| Version 31 (modified by zequi, 4 years ago) (diff) |
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ESGF Local Node Deployment Tutorial
This page shows how to deploy an ESGF Node that provides data, index and idp services and belongs to the esgf-test federation. The purpose of this node is to test the process of publication in the ESGF.
This page assumes that command are executed by the root user (not sudo).
Index
- Prerequisites
- Previous installation clean up
- Installation from scratch
- Configuration for publication
- Publish the test dataset
- Publish CORDEX datasets
- Known issues
- References
0. Prerequisites
- You have to create a globus account - https://www.globusid.org/create
1. Previous installation clean up
Execute /usr/local/bin/esg-node stop in order to stop the current ESGF services (in case they are running).
[root@spock ~]# /usr/local/bin/esg-node stop
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E::::::::::::::::::::ES:::::::::::::::SS GGG::::::GGG:::GF::::::::FF
EEEEEEEEEEEEEEEEEEEEEE SSSSSSSSSSSSSSS GGGGGG GGGGFFFFFFFFFFF.llnl.gov
Checking that you have root privs on spock.meteo.unican.es... [OK]
Checking requisites...
Using IP: 193.144.184.40
Stopping search services...
Using solr_workdir=/usr/local/src/esgf/workbench/esg/solr-5.5.3
Using solr_install_dir=/usr/local/solr-home/slave-8983
Using solr_data_dir=/esg/solr-index/slave-8983
Using solr_server_dir=/usr/local/solr
Using solr_logs_dir=/esg/solr-logs
Using esg_dist_url=http://esg-dn2.nsc.liu.se/esgf/dist
sudo: source: command not found
Sending stop command to Solr running on port 8983 ... waiting 5 seconds to allow Jetty process 16339 to stop gracefully.
Sending stop command to Solr running on port 8984 ... waiting 5 seconds to allow Jetty process 16554 to stop gracefully.
Stopping Globus Services for Data-Node... (GridFTP) stop_globus_services for datanode
globus-gridftp-server: unrecognized service
Stopping Globus Services for Index-Node... (MyProxy server) stop_globus_services for gateway
Stopping myproxy-server: [ OK ]
No MyProxy Process Currently Running...
Tomcat (jsvc) process is running...
stop tomcat: /usr/local/tomcat/bin/jsvc -pidfile /var/run/tomcat-jsvc.pid -stop org.apache.catalina.startup.Bootstrap
(please wait)
postmaster (pid 16024) is running...
Stopping postgresql service: [ OK ]
Stopping httpd: [ OK ]
Running shutdown hooks...
---------------------------
Running Node Services...
node type: [ data index idp compute ] (60)
---------------------------
---------------------------
Execute source /usr/local/bin/esg-purge.sh && esg-purge all
2. Installation from scratch
Change directory to /usr/local/bin/
[root@spock ~]# cd /usr/local/bin/
[root@spock bin]# wget -O esg-bootstrap http://distrib-coffee.ipsl.jussieu.fr/pub/esgf/dist/devel/esgf-installer/2.4/esg-bootstrap --no-check-certificate [root@spock bin]# chmod 555 ./esg-bootstrap [root@spock bin]# ./esg-bootstrap
Your directory should look like this:
[root@spock bin]# ls esg-bootstrap esg-functions esg-init esg-node esg-purge.sh jar_security_scan setup-autoinstall
Check your node's version:
[root@spock bin]# ./esg-node --version Version: v2.4.24-master-release Release: Bifrost Earth Systems Grid Federation (http://esgf.llnl.gov) ESGF Node Installation Script
Set node's type:
[root@spock bin]# ./esg-node --set-type data idp index node type set to: [ index data idp ] (28)
Install the node:
[root@spock bin]# ./esg-node --install
Please select the ESGF distribution mirror for this installation (fastest to slowest):
-------------------------------------------
[1] http://dist.ceda.ac.uk/esgf
[2] http://esg-dn2.nsc.liu.se/esgf
[3] http://aims1.llnl.gov/esgf
[4] http://distrib-coffee.ipsl.jussieu.fr/pub/esgf
-------------------------------------------
select [1] > 1
Are you ready to begin the installation? [Y/n]
Configured host IP address does not match available IPs...
Detected multiple IP addresses bound to this host...
Please select the IP address to use for this installation
-------------------------------------------
[0] : 193.xxx.xxx.xxx
[1] : 192.xxx.xxx.xxx
-------------------------------------------
select [] > (select the one that fits your case)
Welcome to the ESGF Node installation program! :-) What is the fully qualified domain name of this node? [spock.meteo.unican.es]: What is the admin password to use for this installation? (alpha-numeric only) []: Please re-enter password: What is the name of your organization? [unican]: Please give this node a "short" name: []: unican Please give this node a more descriptive "long" name []: unican What is the namespace to use for this node? (set to your reverse fqdn - Ex: "gov.llnl") [es.unican.meteo]: What peer group(s) will this node participate in? (esgf-test|esgf-prod) [esgf-test]: What is the default peer to this node? [spock.meteo.unican.es]: What is the hostname of the node do you plan to publish to? [spock.meteo.unican.es]: What email address should notifications be sent as? []: Is the database external to this node? [y/N]: Please enter the database connection string... (form: postgresql://[username]@[host]:[port]/esgcet) What is the database connection string? [postgresql://dbsuper@localhost:5432/esgcet]: postgresql:// entered: postgresql://dbsuper@localhost:5432/esgcet What is the (low priv) db account for publisher? [esgcet]: What is the db password for publisher user (esgcet)? []:
Enter password for postgres user dbsuper: Re-enter password for postgres user dbsuper: Please Enter PostgreSQL port number [5432]:>
Would you like a "system" or "user" publisher configuration:
-------------------------------------------
*[1] : System
[2] : User
-------------------------------------------
[C] : (Custom)
-------------------------------------------
select [1] >
You have selected: 1
Publisher configuration file -> [/esg/config/esgcet/esg.ini]
Is this correct? [Y/n]
Your publisher configuration file will be: /esg/config/esgcet/esg.ini
What is your organization's id? [unican]:
Would you like to use the DN: (OU=ESGF.ORG, O=ESGF) ? [Y/n]: ... Please enter the password for this keystore :
Enter a single ip address which would be cleared to access admin restricted pages. You will be prompted if you want to enter more ip-addresses Do you wish to allow further ips? y/n n
Create user credentials Please enter username for tomcat [dnode_user]: Please enter password for user, "dnode_user" [********]: Would you like to add another user? [y/N]:
Please Enter the public (i.e. routable) IP address of this host [193.xxx.xxx.xxx]:> Do you wish to use an external IDP peer?(N/y):
Do you want to continue with the Globus installation and setup? [Y/n] : Do you want to register the MyProxy server with Globus? [Y/n]: Please provide a Globus username []: YOUR-GLOBUS-USER Globus password []:
When finished, you should see something like this:
Running Node Services...
node type: [ data index idp ] (29)
---------------------------
myproxy-s 23071 root 5u IPv4 1526752 0t0 TCP *:7512 (LISTEN)
java 26088 solr 28u IPv6 1591850 0t0 TCP 127.0.0.1:7983 (LISTEN)
java 26088 solr 92u IPv6 1591986 0t0 TCP *:8983 (LISTEN)
java 26257 solr 28u IPv6 1592730 0t0 TCP 127.0.0.1:7984 (LISTEN)
java 26257 solr 92u IPv6 1593098 0t0 TCP *:8984 (LISTEN)
postmaste 29509 postgres 3u IPv6 1449862 0t0 TCP [::1]:5432 (LISTEN)
postmaste 29509 postgres 4u IPv4 1449863 0t0 TCP 127.0.0.1:5432 (LISTEN)
httpd 12706 root 4u IPv6 1512235 0t0 TCP *:80 (LISTEN)
---------------------------
Finished!...
In order to see if this node has been installed properly you may direct your browser to:
http://spock.meteo.unican.es/thredds
http://spock.meteo.unican.es/esg-orp
http://spock.meteo.unican.es/
Your peer group membership -- : [esgf-test]
Your specified "default" peer : [spock.meteo.unican.es]
Your specified "index" peer - : [spock.meteo.unican.es] (url = http://spock.meteo.unican.es/)
Your specified "idp" peer --- : [spock.meteo.unican.es] (name = SPOCK.METEO.UNICAN.ES)
Your temporary certificates have been placed in /etc/tempcerts
You can install them by executing this : esg-node --install-keypair /etc/tempcerts/hostcert.pem /etc/tempcerts/hostkey.pem
When promped for the chainfile, specify: /etc/tempcerts/cacert.pem
[Note: Use UNIX group permissions on /esg/content/thredds/esgcet to enable users to be able to publish thredds catalogs from data therein]
%> chgrp -R <appropriate unix group for publishing users> /esg/content/thredds
-------------------------------------------------------
Administrators of this node should subscribe to the
esgf-node-admins@lists.llnl.gov by sending email to: majordomo@lists.llnl.gov
with the body: subscribe esgf-node-admins
-------------------------------------------------------
v2.4.24-master-release
Writing additional settings to db. If these settings already exist, psql will report an error, but ok to disregard.
ERROR: insert or update on table "permission" violates foreign key constraint "permission_user_id_fkey"
DETAIL: Key (user_id)=(1) is not present in table "user".
Node installation is complete.
Execute the following:
[root@spock bin]# ./esg-node --install-keypair /etc/tempcerts/hostcert.pem /etc/tempcerts/hostkey.pem ... Please set the password for this keystore : Please re-enter the password for this keystore: ... certfile> /etc/tempcerts/cacert.pem certfile> ... Is the above information correct? [Y/n] Is the above information correct? [Y/n]
Restart the node:
[root@spock bin]# ./esg-node restart
Check that everything works (https://github.com/ESGF/esgf-installer/wiki/ESGF-Post-Installation-Tests).
If the CoG portal does not work follow the instructions on https://www.earthsystemcog.org/projects/cog/install_or_upgrade.
Now you should be able to log in the CoG portal using the openid "https://spock.meteo.unican.es/esgf-idp/openid/rootAdmin" and the password that you chose in the installation process.
Configuration for publishing
The installation process should have created a user in the postgres database, named rootAdmin. You can check it by running psql -U dbsuper -d esgcet (to access the postgres cli) and visualizing the table esgf_security.user.
esgcet=# select * from esgf_security.user; id | firstname | middlename | lastname | email | username | password | dn | openid | organization | organization_type | city | state | country | status_code | verificat ion_token | notification_code ----+-----------+------------+-------------+------------------------+-----------+------------------------------------+----+---------------------------------------------------------+--------------+-------------------+------+-------+---------+-------------+------------------- -------------------+------------------- 1 | Admin | | User | emailOfTheAdmin | rootAdmin | hashOfThePassword | | https://domain/esgf-idp/openid/rootAdmin | Institution | | City | State | Country | 1 | 79563dfc-ad55-4aa1 -b50e-d43692adc5e5 |
In order to test the publication, create a new user using the CoG web interface (https://[index_node_fqdn]). You should click on 'Create Account' and fill the form. Once the user is created using the CoG interface, it should be visible in the esgf_security.user table of the postgres database.
esgcet=# select * from esgf_security.user; id | firstname | middlename | lastname | email | username | password | dn | openid | organization | organization_type | city | state | country | status_code | verificat ion_token | notification_code ----+-----------+------------+-------------+------------------------+-----------+------------------------------------+----+---------------------------------------------------------+--------------+-------------------+------+-------+---------+-------------+------------------- -------------------+------------------- 1 | Admin | | User | emailOfTheAdmin | rootAdmin | hashOfThePassword | | https://domain/esgf-idp/openid/rootAdmin | Institution | | City | State | Country | 1 | 79563dfc-ad55-4aa1 -b50e-d43692adc5e5 | 0 2 | zequi | | cimadevilla | emailOfZequi | zequi | hashOfThePassword | | https://domain/esgf-idp/openid/zequi | asdf | | asdf | asdf | asdf | 1 | f187f706-b03c-467b-a570-c4ddc7afc70e |
Once the user is created, create permissions and roles as follows:
(reference documentation - https://acme-climate.atlassian.net/wiki/display/ESGF/Guide+to+ESGF+Publishing+and+Best+Practices)
esgcet=# select * from esgf_security.role;
id | name | description
----+-----------+---------------------
1 | super | Super User
2 | none | None
3 | default | Standard
4 | publisher | Data Publisher
5 | admin | Group Administrator
6 | user | user role
(6 rows)
esgcet=# select * from esgf_security.group;
id | name | description | visible | automatic_approval
----+--------------+---------------------+---------+--------------------
1 | wheel | Administrator Group | t | t
2 | test_group | test group | t | t
3 | cordex_group | cordex group | t | t
(3 rows)
esgcet=# select * from esgf_security.permission;
user_id | group_id | role_id | approved
---------+----------+---------+----------
2 | 2 | 4 | t
2 | 2 | 6 | t
2 | 3 | 6 | t
2 | 3 | 4 | t
(4 rows)
Add the following elements to /esg/config/esgf_policies_local.xml
<policy resource=".*test.*" attribute_type="test_group" attribute_value="user" action="Read"/>
<policy resource=".*test.*" attribute_type="test_group" attribute_value="publisher" action="Write"/>
<policy resource=".*cordex.*" attribute_type="cordex_group" attribute_value="user" action="Read"/>
<policy resource=".*cordex.*" attribute_type="cordex_group" attribute_value="publisher" action="Write"/>
Add the following elements to /esg/config/esgf_ats_static.xml
<attribute
type="test_group"
attributeService="https://spock.meteo.unican.es/esgf-idp/saml/soap/secure/attributeService.htm"
description="Test group for test data"
registrationService="https://spock.meteo.unican.es/esgf-idp/secure/registrationService.htm"/>
<attribute
type="cordex_group"
attributeService="https://spock.meteo.unican.es/esgf-idp/saml/soap/secure/attributeService.htm"
description="Test group for cordex data"
registrationService="https://spock.meteo.unican.es/esgf-idp/secure/registrationService.htm"/>
Generate your credentials for publication - globus certificate
myproxy-logon [ -b ] -s <openid_server> -l <your_esgf_username> -p 7512 -t 72 -o $HOME/.globus/certificate-file
The certificate is valid for 72 hours when specified by -t. If you are publishing for the first time, you will need to mkdir $HOME/.globus and use -b to bootstrap its trustroots with the server. The esgf_username is the simply the username portion of your openid rather than the entire openid string, e.g. sashakames, not https://pcmdi.llnl.gov/esgf-idp/openid/sashakames
Publish the test dataset
For esgprep and esgpublish to be available, execute source /etc/esg.env.
[root@spock ~]# esgprep mapfile --project test /esg/data/test/ Collecting files : 1 files Mapfile(s) generation: 100% |████████████████████████████████████████████████████████████| 1/1 files Mapfile(s) generated : 1 (see /root/mapfiles)
[root@spock ~]# esgpublish --service fileservice --map mapfiles/test.test.map --project test --thredds --publish --offline INFO 2017-06-02 14:59:48,405 Replacing files in dataset: test.test, version 1 INFO 2017-06-02 14:59:48,413 File /esg/data/test/sftlf.nc exists, skipping INFO 2017-06-02 14:59:48,416 New dataset version = 2 INFO 2017-06-02 14:59:48,430 Adding file info to database INFO 2017-06-02 14:59:48,469 Writing THREDDS catalog /esg/content/thredds/esgcet/1/test.test.v2.xml INFO 2017-06-02 14:59:48,522 Writing THREDDS ESG master catalog /esg/content/thredds/esgcet/catalog.xml INFO 2017-06-02 14:59:48,533 Reinitializing THREDDS server INFO 2017-06-02 14:59:48,830 Publishing: test.test INFO 2017-06-02 14:59:49,871 Result: SUCCESSFUL
Notes:
- --map must point to the file generated by esgprep mapfile
- --thredds publish data to the data node
- --publish publish data to the index node
- --offline is required for publish the test dataset (Why?)
- This publication works out of the box because esgf installs by default the required /esg/config/esgcet/esg.test.ini file.
Publish CORDEX datasets
Known issues during installation
#error "Psycopg requires PostgreSQL client library (libpq) >= 9.1
This error occurs sometimes during installation but removing the node and installing it from scratch seems to solve it...
Traceback (most recent call last):
File "setup.py", line 110, in <module>
""",
File "/usr/local/uvcdat/2.2.0/lib/python2.7/distutils/core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/dist.py", line 239, in __init__
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/dist.py", line 263, in fetch_build_eggs
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/pkg_resources.py", line 568, in resolve
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/pkg_resources.py", line 806, in best_match
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/pkg_resources.py", line 818, in obtain
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/dist.py", line 313, in fetch_build_egg
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/command/easy_install.py", line 609, in easy_install
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/command/easy_install.py", line 639, in install_item
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/command/easy_install.py", line 825, in install_eggs
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/command/easy_install.py", line 1031, in build_and_install
File "/usr/local/uvcdat/2.2.0/lib/python2.7/site-packages/setuptools-1.4-py2.7.egg/setuptools/command/easy_install.py", line 1019, in run_setup
distutils.errors.DistutilsError: Setup script exited with error: command 'gcc' failed with exit status 1
Sorry...
This action did not complete successfully
Please re-run this task until successful before continuing further
Also please review the installation FAQ it may assist you
https://github.com/ESGF/esgf.github.io/wiki/ESGFNode%7CFAQ
Failed building wheel for Pillow
This error seems unavoidable but it also seems that it doesn't affect the esgf functionality.
Installing a custom certificate in the ESGF Node
You should own your certificate file (hostcert.crt) and your private key (hostkey.key). Your /etc/httpd/conf/esgf-httpd.conf must reference your certificate and key:
228 SSLVerifyClient optional
229 SSLVerifyDepth 10
230 SSLCertificateFile /etc/certs/hostcert.crt
231 #SSLCACertificateFile /etc/certs/esgf-ca-bundle.crt
232 SSLCertificateKeyFile /etc/certs/hostkey.key
233 #SSLCertificateChainFile /etc/certs/cachain.pem
234 SSLOptions +StdEnvVars? +ExportCertData?
Then you have to import your certificate and your key into your tomcat keystore (located in /esg/config/tomcat/ and named esg-truststore.ts and keystore-tomcat). They are configurated in /usr/local/tomcat/conf/server.xml.
- If the self-signed certificate is installed in keystore-tomcat, remove it with keytool -delete -alias ALIAS -keystore keystore-tomcat, where alias can be obtained with keytool -v -list -keystore keystore-tomcat.
- Execute # openssl pkcs12 -export -in /etc/certs/hostcert.crt -inkey /etc/certs/hostkey.key -out server.p12 -name my-esgf-node -CAfile /etc/certs/hostcert.crt -caname root and keytool -importkeystore -deststorepass PASSWORD -destkeypass PASSWORD -destkeystore keystore-tomcat -srckeystore server.p12 -srcstoretype PKCS12 -srcstorepass PASSWORD -alias my-esgf-node
- Ensure it has been correctly installed with keytool -v -list -keystore keystore-tomcat.
- Restart the node: esg-node restart
