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Migrate dnb03 mount point to dnb-ds03 #970

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merged 2 commits into from
Nov 6, 2023
Merged

Migrate dnb03 mount point to dnb-ds03 #970

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ce419e8
Migrate dnb03 mount point to dnb-ds03
kysrpex Oct 30, 2023
249f5a0
Merge branch 'master' into dnb03_to_dnb-ds03
kysrpex Oct 30, 2023
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8 changes: 4 additions & 4 deletions files/galaxy/tpv/tools.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -778,7 +778,7 @@ tools:
params:
submit_requirements: 'GalaxyGroup == "compute_mothur"'
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
Expand All @@ -792,7 +792,7 @@ tools:
params:
submit_requirements: 'GalaxyGroup == "compute_mothur"'
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
Expand All @@ -803,7 +803,7 @@ tools:
'.*bioext_bam2msa.*':
params:
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,,/data/dnb08/galaxy_db/:rw,/data/dnb-ds02/galaxy_db/:ro,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
Expand All @@ -813,7 +813,7 @@ tools:
'last_*':
params:
docker_run_extra_arguments: --pids-limit 10000 --ulimit fsize=1000000000 --env TERM=vt100
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_volumes: "$_CONDOR_SCRATCH_DIR:rw,$job_directory:rw,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro,/data/dnb-ds03/galaxy_db/:ro,/data/dnb05/galaxy_db/:ro,/data/dnb06/galaxy_db/:rw,/data/dnb07/galaxy_db/:rw,/data/dp01/galaxy_db/:rw,/data/0/galaxy_db/:ro,/data/1/galaxy_db/:ro,/data/2/galaxy_db/:ro,/data/3/galaxy_db/:ro,/data/4/galaxy_db/:ro,/data/5/galaxy_import/galaxy_user_data/:ro,/data/6/galaxy_db/:ro,/data/7/galaxy_db/:ro,/usr/local/tools/:ro"
docker_default_container_id: centos:8.3.2011
scheduling:
require:
Expand Down
2 changes: 1 addition & 1 deletion group_vars/all.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ autofs_conf_files:
- dnb02 -rw,hard,nosuid ufr-dyn.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb-ds01 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb01-legacy
- dnb-ds02 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb02-legacy
- dnb03 -rw,hard,nosuid ufr-dyn.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb-ds03 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb03-legacy
- dnb04 -rw,hard,nosuid ufr-dyn.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb05 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb01/&
- dnb06 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb06
Expand Down
4 changes: 2 additions & 2 deletions group_vars/maintenance.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ fsm_scripts:
- /data/2/galaxy_db/tmp
- /data/dnb01/galaxy_db/tmp
- /data/dnb02/galaxy_db/tmp
- /data/dnb03/galaxy_db/tmp
- /data/dnb-ds03/galaxy_db/tmp
- /data/dnb05/galaxy_db/tmp
- /data/dnb06/galaxy_db/tmp
- /data/jwd/tmp
Expand All @@ -136,7 +136,7 @@ fsm_scripts:
group: "{{ fsm_galaxy_user.groupname }}"
paths:
- "{{ galaxy_config['galaxy']['job_working_directory'] }}"
- /data/dnb03/galaxy_db/job_working_directory
- /data/dnb-ds03/galaxy_db/job_working_directory
- /data/jwd/main
- /data/jwd01/main
- /data/jwd02f/main
Expand Down
4 changes: 2 additions & 2 deletions group_vars/sn07.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ conda_prefix: /opt/miniconda
# - /data/2/galaxy_db/tmp
# - /data/dnb01/galaxy_db/tmp
# - /data/dnb02/galaxy_db/tmp
# - /data/dnb03/galaxy_db/tmp
# - /data/dnb-ds03/galaxy_db/tmp
# - /data/jwd/tmp
# time: "{{ fsm_intervals.long }}"
# upload_dirs:
Expand All @@ -64,7 +64,7 @@ conda_prefix: /opt/miniconda
# group: "{{ fsm_galaxy_user.groupname }}"
# paths:
# - "{{ galaxy_config['galaxy']['job_working_directory'] }}"
# - /data/dnb03/galaxy_db/job_working_directory
# - /data/dnb-ds03/galaxy_db/job_working_directory
# - /data/jwd/main
# time: "{{ fsm_intervals.long }}"
# Docker is not used on headnode anymore, gxadmin cleanup needs to run only once - commented 11/29/2022
Expand Down
2 changes: 1 addition & 1 deletion roles/hxr.autofs/defaults/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ data_conf:
- 7 -rw,hard,nosuid,quota sn03.bi.uni-freiburg.de:/export/galaxy1/data/&
- dnb01 -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb02 -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb03 -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- dnb-ds03 -rw,hard,nosuid,nconnect=2 denbi.svm.bwsfs.uni-freiburg.de:/dnb03-legacy
- dnb04 -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- db -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
- jwd -rw,hard,nosuid,quota ufr.isi1.public.ads.uni-freiburg.de:/ifs/isi1/ufr/bronze/nfs/denbi/&
Expand Down
4 changes: 2 additions & 2 deletions roles/usegalaxy-eu.monitoring/tasks/network_disks_access_time.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@
timeout 3m pssh -h /etc/pssh/cloud -l centos 'time timeout 1m ls /data/dnb02/galaxy_db/' > $TIMES
cat $TIMES | awk 'v && /real/{print v,$2}/SUCCESS/{v=$4}' | sed 's/\([0-9]*\)m\([0-9.]*\)s/\1\t\2/g' | awk '{print $1,$2"\t"$2 * 60 + $3}' | sed 's/://g' | awk '{print "disk-access-time,server="$1",disk=dnb02 seconds="$3}'

timeout 3m pssh -h /etc/pssh/cloud -l centos 'time timeout 1m ls /data/dnb03/galaxy_db/' > $TIMES
cat $TIMES | awk 'v && /real/{print v,$2}/SUCCESS/{v=$4}' | sed 's/\([0-9]*\)m\([0-9.]*\)s/\1\t\2/g' | awk '{print $1,$2"\t"$2 * 60 + $3}' | sed 's/://g' | awk '{print "disk-access-time,server="$1",disk=Isilon_dnb03_cluster seconds="$3}'
timeout 3m pssh -h /etc/pssh/cloud -l centos 'time timeout 1m ls /data/dnb03-legacy/galaxy_db/' > $TIMES
cat $TIMES | awk 'v && /real/{print v,$2}/SUCCESS/{v=$4}' | sed 's/\([0-9]*\)m\([0-9.]*\)s/\1\t\2/g' | awk '{print $1,$2"\t"$2 * 60 + $3}' | sed 's/://g' | awk '{print "disk-access-time,server="$1",disk=dnb03-legacy seconds="$3}'

timeout 3m pssh -h /etc/pssh/cloud -l centos 'time timeout 1m ls /data/dnb05/galaxy_db/' > $TIMES
cat $TIMES | awk 'v && /real/{print v,$2}/SUCCESS/{v=$4}' | sed 's/\([0-9]*\)m\([0-9.]*\)s/\1\t\2/g' | awk '{print $1,$2"\t"$2 * 60 + $3}' | sed 's/://g' | awk '{print "disk-access-time,server="$1",disk=dnb05 seconds="$3}'
Expand Down
8 changes: 4 additions & 4 deletions templates/galaxy/config/object_store_conf.xml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no
</description>
<files_dir path="/data/dnb-ds01/galaxy_db/files"/>
<extra_dir type="temp" path="/data/dnb-ds01/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/dnb03/galaxy_db/job_working_directory"/>
<extra_dir type="job_work" path="/data/dnb-ds03/galaxy_db/job_working_directory"/>
</backend>
<backend id="files9" type="disk" weight="0" store_by="id" name="University of Freiburg Isilon storage (id=files9)">
<description>
Expand Down Expand Up @@ -87,7 +87,7 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no
</description>
<files_dir path="/data/dnb-ds02/galaxy_db/files"/>
<extra_dir type="temp" path="/data/dnb-ds02/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/dnb03/galaxy_db/job_working_directory"/>
<extra_dir type="job_work" path="/data/dnb-ds03/galaxy_db/job_working_directory"/>
</backend>
<backend id="files10" type="disk" weight="0" store_by="uuid" name="University of Freiburg Isilon storage (id=files10)">
<description>
Expand All @@ -114,9 +114,9 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no
</table>
</div>
</description>
<files_dir path="/data/dnb03/galaxy_db/files"/>
<files_dir path="/data/dnb-ds03/galaxy_db/files"/>
<extra_dir type="temp" path="/data/dnb-ds02/galaxy_db/tmp"/>
<extra_dir type="job_work" path="/data/dnb03/galaxy_db/job_working_directory"/>
<extra_dir type="job_work" path="/data/dnb-ds03/galaxy_db/job_working_directory"/>
</backend>
<backend id="files11" type="disk" weight="0" store_by="uuid">
<files_dir path="/data/dnb05/galaxy_db/files"/>
Expand Down
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