Everything you need to know about Discovery HPC
Discovery is a HPC cluster which DBIC users can utilize to run heavy computation. Discovery Overview and pages within provide official generic information about Discovery - what it provides and how to use it. This section provides additional, typically DBIC users specific information and hints.
Getting Access
MUST KNOWs
- Please be considerate about the nodes you are using. When you login, you
are on a login-node, but no work should be done here! Instead, use an interactive node
x01
, scheduling node,s01
, or if you have permission, the fancy IT nodendoli
. - Home dir limited 50gigs for large datasets, use
/dartfs/rc/lab/D/DBIC/DBIC/
Recommended .bashrc
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
# Install conda
source /optnfs/common/miniconda3/etc/profile.d/conda.sh
# use DBIC-installed git-annex
# https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#discovery-filesystem
ANNEX_BIN_PATH=/dartfs/rc/lab/D/DBIC/DBIC/archive/git-annex/usr/lib/git-annex.linux/
echo $PATH | grep -q "$ANNEX_BIN_PATH" || export PATH="$ANNEX_BIN_PATH:$PATH"
export TERM=xterm
export EDITOR=vim
alias dog="pygmentize -g"
Installing Software
Make sure datalad --version
> 0.19.3
Containers
Notes for why and how to use containers on Discovery can be found in the Research ITC containers repo.
Conda
"modules"
TODO: brief intro into modules - the system used a collection of available environments.
For the purpose of using DataLad, please use python/3.7-Anaconda-datalad
module which you can enable via module load python/3.7-Anaconda-datalad
:
[d31548v@discovery7 ~]$ which datalad
/usr/bin/which: no datalad in (/dartfs-hpc/admin/opt/el7/intel/...
[d31548v@discovery7 ~]$ module load python/3.7-Anaconda-datalad
[d31548v@discovery7 ~]$ which datalad
/optnfs/common/miniconda3-datalad/bin/datalad
POSIXy filesystem(s) for git-annex/DataLad inspired
TODO
Installing Data
TODO limit of home dir, DBIC, and the ACL
Unfortunately the filesystem used on discovery by default does not support smooth git-annex and thus DataLad operation.
If you use datalad install
or datalad clone
as instructed above, you would likely to endup in "adjusted" git-annex branch which would complicate your interactions with the data, etc.
We recommend to use new feature of git-annex allowing for custom protection of data on discovery.
For that:
Step 1: make sure you are using recent git-annex
Make sure that you are using recent (at least as of January 2023) version of git-annex.
For that you could use the version we provide and just adjust your ~/.bashrc
with the following content:
ANNEX_BIN_PATH=/dartfs/rc/lab/D/DBIC/DBIC/archive/git-annex/usr/lib/git-annex.linux/
echo $PATH | grep -q "$ANNEX_BIN_PATH" || export PATH="$ANNEX_BIN_PATH:$PATH"
(TODO note that setting this needs to be after the venv activation)
So whenever you re-login (or open a new bash
) and type git annex version
you should get version past above date.
Step 2: configure git-annex to use custom data protection
Adjust you global ~/.gitconfig
with the following section
[annex]
thawcontent-command = /dartfs/rc/lab/D/DBIC/DBIC/archive/bin-annex/thaw-content %path
freezecontent-command = /dartfs/rc/lab/D/DBIC/DBIC/archive/bin-annex/freeze-content %path
which also could be done via running commands
git config --global annex.thawcontent-command '/dartfs/rc/lab/D/DBIC/DBIC/archive/bin-annex/thaw-content %path'
git config --global annex.freezecontent-command '/dartfs/rc/lab/D/DBIC/DBIC/archive/bin-annex/freeze-content %path'
Step 3: make sure that directory has group ACL to remove children
It is the D
ACE Permission: if folder lacks it, then git-annex
will be unable to move read-only file under .git/annex
.
So, if you get a "Permission error" while trying to git annex add
or datalad save
, you might need to add that to the group permissions.
Use /dartfs/rc/lab/D/DBIC/DBIC/archive/bin-annex/fix-dir-group-perm
script with the folder under which you want to create/clone repo to add that D
.
Now, after these 3 steps, whenever you datalad install
data from rolando you should end up in master
branch.
If that doesn't happen - file an issue.
Parallel get - multiple passwords
If you are get
ing data to discovery, to non-POSIX compliant filesystem, then you must provide option -J1
to datalad get
to prevent parallel downloads and multiple password prompts.