From ce419e8bcbbca21c79969bc3a5fdb2ea95aea07f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?= Date: Mon, 30 Oct 2023 14:02:33 +0100 Subject: [PATCH] Migrate dnb03 mount point to dnb-ds03 --- files/galaxy/tpv/tools.yml | 8 ++++---- group_vars/all.yml | 2 +- group_vars/maintenance.yml | 4 ++-- group_vars/sn07.yml | 4 ++-- roles/hxr.autofs/defaults/main.yml | 2 +- .../tasks/network_disks_access_time.yml | 4 ++-- templates/galaxy/config/object_store_conf.xml.j2 | 8 ++++---- 7 files changed, 16 insertions(+), 16 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 6806f957f..929ac23da 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -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: @@ -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: @@ -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: @@ -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: diff --git a/group_vars/all.yml b/group_vars/all.yml index 47008d132..e86da5afb 100644 --- a/group_vars/all.yml +++ b/group_vars/all.yml @@ -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 diff --git a/group_vars/maintenance.yml b/group_vars/maintenance.yml index ebf79138d..5f1a6a4dc 100644 --- a/group_vars/maintenance.yml +++ b/group_vars/maintenance.yml @@ -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 @@ -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 diff --git a/group_vars/sn07.yml b/group_vars/sn07.yml index 139c56540..3eac16461 100644 --- a/group_vars/sn07.yml +++ b/group_vars/sn07.yml @@ -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: @@ -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 diff --git a/roles/hxr.autofs/defaults/main.yml b/roles/hxr.autofs/defaults/main.yml index f205750cb..53989d4f0 100644 --- a/roles/hxr.autofs/defaults/main.yml +++ b/roles/hxr.autofs/defaults/main.yml @@ -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/& diff --git a/roles/usegalaxy-eu.monitoring/tasks/network_disks_access_time.yml b/roles/usegalaxy-eu.monitoring/tasks/network_disks_access_time.yml index 527743506..55550c06d 100644 --- a/roles/usegalaxy-eu.monitoring/tasks/network_disks_access_time.yml +++ b/roles/usegalaxy-eu.monitoring/tasks/network_disks_access_time.yml @@ -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}' diff --git a/templates/galaxy/config/object_store_conf.xml.j2 b/templates/galaxy/config/object_store_conf.xml.j2 index 317e1ebbe..b2ed8f1de 100644 --- a/templates/galaxy/config/object_store_conf.xml.j2 +++ b/templates/galaxy/config/object_store_conf.xml.j2 @@ -58,7 +58,7 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no - + @@ -87,7 +87,7 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no - + @@ -114,9 +114,9 @@ The storage consists of 16 Gen6 type A200 storage nodes and 16 Gen5 type X410 no - + - +