diff options
| -rw-r--r-- | topics/octopus/lizardfs/README.gmi | 53 | ||||
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 6 |
2 files changed, 58 insertions, 1 deletions
diff --git a/topics/octopus/lizardfs/README.gmi b/topics/octopus/lizardfs/README.gmi index 3a07505..78316ef 100644 --- a/topics/octopus/lizardfs/README.gmi +++ b/topics/octopus/lizardfs/README.gmi @@ -118,13 +118,64 @@ It has not yet been tested to see how much this affects reading and writing to t # Adding a node to the pool +We can add a mount point using mfsmount using systemd + +``` +[Unit] +Description=LizardFS mounts +After=syslog.target network.target + +[Service] +Type=forking +TimeoutSec=600 +ExecStart=/usr/local/guix-profiles/octo/bin/mfsmount -c /etc/lizardfs/mfsmount.cfg +ExecStop=/usr/bin/umount /lizardfs + +[Install] +WantedBy=multi-user.target +``` + +note it runs as the root user. + +It is a good idea to also run a chunk server on the node, so it effectively can cache information locally. For this we create a lizard account: + ``` addgroup -gid 600 lizardfs adduser -uid 600 -gid 600 lizardfs ``` -In password +In password file ``` lizardfs:x:600:600:Lizard,,,:/var/lib/lizardfs:/bin/sbin/nologin ``` + +Now we can run + +``` +/usr/local/guix-profiles/octo/sbin/mfschunkserver -c /etc/lizardfs/mfschunkserver_hdd.cfg -d start +``` + +and set up systemd with something like + +``` +[Unit] +Description=LizardFS chunkserver daemon +Documentation=man:mfschunkserver +After=local-fs.target network.target lizardfs-master.service +Wants=local-fs.target network-online.target + +[Service] +Type=notify +ExecStart=/usr/local/guix-profiles/octo/sbin/mfschunkserver -c /etc/lizardfs/mfschunkserver_hdd.cfg -d start +ExecReload=/bin/kill -HUP $MAINPID +Restart=on-abort +OOMScoreAdjust=-999 +IOAccounting=true +IOWeight=250 +StartupIOWeight=100 +KeyringMode=inherit + +[Install] +WantedBy=multi-user.target +``` diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi index caad794..12c21da 100644 --- a/topics/systems/mariadb/precompute-mapping-input-data.gmi +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -918,6 +918,12 @@ select * from StrainXRef WHERE InbredSetId=1 AND Used_for_mapping="Y" so it looks like we need some extra logic to fetch the used individuals from the actual genotype file(s). +For development I am running: + +``` +.guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm +``` + ## Writing the phenotype file For gemma we need to feed a phenotype file that has only the individuals that are in the genotype file (the other 'missing' phenotype values should be NAs). |