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This page was last updated on Monday, 19-Mar-2018 12:54:06 CDT
Link to running instance https://daucus.vcru.wisc.edu:8243/sl
smrtanalysis soft nofile 8192 smrtanalysis hard nofile 8192
… Use the 'smrtanalysis' as the SMRT Analysis user? [Y/n]: y … Specify the Local File System Root Directory: [/opt/pacbio/smrtlink]: … Enter the SMRT Link GUI (http) port [9090]: Enter the SMRT Link Services port [9091]: Enter the SMRT Link GUI Shutdown port [9092]: Enter the SMRT Link GUI AJP port [9093]: … Enter the SMRT Link Services initial memory (in MB) [32768]: Enter the SMRT Link Services maximum memory (in MB) [32768]: Enter the SMRT Link GUI initial memory (in MB) [8192]: Enter the SMRT Link GUI maximum memory (in MB) [8192]: … Enter the SMRT View Server (http) port [9094]: … Enter the initial memory SMRT View Server (in MB) [32768]: Enter the maximum memory SMRT View Server (in MB) [32768]: … Enter the SMRT Link Database port [9095]: Enter the full path to the 'dbdatadir' directory [/opt/pacbio/smrtlink/userdata/db_datadir.default]: Directory '/opt/pacbio/smrtlink/userdata/db_datadir.default' does not exist. Create it? [Y/n]: … The following directories should be configured to point to the actual locations: data_root jobs_root tmp_dir data_root - This directory stores PacBio instrument data and needs to be large (> 30TB). Enter the full path to the 'data_root' directory [/opt/pacbio/smrtlink/userdata/data_root.default]: Directory '/opt/pacbio/smrtlink/userdata/data_root.default' does not exist. Create it? [Y/n]: Creating directory '/opt/pacbio/smrtlink/userdata/data_root.default'... jobs_root - This directory stores output from SMRT Analysis and needs to be large (> 15TB). Enter the full path to the 'jobs_root' directory [/opt/pacbio/smrtlink/userdata/jobs_root.default]: Directory '/opt/pacbio/smrtlink/userdata/jobs_root.default' does not exist. Create it? [Y/n]: Creating directory '/opt/pacbio/smrtlink/userdata/jobs_root.default'... tmp_dir - This directory is used for fast I/O operations, and should be a local directory (not NFS mounted) and needs to be large for large genome assembly jobs (>500Gb minimum, 1Tb recommended). This directory will be automatically created, as needed, on compute cluster nodes. Enter the full path to the 'tmp_dir' directory [/tmp/smrtlink]: Directory '/tmp/smrtlink' does not exist. Create it? [Y/n]: … Enable SMRT Link Event Service? [Y/n]: Enable SMRT Link Update Service? [Y/n]: Test connectivity to the remote URLs? [Y/n]: … Pick an option: 1) None (Non-Distributed Mode) 2) Other JMS Choice [1]: 1 Enter the max number of workers 'NWORKERS' [50]: NPROC - Specifies the maximum number of processors per task Enter the number of processors per task 'NPROC [63]: TOTAL_NPROC - Specifies the maximum number of total processors/slots a pbsmrtpipe job will use concurrently. Enter the total number of processors 'TOTAL_NPROC' [1000]: 64 CHUNKING - Specifies whether large files should be broken up into smaller chunks Enable chunking 'CHUNKING'? [Y/n]: MAXCHUNKS - Specify the maximum number of chunks when breaking up large files Enter the max number of chunks 'MAXCHUNKS' [24]: …
Starting SMRT View Server Node... Tomcat started. SMRT View Server Node started successfully.. Step #1 Attempting to apply-config Successfully Completed apply-config Successfully completed running smrtflow.tools.apply_config 0.2.0 (smrtflow 0.6.7+9513.aef53eb) in 1 sec. completed applying config Step #2 Checking system requirements (e.g., ulimits) No conflicts with SMRT Link detected. Successfully completed checking system requirements Step #3 Checking if db is up and running Successfully completed check for Postgres database (db is up and running) Step #4a Checking SMRT Link Analysis services daemon... Successfully completed checking SMRT Link Analysis services daemon is NOT running. Step #4b Checking Tomcat GUI webserver daemon... Successfully completed checking Tomcat GUI webserver daemon is NOT running. Step #4c Checking WSO2 API Manager daemon... Successfully completed checking WSO2 API Manager daemon is NOT running. Completed check of sub-components; SLA, Tomcat and WSO2 API Manager. No sub-component is running Step #5 Attempting to Start SMRTLink Analysis services daemon... Successfully started up SMRT Link Analysis services on PID 60639 Successfully got status Services have been up for 10.744 seconds. Successfully completed running smrtflow.tools.get_system_status 0.1.0 (smrtflow 0.6.7+9513.aef53eb) in 14 sec. Step #6 Attempting to start Tomcat GUI webserver daemon... Tomcat started. Successfully got status of http://localhost:9090/sl Successfully completed running smrtflow.tools.get_system_status 0.1.0 (smrtflow 0.6.7+9513.aef53eb) in 3 sec. Successfully started up tomcat GUI webserver Attempting to start WSO2 API Manager... Attempting to configure API Manager for SL Analysis backend... added roles updated API b7f69d91-21ec-41e1-9f5f-98c80a8ce613 Attempting to configure API Manager admin proxy... updated API 7c20cecd-a8f8-4847-96c3-7590e82cf7f2 created ReadOnlyRemoteUserStoreService definition Successfully started up and configured WSO2 API Manager for SL Analysis backend Completed starting the SMRT Link Analysis services, tomcat UI server and WSO2 API Manager Waiting for services to start... Checking SMRT Link status... Checking SMRT View status... Status summary: SMRT Link status: ok SMRT View status: ok Services started successfully.