Skip to content

Configuring SMRT Link

SMRT Link configuration is done interactively during the installation process (see Installing SMRT Link). For example, during installation you will setup:

  • The SMRT Link server domain name (DNS)
  • The location of db_datadir, jobs_root, and tmp_dir (see System Requirements)
  • SMRT Analysis job email notifications
  • Compute configurations
    • You can setup multiple compute configurations, for example:
      1. SLURM distributed analysis (general partition)
      2. SLURM distributed analysis (high-mem or CPU partition)
      3. Local analysis (non-distributed analysis)

Expand the Configuration Details section below to see an example configuration file generated during a SMRT Link installation. This file can be found at $SMRT_ROOT/userdata/config/smrtlink.config following installation.

Configuration Details 
# smrtlink config

# 'install' settings
install__user='smrtanalysis';
install__group='smrtanalysis';
install__sluuid='859d2df1-cc8a-4e56-bc5b-0c83df4a5c79';
install__umask='__USE_DEFAULT__';                # Current val: '0022'

# 'system' settings
system__memtotal='__USE_DEFAULT__';              # Current val: '12884901888'

# 'smrtlink' settings
smrtlink__dnsname='smrtlinkhost.mydomain.com';
smrtlink__gui_port='__USE_DEFAULT__';            # Current val: '9090'
smrtlink__services_port='__USE_DEFAULT__';       # Current val: '9091'
smrtlink__services_minmem='__USE_DEFAULT__';     # Current val: '3072'
smrtlink__services_maxmem='__USE_DEFAULT__';     # Current val: '3072'
smrtlink__ics_services_minmem='__USE_DEFAULT__';  # Current val: '1216'
smrtlink__ics_services_maxmem='__USE_DEFAULT__';  # Current val: '1216'
smrtlink__mail_host='__USE_DEFAULT__';           # Current val: ''
smrtlink__mail_port='__USE_DEFAULT__';           # Current val: '25'
smrtlink__mail_user='__USE_DEFAULT__';           # Current val: ''
smrtlink__mail_password='__USE_DEFAULT__';       # Current val: ''
smrtlink__nworkers='__USE_DEFAULT__';                 # Current val: '8'
smrtlink__extended_cell_use_enable='__USE_DEFAULT__';  # Current val: 'false'
smrtlink__pacbio_internal='__USE_DEFAULT__';     # Current val: 'false'

# 'remote' settings
remote__eve_server_select='__USE_DEFAULT__';     # Current val: 'production'
remote__eve_url='__USE_DEFAULT__';               # Current val: ''
remote__update_server_select='__USE_DEFAULT__';  # Current val: 'production'
remote__update_url='__USE_DEFAULT__';            # Current val: ''
remote__update_enable='__USE_DEFAULT__';         # Current val: 'true'

# 'cromwell' settings
cromwell__port='__USE_DEFAULT__';                # Current val: '9096'

# 'database' settings
database__dbport='__USE_DEFAULT__';              # Current val: '9095'
database__dbdatadir='/opt/pacbio/smrtlink/userdata/db_datadir.default';

# 'datadirs' settings
datadirs__jobsroot_dir='/opt/pacbio/smrtlink/userdata/jobs_root.default';
datadirs__jobsroot_umask='__USE_DEFAULT__';   # Current val: '0022'
datadirs__tmpdir_dir='/tmp';

# 'computecfg_00' settings
computecfg_00__name='__USE_DEFAULT__';                # Current val: 'SMRT Analysis Compute Configuration'
computecfg_00__enable='__USE_DEFAULT__';              # Current val: 'true'
computecfg_00__menuorder='__USE_DEFAULT__';           # Current val: '1'
computecfg_00__nproc='8';
computecfg_00__maxchunks='__USE_DEFAULT__';           # Current val: '24'
computecfg_00__jmstype='Slurm';
computecfg_00__cromwell_loglevel='__USE_DEFAULT__';   # Current val: 'INFO'
computecfg_00__cromwell_concurrent_job_limit='__USE_DEFAULT__';  # Current val: '500'
computecfg_00__slurm_bindir='/usr/bin';
computecfg_00__slurm_partition='__USE_DEFAULT__';     # Current val: ''
computecfg_00__slurm_startargs='__USE_DEFAULT__';     # Current val: ''
computecfg_00__slurm_useraccting='__USE_DEFAULT__';   # Current val: 'false'
computecfg_00__slurm_memrequest='__USE_DEFAULT__';    # Current val: 'false'
computecfg_00__slurm_slurmconf='__USE_DEFAULT__';     # Current val: ''

# 'computecfg_01' settings
computecfg_01__name='Local Analysis';
computecfg_01__enable='__USE_DEFAULT__';              # Current val: 'true'
computecfg_01__menuorder='__USE_DEFAULT__';           # Current val: '2'
computecfg_01__nproc='8';
computecfg_01__maxchunks='__USE_DEFAULT__';           # Current val: '24'
computecfg_01__jmstype='NONE';
computecfg_01__cromwell_loglevel='__USE_DEFAULT__';   # Current val: 'INFO'
computecfg_01__cromwell_concurrent_job_limit='__USE_DEFAULT__';  # Current val: '500'

# 'internal' settings
internal__version='smrtlink-release_25.3.0.273777';

Note

This configuration file has two compute configurations (computecfg_00 and computecfg_01) setup for SLURM distributed analysis and local (non-distributed) analysis.


Following installation – if you need to change a given setting – you can do so by stopping SMRT Link services and using the smrt_reconfig command. The smrt_reconfig command – similar to the installation script – provides interactive prompts for each configuartion settings.

Stop Services: $SMRT_ROOT/admin/bin/services-stop

Reconfigure: $SMRT_ROOT/admin/bin/smrt_reconfig

Start Services: $SMRT_ROOT/admin/bin/services-start

Changing a specific setting

If you know exactly what setting you want to change, you can also perform smrt_reconfig non-interactively.

See all the options available: $SMRT_ROOT/admin/bin/smrt_reconfig --help

Example: To change the temporary directory (tmp_dir) from the default /tmp/smrtlink to /tmp, you could run:

$SMRT_ROOT/admin/bin/smrt_reconfig --datadirs-tmpdir-dir /tmp --batch

Note

The --batch option allows you to run the command without interactive prompts, applying the specified changes directly.


Advanced Topics

See Advanced Topics for additional configuartion options including the following: