVO DC's software distribution pages for details on those.
The preferred way to run DaCHS is on Debian stable or compatible systems. Starting with Debian bullseye (11.0), DaCHS is part of Debian. On a suitably recent system, just execute:
sudo apt install gavodachs2-server
With that, you are ready to proceed to the tutorial.
This is the recommended way to get up to speed with DaCHS regardless of whether you want to run the bleeding-edge version. You can switch later.
On older systems, you need to add our APT repository to your /etc/apt/sources.list before running the apt install.
You are probably saving yourself quite a bit of grief if you just choose Debian stable as your platform when you are going for Debian derivatives. If you insist on running, say, Ubuntu, please note that they do not package DaCHS (so you have to add our APT repo no matter what) and that they do not package the q3c and pgsphere packages that DaCHS cannot live without.
A workable fix is to install the packages from postgres' APT repository (these are basically equivalent to what Debian has). However, these have multiple postgres versions at the same time, and hence you will need to manually make sure that the postgres server and the extensions match.
Hence, on dpkg-based distributions more remote from Debian, try a sequence more or less like:
If this fails, make sure the postgres instance listening on your port 5432 really is the one you got from the postgres repo, not the one from Ubuntu.
The following instructions were mainly written by Chris Piker (U Iowa) – thanks! – and reflect the state on CentOS 7. The systemd parts are probably applicable beyond the RPM universe.
Install postgres if needed:
$ sudo yum install postgresql-server postgresql-devel
If postgres is running shut it down:
$ sudo systemctl stop postgresql.service
Moving the database cluster: The database cluster is typically in the $HOME/data directory of the postgres user. Changing this under CentOS 7 which uses systemd is a bit different. Configuration files are now .ini style files (not bash scripts) and they live under /usr/lib/systemd/system/.
The default configuration file for postgres is /usr/lib/systemd/system/postgresql.service.
The files in /usr/lib/systemd are maintained by the package manager so you should leave them alone. Forturnatly, systemd looks for overrides in an alternate directory first before loading the deflault service configuration.
Local user defined overrides for services go in the /etc/systemd/system directory. So, put:
# Include the default config: .include /usr/lib/systemd/system/postgresql.service [Service] Environment=PGDATA=<your path here>/data
into /etc/systemd/system/postgresql.service; of course <your path here> needs to be substituted with the path to somewhere where there's enough space for what you expect in your database; it's usually a good idea to use a directory on a separate partition here. The examples below assume /disk/1/pgsql (and need to be adjusted accordingly in the likey event that you chose something else).
Let systemd know that you've changed something:
$ sudo /bin/systemctl daemon-reload
Also, the home directory for the postgres user should be changed to:
$ $EDITOR /etc/passwd (change postgres user home directory) $ sudo mkdir /disk/1/pgsql $ sudo cp /var/lib/pgsql/.bash_profile /disk/1/pgsql $ sudo chown -R postgres:postgres /disk/1/pgsql
Now initialize the db-cluster:
$ sudo su -l postgres $ initdb -D $HOME/data --locale=C --lc-collate=C --lc-ctype=C -E UTF8 $ $EDITOR data/pg_hba.conf > change 'trust' authentication to 'ident'
Start up the service:
$ sudo systemctl enable postgresql.service $ sudo systemctl start postgresql.service
Test the service:
$ sudo su -l postgres postgres$ psql postgres# \l
Make sure postgresql account has a password and will listen on the loop-back interface:
$ sudo su -l postgres
$ psql
postgres# alter user postgres encrypted password '*********'; (remember this)
postgres# \q
$ rm .psql_history (or else the password is stored on disk)
$ cd data
$ vim pg_hba.conf
<<< change <<<
host all all 127.0.0.1/32 ident
host all all ::1/128 ident
>>> to >>>>
host all all 127.0.0.1/32 md5
host all all ::1/128 md5
and restart the postmaster:
$ exit (postgres account) $ sudo systemctl restart postgresql.service
Test that it works, you should get a password prompt:
$ sudo -u postgres psql -h 127.0.0.1 -U postgres template1
This is realatively straighforward:
$ sudo yum install python3-twisted #has lots of dependencies, yum gets them $ sudo yum install python3-pyparsing $ sudo yum install python3-astropy $ sudo yum install python3-matplotlib $ sudo yum install python3-setuptools $ sudo yum install python3-docutils $ sudo yum install python3-pillow #New name for Python Image Manipulation Lib
The RedHat/CentOS package universe is smaller than that available to Fedora and Debian. Instead of searching for rpms that may or may not be compatible with your OS, is ususally more reliable to just build packages from source if they are not available in the primary repositories.
$ git clone https://github.com/akorotkov/pgsphere.git $ cd pgsphere $ make USE_PGXS=1 PG_CONFIG=/usr/bin/pg_config $ sudo make USE_PGXS=1 PG_CONFIG=/usr/bin/pg_config install
Test (difficult due to user permissions, but possible):
$ mkdir results $ sudo chmod 777 . results $ sudo su postgres $ make USE_PGXS=1 installcheck $ exit $ rm regression.* $ sudo su postgres $ make USE_PGXS=1 crushtest $ exit
$ git clone https://github.com/segasai/q3c.git $ cd q3c $ make $ sudo make install
There are finite-state machines for python, need by twisted. Version 0.3.0 is the newest that will work with the system supplied python (Python 2.7.5):
$ wget https://github.com/glyph/automat/archive/v0.3.0.tar.gz $ tar -xvzf v0.3.0.tar.gz $ $EDITOR setup.py # (look for potential issues) $ sudo python setup.py install --dry-run #(look for potential issues) $ sudo python setup.py install
Getting the source is an easy download; these instructions were tested with SVN revision 6511:
$ svn http://svn.ari.uni-heidelberg.de/svn/gavo/python/trunk dachs $ cd dachs
Run setup:
$ python setup.py install --dry-run # (Look for problems) $ sudo python setup.py install
From here follow the standard instructions to test dachs. With this, you should be all set to try out stuff from tutorial.html.
The final step is to make DaCHS start as part of the system boot.
Use the following systemd unit file (put it into /etc/systemd/system/dachs.service):
[Unit] Description=The DaCHS VO server After=network.target [Service] ExecStart=/usr/local/bin/dachs serve start -f Type=simple Restart=on-abnormal [Install] WantedBy=multi-user.target
You may need to adapt the path to the dachs binary.
Before activating DaCHS through systemd, make sure you have shutdown any instances of dachs that you may have running:
$ sudo su -l gavo $ dachs serve stop $ exit
Let systemd know a config file has changed:
$ sudo /bin/systemctl daemon-reload
Then enable and start the service:
$ sudo systemctl enable dachs.service $ sudo systemctl start dachs.service $ sudo systemctl status dachs.service
Unfortunately, DaCHS has quite a few dependencies; here's the list of dependencies of our Debian package as of version 2.1. This should give you some clue as to what might be necessary on other systems:
python3-astropy, python3-docutils, python3-numpy, python3-pil, python3-pkg-resources, python3-psycopg2, python3-pyparsing, python3-cryptography, python3-docutils, python3-lxml, python3-matplotlib, python3-pkg-resources, python3-psycopg2, python3-pymoc, python3-rjsmin, python3-testresources, python3-twisted, postgresql-q3c, postgresql-pgsphere
One thing you could also try is comment in the install_requires line in DaCHS' setup.py (see below) and try to pull in the dependencies via pip. Expect minor breakage in that case, though, as we don't do versioned dependencies there, and as libraries develop, their APIs do change.
If you want to use boosters, you will additionally need:
build-essential libcfitsio3-dev
To install from our version control system (see below), you will also need:
subversion
Of course, you'll need postgres itself on top of that. We currently require postgres 9.6 or newer. If you actually need support for older Postgres releases, let us know – it's not hard to restore.
PgSphere is a postgres extension for spherical geometry. It is needed for support of the geometric types in DaCHS' ADQL implementation and in the preferred SIAP backend, so you should definitely install it. So build it, install the server development packages for postgres (such as postgresql-server-dev-9.x or postgresql-devel), check out https://github.com/pgsphere/pgsphere, and in the source directory run:
USE_PGXS=1 make sudo USE_PGXS=1 make install
DaCHS uses the Q3C library by Sergey Koposov and Oleg Bartunov, http://www.sai.msu.su/~megera/oddmuse/index.cgi/SkyPixelization for positional indexes. DaCHS uses it for positional indexes (the scs#q3cindex mixin) and in the interpretation of ADQL. It is therefore highly recommended to install it.
To do that, get the source directly from https://github.com/segasai/q3c/releases/, install the server development packages for postgres (such as postgresql-server-dev-9.x or postgresql-devel), and in the source directory run:
make sudo make install
If you cannot use the Debian package (or do not want to), you can grab a gavodachs package from our distribution page. Choose whatever gavodachs-latest.tar.gz points to.
If you want to follow the bleeding edge closely – DaCHS is being actively developed – check out whatever is in the subversion repository right now. For a read-only copy, say:
svn co http://svn.ari.uni-heidelberg.de/svn/gavo/python/trunk/ dachs
After that, the current source code is in the dachs subdirectory. This is development code, so please do not hesitate to contact us if something weird is going on with it. We mean it; even trivial reports help us to gauge where our software behaves contrary to expectations. Plus, we don't have oodles of users, so chances are you won't get on our nerves. For contact options see http://docs.g-vo.org/DaCHS/#support.
The DaCHS installer is based on setuptools; we do not use setuptools' dependency management, though, since in practice it seems more trouble than it's worth, which means you need to manually install Dependencies.
To install the software, in the dachs directory you checked out above, say:
sudo python setup.py develop
(there are various options to get the stuff installed when you prefer not to install as root; refer to the setuptools documentation if necessary). The checkout itself needs to be readable by whoever later runs the server in this mode. You can also use install instead of develop; in that case, you will have to rerun setup.py everytime you update the source.
Note: If running from SVN, do not forget to run dachs upgrade after an svn update. The on-disk structures of DaCHS sometimes change, and dachs upgrade makes sure they are properly updated if necessary. Technically, you would only need to run gavo upgrade if, in gavo --version, the two numbers behind “Schema” are different, but since dachs upgrade is smart enough to figure out when there's no need to do anything, just make it a routine to run it.
Note: python setup.py install and friends do not install DaCHS' man page. Either do that manually (it's in docs/dachs.1) or use the online version at dachs.1.html
All this is taken care of by the Debian package, so don't do any of this if you installed from .deb.
GAVO DaCHS is quite sensitive to a correct setup as regards permissions. Experience has shown that user setup is the number one reason for installation problems. So, up front, here's what the steps given below should create:
On the database side, the following must be ascertained:
You should first create a user that the DaCHS server runs as later, and a group for running DC-related processes in:
sudo adduser --system gavo sudo addgroup --system gavo sudo adduser gavo gavo
(or similar, depending on your environment). This user should not be able to log in, but it should have a home directory. Everyone that may issue a dachs serve debug must be in the group created (this is because the log directory will be writable by this group); in particular, you should add yourself:
sudo adduser `id -nu` gavo
You may want to create another account for "maintenance", or just use your normal account; if more than one person will feed the data center, you'll need more elaborate schemes.
To update the system's idea of your group membership, say newgrp gavo or log in and out now.
All users that are to ingest data into the database using DaCHS must be part of this gavo group.
The most complicated step in setting up DaCHS is actually setting up the database. We currently only support postgres.
While it is conceivable to use DaCHS together with an existing postgres database, we do not recommend trying this the first time. Experiment with a database dedicated to DaCHS first, then consider whether it's worth interfacing to your existing database or whether a copy of that data is more convenient.
You first need a database to play with, preferably in a suitable cluster (you could skip this, but the all bets are off as to whether you'll be able to store non-ASCII characters in strings).
It is recommended to create a dedicated cluster first even if you want to connect DaCHS to a pre-existing database later to get a feeling for how it works. See Connecting to a remote database for information on what setup is necessary in this case.
Database cluster generator is very system-dependent, and ideally a database admin would assist you.
On Debian systems dedicated for GAVO DaCHS, you can try the following (Warning: This will destroy any previous content anyone put in postgres databases on that particular system):
Find out the version of the server you will be running (e.g., using dpkg -l; in Debian, more than one version may be installed in parallel. It's probably a good idea to use the most recent one. Set your desired version for subsequent use:
export PGVERSION=11
Drop the Debian default cluster (this will delete everything in there -- for a fresh install, that doesn't matter, but don't do this if other people use the database). If you don't do this, your database will listen do a different port, and you will have to adapt the default profiles:
sudo pg_dropcluster --stop $PGVERSION main
Create the new cluster used by DaCHS:
sudo pg_createcluster -d /<path-to-where-your-db-should-reside> \ --locale=C -e UNICODE\ --lc-collate=C --lc-ctype=C $PGVERSION main
The locale should currently be C, because only the C locale will allow you databases with all kinds of encodings. The database stores descriptions and similar entities, and you may encounter funny characters in there. It would be a shame if you couldn't store them (plus, you would get odd error messages for those).
If unsure where to put the cluster: Debian's default is /var/lib/postgresql/<postgres-version>/main.
Start the server:
sudo /etc/init.d/postgresql start
Create the database itself:
sudo -u postgres createdb -Ttemplate0 --encoding=UTF-8 --locale=C gavo
On Debian, the configuration files for this cluster are at /etc/postgresql/$PGVERSION/pgdata/.
At least during setup, you also need superuser privileges on the database. For dachs init below to work, your normal account must have such privileges. On Debian systems, you can simply say:
sudo -u postgres createuser -s `id -nu`
You can drop those privileges later if they make you nervous, but for gavo init you need to be DB superuser. Also note that DaCHS assumes your server is trusted, and if people have managed to take over an account in the gavo group, they can do with your database whatever they please anyway. In particular (don't complain we didn't tell you), DaCHS currently encrypts no passwords; for the DB passwords, sensible encryption would mean the software requires some passphrase during startup, which we don't want. For user passwords (for protecting web resources), it would make no sense since with HTTP basic authentication as employed by DaCHS, they travel through the net unencrypted anyway (which is sometimes called "mild security").
Next, you need to decide on a "root" directory for DaCHS. Below it, there are data descriptions, cache files, logs, etc. (these locations can be changed later, but for a simple setup we recommend keeping everything together). By default, this is /var/gavo.
DaCHS is configured in an INI-style configuration file in /etc/gavo.rc (overridable using the envirvonment variable GAVOSETTINGS). In addition, users, in particular the gavo user, can have ~/.gavorc files, the contents of which override settings in /etc/gavo.rc.
Configuration Settings gives a walkthrough through the most important settings; for now, you must set the DaCHS root dir if you are not happy with /var/gavo:
[general] rootDir: /data/gavo
as /etc/gavo.rc.
Whatever rootDir is, it must exist and be writable by you, or you must have sufficient privileges to create it. Do not run dachs init as root, since the files and directories it creates will be owned by whoever ran the program. In the typical situation in which you may not write to rootDir's parent, do something like:
sudo mkdir -p /data/gavo sudo chown `id -nu`:gavo /data/gavo
You can now let DaCHS create its file system hierarchy:
dachs init
dachs init will spit out a warning about a missing file defaultmeta.txt on the first run. On that first run, you can ignore the warning; the missing file will be created by DaCHS.
If your database server is not on the same machine as your web server (which is not recommended for a test setup), you have to pass a complete DSN that lets DaCHS connect as a superuser to dachs init. A DSN ("Data Source Name") is a sequence of key-values pairs as used by ODBC or Postgres itself (with keys discussed in Database Connection Control Functions in the postgres documentation). You would say something like:
dachs init --dsn "host=myhost.xy port=5546 user=super password=secret dbname=wisdom"
– make sure you give at least dbname and whatever role DaCHS ends up using has superuser privileges during setup (that role is not used during normal DaCHS operation any more).
You can later run gavo init again. It will not clobber anything you did in the meantime (well, if it does, it's a bug and you should fiercely complain). In particular, this is the most convenient way to create directories if you changed locations in gavo.rc.
Though you can operate the server manually through dachs serve (start|stop|reload), you will probably want to have your init system automatically start it. See https://docs.g-vo.org/DaCHS/tutorial.html#starting-and-stopping-the-server for details on integrating DaCHS with either sysvinit or systemd.
We do not really recommend using Docker containers on production machines. We do, however, use Docker in our internal QA to check installability and upgradeability; in case you are curious what we do, see http://svn.ari.uni-heidelberg.de/svn/integration/dockerbased .
Still, if you want to build a Docker-able DaCHS take a look at the corresponding Git or, analogously, Docker repositories.