Skip to content

Latest commit

 

History

History
139 lines (92 loc) · 5.52 KB

Using.rst

File metadata and controls

139 lines (92 loc) · 5.52 KB
Raw
.. hightlight:: rest

Using Lifemapper Server roll

Contents

After the roll is installed, the initial database schema, and user authentication are set up and postgres and pgbouncer are configured.

Populate the database

  1. Initialize the database happens on reboot, called by rocks/bin/initLM

    Examine the script output in /tmp/catalogDefaultDataInputs.log (and /tmp/initLM.log).

    Check the available memory

    # free -m

    If the output indicates 200-300 Mb, reboot the VM:

    # reboot

Add a new LmCompute

  1. Register LmCompute instance(s) as root

    As user root, add the section [LmServer - registeredcompute] in config/site.ini to include

    [LmServer - registeredcompute]
COMPUTE_NAME: <required>
COMPUTE_IP:  <required  **private IP if compute nodes from this cluster**>
COMPUTE_IP_MASK:  <required **CIDR if compute nodes from this cluster**>
COMPUTE_CONTACT_USERID:  <required>
COMPUTE_CONTACT_EMAIL:  <required **only if new user**>

    The new record requires COMPUTE_NAME, COMPUTE_IP, and COMPUTE_CONTACT_USERID. If the COMPUTE_CONTACT_USERID does not already exist in the database, COMPUTE_CONTACT_EMAIL is also required.

    IMPORTANT: When running LmServer and LmCompute on the same cluster, nodes (in LmCompute functions) will contact the frontend through the private network. In this case, make sure to put the private network in the COMPUTE_IP, and a CIDR in the COMPUTE_MASK. **TODO: Rename those variables! **

    As user root, run the script to install LmCompute instance configured for this LmServer

    $ $PYTHON /opt/lifemapper/LmDbServer/tools/registerCompute.py

Test the LmWebServer setup

  1. Begin by checking the webservices. Open a web browser to the FQDN or IP of the server, then append '/services' to the address. If the webserver returns an error message, look at the following to determine the cause

    1. Make sure web access is enabled (instructions at http://yeti.lifemapper.org/roll-documentation/base/6.2/enable-www.html)
    2. /var/log/httpd/lifemapper_error
    3. /var/log/messages
    4. /opt/lifemapper/log/cherrypyErrors.log
    5. /opt/lifemapper/log/web.log

  2. The following commands must be executed as user lmwriter. To become lmwriter do:

    # su - lmwriter

  3. Create a test user:

    $ $PYTHON /opt/lifemapper/LmWebServer/tests/scripts/createTestUser.py  > /tmp/createTestUser.log 2>&1
  Successfully created user

    TODO: Move to command lm test user

  4. Check job server:

    $ $PYTHON /opt/lifemapper/LmWebServer/tests/scripts/checkJobServer.py > /tmp/checkJobServer.log 2>&1

  27 Sep 2015 13:57 MainThread.log.debug line 80 DEBUG    {'epsgcode': '4326', 'displayname': 'Test Chain57292.8734326', 'name': 'Test points57292.8734326', 'pointstype': 'shapefile'}
  27 Sep 2015 13:57 MainThread.log.debug line 80 DEBUG    Test Chain57292.8734326
  27 Sep 2015 13:57 MainThread.log.warning line 136 WARNING  Database connection is None! Trying to re-open ...
  27 Sep 2015 13:57 MainThread.log.debug line 80 DEBUG       inserted job to write points for occurrenceSet 1 in MAL
  Closed/wrote dataset /share/lmserver/data/archive/unitTest/000/000/000/194/pt_94.shp
  creating index of new  LSB format
  27 Sep 2015 13:57 MainThread.log.debug line 80 DEBUG       inserted job to write points for occurrenceSet 94 in MAL
  Occurrence job id: 148
  Model job id: 149
  Projection job id: 150

    TODO: Move to command lm test jobserver (or 'lm test makeflow' when creating makeflow documents and starting makeflow processes replace the jobserver)

  5. Check local URLs. This test shows the result of URLs on the local server. EML is not configured, so errors for this format may be ignored. We will add configuration to identify installed formats.

    $ $PYTHON /opt/lifemapper/LmWebServer/tests/scripts/checkLmWeb.py  > /tmp/checkLmWeb.log 2>&1
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public/services/
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public/services/sdm/
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public/services/sdm/experiments
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public/services/sdm/layers
  ...
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG     returned HTTP code: 500
  27 Sep 2015 14:38 MainThread.log.debug line 80 DEBUG    Url: http://lm.public/services/sdm/layers/94/atom
  ...

    TODO: Move to command lm test web

Run the archivist

  1. To start the archivist as user lmwriter do

    $ $PYTHON /opt/lifemapper/LmDbServer/pipeline/archivist.py start

    TODO: Move to command lm start archivist

  2. To stop the archivist:

    $ $PYTHON /opt/lifemapper/LmDbServer/pipeline/archivist.py stop

    TODO: Move to command lm stop archivist

  3. After the archivist has run for awhile and LmCompute has pulled, computed, and returned some jobs, check URLs on completed jobs (as user lmwriter)

    $ $PYTHON /opt/lifemapper/LmWebServer/tests/scripts/checkLmWeb.py