| Version 83 (modified by carlos, 9 years ago) (diff) |
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Page Contents
This installation guide will provide instructions about how to install an ESGF data/compute node. In order to do it, the VM should have 1 core, 2GB of RAM memory and 20GB of Hard Disk.
For the installation process, it is highly recommendable to provide more than 1 core
Pre-requisites
TCP and UDP ports firewall configuration
Corporate Firewall
| Port | Direction | Type | Application | Description |
| 80 | in | tcp | Tomcat | Web server access |
| 443 | in | tcp | Tomcat | SSL - Secure Web Server Access. |
| 5432 | in | tcp | Postgres | Postgres Access. (not external: by default bound ONLY TO LOCAL INTERFACE) |
| 2811 | in | tcp | GridFTP | user-configured GridFTP Server control channel |
| (60000-61000) | in/out | tcp | GridFTP | user-configured GridFTP Server data channel (or as defined in the global variable GLOBUS_TCP_PORT_RANGE) |
| 2812 | in | tcp | GridFTP | BDM-configured GridFTP Server control channel. May run together with the user-configured one though not recommended - system resource intensive! |
| (60000-61000) | in/out | tcp | GridFTP | BDM-configured GridFTP Server data channel. May run together with the user-configured one though not recommended - system resource intensive! |
| 7512 | out | tcp | MyProxy | MyProxy client access to the certificate repository |
| 8984 | - | tcp | esgf-search (Tomcat) | local connection to the Solr master instance (not external!) |
| 8983 | in/out | tcp | esgf-search (Tomcat) | Connection to remotes Solr slave instance. Used in distributed search (shard). |
| 80 | out | tcp | esg-publisher | Local connection to THREDDS server (e.g., to check catalogs) and other nodes (node-manager) |
| 443 | out | tcp | esg-publisher | Local secure connection to THREDDS server (e.g., to restart the application) and to the idp |
IPTables configuration
Add the rules below to the IPTables configuration file, i.e. /etc/sysconfig/iptables
-A INPUT -m state --state NEW -m tcp -p tcp --dport 22 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 443 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 2811 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 2812 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 8984 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 8983 -j ACCEPT -A INPUT -m state --state NEW -m tcp -p tcp --dport 60000:61000 -j ACCEPT
then, restart the IPTables services
$ services iptables restart
Install RPM packages
First, install the sourceforge RPM repository for the *ExtUtils* packages:
$ rpm -iv http://dag.wieers.com/packages/rpmforge-release/rpmforge-release-0.3.6-1.el4.rf.x86_64.rpm
after that, the ESGF required RPM packages :
$ yum install autoconf automake bison file flex gcc gcc-c++ gettext-devel libtool libuuid-devel libxml2 libxml2-devel libxslt libxslt-devel lsof make openssl-devel pam-devel pax readline-devel tk-devel wget zlib-devel perl-Archive-Tar perl-XML-Parser libX11-devel libtool-ltdl-devel e2fsprogs-devel.x86_64 gcc-gfortran libicu-devel.x86_64 libgtextutils-devel.x86_64 perl-ExtUtils-AutoInstall.noarch perl-ExtUtils-Depends.noarch perl-ExtUtils-CBuilder.x86_64 perl-ExtUtils-CChecker.x86_64 perl-ExtUtils-Config.noarch perl-ExtUtils-DynaGlue.noarch perl-ExtUtils-Embed.x86_64 perl-ExtUtils-F77.noarch perl-ExtUtils-FakeConfig.noarch perl-ExtUtils-FindFunctions.noarch perl-ExtUtils-H2PM.noarch perl-ExtUtils-Helpers.noarch perl-ExtUtils-InstallPaths.noarch perl-ExtUtils-MakeMaker.x86_64 perl-ExtUtils-MakeMaker-Coverage.noarch perl-ExtUtils-ParseXS.x86_64 perl-ExtUtils-PerlPP.noarch perl-ExtUtils-PkgConfig.noarch perl-ExtUtils-TBone.noarch perl-ExtUtils-XSBuilder.noarch
Please make sure that the ntp package is installed $ rpm -qa | grep ntp, otherwise instal it $ yum install ntp
ESGF user configuration
Fist, add a esgf user:
$ adduser esgf
...
After that, change the password:
$ passwd esgf
...
To finish, configure the esgf user with sudoers privileges. Add the following line to /etc/sudoers file:
esgf ALL=(ALL) ALL
Install the ESGF data/compute node
The instructions have been provided by the IPSL1.
Do it as esgf user
$ whoami esgf $ cd /usr/local/bin $ wget -O esg-bootstrap http://198.128.245.140/dist/esgf-installer/esg-bootstrap $ diff <(md5sum esg-bootstrap | tr -s " " | cut -d " " -f 1) <(curl -s http://198.128.245.140/dist/esgf-installer/esg-bootstrap.md5 | tr -s " " | cut -d " " -f 1) $ chmod 555 esg-bootstrap $ esg-bootstrap --devel
In our case, we are going to configure only data and compute types:
$ sudo ./esg-node --type data compute --install
-------------------------------------------------------
During the installation, you will have to fill in several questionnaires:
Welcome to the ESGF Node installation program! :-) What is the fully qualified domain name of this node? [data.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: []: data-unican Please give this node a more descriptive "long" name []: data-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? (if not sure, use default) [esgf-test]: What is the default peer to this node? [esgf-node1.llnl.gov]: data.meteo.unican.es What is the hostname of the node do you plan to publish to? [esgf-node1.llnl.gov]: vesgdev-idx.ipsl.jussieu.fr What email address should notifications be sent as? []: meteo@unican.es 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]:
Finished processing dependencies for esgcet==2.12.1 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]
Looking for keystore [/esg/config/tomcat/keystore-tomcat]... (don't see one)... Keystore setup: Launching Java's keytool: store_password = ****** Would you like to use the DN: (OU=ESGF.ORG, O=ESGF) ? [Y/n]: Using keystore DN = CN=data.meteo.unican.es, OU=ESGF.ORG, O=ESGF Enter key password for <my_esgf_node> (RETURN if same as keystore password): Re-enter new password: Do you wish to generate a Certificate Signing Request at this time? [Y/n]
Please enter the password for this keystore : Please re-enter the password for this keystore:
Create user credentials Please enter username for tomcat [dnode_user]: dnode_user Please enter password for user, "dnode_user" [********]: 73769edbd97410aacfb3560ebb817f882d141517 Would you like to add another user? [y/N]:
Please Enter the IP address of this host [134.157.179.48]:>
Using IP: 134.157.179.48
Please select the IDP Peer for this node:
-------------------------------------------
*[1] : ESGF-PCMDI-9 -> pcmdi9.llnl.gov
[2] : ESGF-PCMDI -> pcmdi3.llnl.gov
[3] : ESGF-JPL -> esg-gateway.jpl.nasa.gov
[4] : ESGF-ORNL -> esg2-gw.ccs.ornl.gov
[5] : ESGF-BADC -> cmip-gw.badc.rl.ac.uk
[6] : ESGF-DKRZ -> ipcc-ar5.dkrz.de
[7] : ESGF-PNNL -> esg1-gw.pnl.gov
[8] : ESGF-ANL -> dev.esg.anl.gov
[9] : ESGF-PCMDI-TEST3 -> esgf-node3.llnl.gov
-------------------------------------------
[C] : (Manual Entry)
-------------------------------------------
select [1] > C
Please enter the IDP Peer's name [ESGF-PCMDI-9] ESGF-TEST
Please enter the IDP Peer's hostname [pcmdi9.llnl.gov] data.meteo.unican.es
You have selected: (Manual Entry)
ESGF-TEST -> data.meteo.unican.es
Is this correct? [Y/n] Y
Creating directory /esg/content/thredds/esgcet INFO 2013-08-02 16:48:46,144 Writing THREDDS ESG master catalog /esg/content/thredds/esgcet/catalog.xml INFO 2013-08-02 16:48:46,173 Writing THREDDS root catalog /esg/content/thredds/catalog.xml THREDDS dataset root directories (option=thredds_dataset_roots) Each entry has the form 'path_identifier | absolute_directory_path': Current value is: esg_dataroot | /esg/data Enter lines, or <RETURN> to end Add new line:
# ESGF cronjob BEGIN ### 35 0,12 * * * ESG_USAGE_PARSER_CONF=/esg/config/gridftp/esg-bdm-usage-gridftp.conf /esg/tools/esg_usage_parser # ESGF cronjob END ### Is this ok ? [Y/n]Y
# ESGF cronjob BEGIN ### 35 0,12 * * * ESG_USAGE_PARSER_CONF=/esg/config/gridftp/esg-bdm-usage-gridftp.conf /esg/tools/esg_usage_parser 5 0,12 * * * ESG_USAGE_PARSER_CONF=/esg/config/gridftp/esg-server-usage-gridftp.conf /esg/tools/esg_usage_parser # ESGF cronjob END ### Is this ok ? [Y/n]Y
Server sent 2 certificate(s): 1 Subject CN=vesgdev-idx.ipsl.fr, OU=simpleCA-vesgdev-idx.ipsl.fr, OU=GlobusTest, O=Grid Issuer CN=Globus Simple CA, OU=simpleCA-vesgdev-idx.ipsl.fr, OU=GlobusTest, O=Grid sha1 cf f9 20 2b ce a6 bc b0 5d b4 a7 bb 0c 08 18 99 14 47 a6 86 md5 bd 6d ab cb 0b 75 58 fb 54 52 89 60 8e 1b 44 b8 2 Subject CN=Globus Simple CA, OU=simpleCA-vesgdev-idx.ipsl.fr, OU=GlobusTest, O=Grid Issuer CN=Globus Simple CA, OU=simpleCA-vesgdev-idx.ipsl.fr, OU=GlobusTest, O=Grid sha1 06 09 9b cc b6 70 6f 3e 59 00 34 b9 fa 0a ba 87 0b f1 16 10 md5 0b b0 a3 56 f6 a7 c7 32 7e 35 b5 b9 e3 bb cd 26 Enter certificate to add to trusted keystore or 'q' to quit: [1] > 1
After that, you should restart the esg-node:
$ sudo ./esg-node restart
If you want to re-install it, you have to use the force option :
$ sudo ./esg-node --type data compute --install --force
Index peer configuration
Do it as root user
In order to configure the host certificate and CA public key, you have to send the csr file located under /esg/config/tomcat/ directory to the CA.
$/esg/config/tomcat/data.meteo.unican.es-esg-node.csr
Then you should put the signed csr under the /etc/grid-security/ directory.
$ /etc/grid-security/data.meteo.unican.es-esg-node-globus.csr.signed.pem
And, if the tomcat key is not in /etc/grid-security directory, copy it inside:
$ cd /etc/grid-security $ cp /esg/conf/tomcat/hostkey.pem ./
Install the key pair in tomcat. You will be prompted to enter the cacert file; enter the url to the index node cacert.pem:
$ esg-node --install-keypair data.meteo.unican.es-esg-node-globus.csr.signed hostkey.pem Please enter your Certificate Athority's certificate chain file(s): [enter each cert file/url press return, press return with blank entry when done] certfile> http://vesgint-idx.ipsl.jussieu.fr/cacert.pem ................................... ...................................
Set auto fetch certs false, otherwise /etc/grid-security/certificates/* will be overwritten by esgf-prod peer groups certificates
$ esg-node --set-auto-fetch-certs false $ esg-node restart
Register connects to desired node, fetches and stores their certificate to enable ingress SSL connections
$ esg-node --register vesgint-idx.ipsl.jussieu.fr
$ cd /etc/grid-security/certificates/ $ grep vesgint-idx.ipsl.jussieu.fr * 373bd876.signing_policy: access_id_CA X509 '/O=ESGF/OU=ESGF.ORG/OU=ESGF-vesgint-idx.ipsl.jussieu.fr/CN=ESGF CA' 373bd876.signing_policy: cond_subjects globus '"/O=ESGF/OU=ESGF.ORG/OU=ESGF-vesgint-idx.ipsl.jussieu.fr/*"'
This process should fetch the CA cert to /etc/grid-security/certificates
Then rebuild the Tomcat's trustsore
$ esg-node --rebuild-truststore
Data Publishing
Configuring a new project for ESGF publication
See the ESGF publication reference for details.
In order to publish, you have to configure a text file, /esg/config/esgcet/esg.ini. For this propose, we are going to create a new project called cordex:
[initialize][initialize] log_level = DEBUG initial_models_table = /esg/config/esgcet/esgcet_models_table.txt [DEFAULT] thredds_dataset_roots = esg_dataroot | /datasets project_options = cordex | CORDEX Output data | 1 [project:cordex] # name | category_type | is_mandatory | is_thredds_property | display_order categories = project | enum | true | true | 0 domain | enum | true | true | 1 institute | enum | true | true | 2 driving_model | enum | false | true | 3 experiment | enum | false | true | 4 ensemble | enum | false | true | 5 model | enum | false | true | 6 time_frequency | enum | false | true | 7 version | enum | false | true | 8 rcm_model | enum | false | true | 9 rcm_version | enum | false | true | 10 description | text | false | false | 99 category_defaults = domain | EUR-22 institute | UCAN driving_model | ERAINT ensemble | r1i1p1 model | WRF331G time_frequency| mon dataset_id = cordex.%(domain)s.%(institute)s.%(driving_model)s.%(experiment)s.%(ensemble)s.WRF331G_v02.%(time_frequency)s.%(variable)s directory_format = /datasets/CORDEX/output/%(domain)s/%(institute)s/%(driving_model)s/%(experiment)s/%(ensemble)s/%(rcm_model)s/%(rcm_version)s/%(time_frequency)s/%(variable)s/%(version)s domain_map = map(project_id,domain : domain_description) cordex | SAM-44 | South America cordex | CAM-44 | Central America cordex | NAM-44 | North America cordex | EUR-44 | Europe cordex | EUR-22 | Europe cordex | AFR-44 | Africa cordex | WAS-44 | West Asia cordex | EAS-44 | East Asia cordex | CAS-44 | Central Asia cordex | AUS-44 | Australasia cordex | ANT-44 | Antarctica cordex | ARC-44 | The Arctic cordex | MED-44 | HYMEX Mediterranean cordex | EUR-11 | High-res. Europe cordex | SAM-44i | South America cordex | CAM-44i | Central America cordex | NAM-44i | North America cordex | EUR-44i | Europe cordex | AFR-44i | Africa cordex | WAS-44i | West Asia cordex | EAS-44i | East Asia cordex | CAS-44i | Central Asia cordex | AUS-44i | Australasia cordex | ANT-44i | Antarctica cordex | ARC-44i | The Arctic cordex | MED-44i | HYMEX Mediterranean cordex | EUR-11i | High-res. Europe cordex | MNA-44 | Middle East and North Africa cordex | MNA-44i | Middle East and North Africa cordex | MNA-22 | Middle East and North Africa cordex | MNA-22i | Middle East and North Africa domain_options = SAM-44,CAM-44,NAM-44,EUR-44,EUR-22,EUR-44i,AFR-44,AFR-44i,WAS-44,EAS-44,CAS-44,AUS-44,ANT-44,ARC-44,MED-44,EUR-11,SAM-44i,CAM-44i,NAM-44i,EUR-44i,AFR-44i,WAS-44i,EAS-44i,CAS-44i,AUS-44i,ANT-44i,ARC-44i,MED-44i,EUR-11i,MNA-44,MNA-44i,MNA-22,MNA-22i driving_model_options = ERAINT, ECMWF-ERAINT, CCCma-CanESM2, CNRM-CERFACS-CNRM-CM5, ICHEC-EC-EARTH, MIROC-MIROC5, MOHC-HadGEM2-ES, MPI-M-MPI-ESM-LR, NCC-NorESM1-M, NOAA-GFDL-GFDL-ESM2M, IPSL-IPSL-CM5A-MR ensemble_options = r1i1p1, r12i1p1, r0i0p0 experiment_options = cordex | evaluation | no description cordex | historical | no description cordex | rcp4 | no description cordex | rcp26 | no description cordex | rcp45 | no description cordex | rcp85 | no description institute_map = map(project_id,model : institute) cordex | WRF331G | UCAN institute_options = UCAN las_configure = false las_time_delta_map = map(time_frequency : las_time_delta) mon | 1 month day | 1 day fx | fixed sem | semi maps = institute_map, las_time_delta_map, domain_map model_options = WRF331G parent_id = wdcc2.cordex project_handler_name = basic_builtin rcm_model_options = UCAN-WRF331G rcm_version_options = v02 thredds_exclude_variables = a, a_bnds, alev1, alevel, alevhalf, alt40, b, b_bnds, basin, bnds, bounds_lat, bounds_lon, dbze, depth, depth0m, depth100m, depth_bnds, geo_region, height, height10m, height2m, Lambert_Conformal, lat, lat_bnds, lat_bounds, latitude, latitude_bnds, layer, lev, lev_bnds, location, lon, lon_bnds, lon_bounds, longitude, longitude_bnds, olayer100m, olevel, oline, p0, p220, p500, p560, p700, p840, plev, plev3, plev7, plev8, plev_bnds, plevs, pressure1, region, rho, rlat, rotated_pole, rlon, scatratio, sdepth, sdepth1, sza5, tau, tau_bnds, time, time1, time2, time_bnds, vegtype, x, y time_frequency_options = day,fx,mon,sem,3hr,6hr variable_locate = ps,ps_ | vas,vas_ | uas,uas_ |tasmin,tasmin_|tasmax,tasmax_| tas,tas_ | sfcWindmax,sfcWindmax_ | sfcWind,sfcWind_ |rsds,rsds_|rlds,rlds_| pr,pr_ | prc,prc_| mrso,mrso_| mrros,mrros_|huss,huss_| hfss,hfss_|hfls,hfls_ variable_per_file = true version_options = 20131108
Therefore, if you use the above configuration file, you will have to create a tree directory like this:
[esgf@data datasets]# tree
.
`-- CORDEX
`-- output
`-- EUR-22
`-- UCAN
`-- ECMWF-ERAINT
`-- evaluation
`-- r1i1p1
`-- UCAN-WRF311G
`-- v02
|-- 3hr
| |-- hfls
| | `-- 20131108
| | |-- hfls_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | `-- hfls_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- hfss
| | `-- 20131108
| | |-- hfss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | |-- hfss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19800101-19801231.nc
| | `-- hfss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- huss
| | `-- 20131108
| | |-- huss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | |-- huss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19800101-19801231.nc
| | `-- huss_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- pr
| | `-- 20131108
| | |-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | `-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- prc
| | `-- 20131108
| | |-- prc_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | `-- prc_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- ps
| | `-- 20131108
| | |-- ps_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | `-- ps_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- rlds
| | `-- 20131108
| | |-- rlds_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | |-- rsds_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20090101-20091231.nc
| | `-- rsds_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| |-- sfcWind
| | `-- 20131108
| | |-- sfcWind_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| | |-- sfcWind_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19800101-19801231.nc
| | |-- sfcWind_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20090101-20091231.nc
| | `-- sfcWind_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
| `-- tas
| `-- 20131108
| |-- tas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_19790101-19791231.nc
| `-- tas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_3hr_20100101-20101231.nc
|-- 6hr
| |-- mrros
| | `-- 20131108
| | |-- mrros_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_19790101-19791231.nc
| | |-- mrros_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20090101-20091231.nc
| | `-- mrros_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20100101-20101231.nc
| |-- uas
| | `-- 20131108
| | |-- uas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_19790101-19791231.nc
| | |-- uas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20090101-20091231.nc
| | `-- uas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20100101-20101231.nc
| `-- vas
| `-- 20131108
| |-- vas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_19790101-19791231.nc
| |-- vas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20090101-20091231.nc
| `-- vas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_6hr_20100101-20101231.nc
|-- day
| |-- mrso
| | `-- 20131108
| | |-- mrso_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_19790101-19801231.nc
| | `-- mrso_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20060101-20101231.nc
| |-- pr
| | `-- 20131108
| | |-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_19790101-19801231.nc
| | `-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20060101-20101231.nc
| |-- sfcWindmax
| | `-- 20131108
| | |-- sfcWindmax_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_19790101-19801231.nc
| | |-- sfcWindmax_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20010101-20051231.nc
| | `-- sfcWindmax_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20060101-20101231.nc
| |-- tasmax
| | `-- 20131108
| | |-- tasmax_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_19790101-19801231.nc
| | `-- tasmax_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20060101-20101231.nc
| `-- tasmin
| `-- 20131108
| |-- tasmin_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_19790101-19801231.nc
| `-- tasmin_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_day_20060101-20101231.nc
`-- mon
|-- pr
| `-- 20131108
| |-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_mon_19790101-19801231.nc
| `-- pr_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_mon_20010101-20101231.nc
`-- tas
`-- 20131108
|-- tas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_mon_19790101-19801231.nc
|-- tas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_mon_19910101-20001231.nc
`-- tas_EUR-22_ECMWF-ERAINT_evaluation_r1i1p1_UCAN-WRF331G_v02_mon_20010101-20101231.nc
Then you have to add the project name to the esgcet_models_table.txt file
$ echo " cordex | WRF331G | http://meteo.unican.es | UNICAN WRF3.3.1 Model version, 2.0" >> /esg/config/esgcet/esgcet_models_table.txt
After modifying esgcet_models_table.txt and esg.ini files, you have to update the data base by executing :
$ cd /usr/local/uvcdat/1.4.0/bin/ $ ./esginitialize -i /esg/config/esgcet/esg.ini -c
- ./esginitialize -d 0: To remove all tables
- ./esginitialize -c : Upgrade the database schema to the latest version, and initialize projects, models, experiments, and standard names from configuration files.
Using the ESGF Publisher
This takes place in three steps:
- Scan each file for metadata and save the metadata in the node database. (This is in contrast to running esgscan_directory, which just scans the directory structure.)
- Generate a THREDDS catalog based on the scanned information. THREDDS is a data and metadata server used by ESGF.
- Notify the idx that one or more catalogs have been generated.
File Scan Phase
In order to scan the cordex files for metadata, run esgscan_directory to generate a mapfile and after that run esgpublish with input from a mapfile:
$ whoami esgf $ cd /usr/local/uvcdat/1.4.0/bin $ ./esgscan_directory -i /esg/config/esgcet/esg.ini --project cordex -o ~/cordex.txt /datasets/CORDEX $ sudo ./esgunpublish -i /esg/config/esgcet/esg.ini --map ~/cordex.txt INFO 2013-11-19 19:32:44,981 Deleting cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls INFO 2013-11-19 19:32:45,162 Result: SUCCESSFUL INFO 2013-11-19 19:32:45,173 Deleting cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss INFO 2013-11-19 19:32:45,345 Result: SUCCESSFUL ..........................................
In order to check that the datasets were entered correctly into the database, list the datasets for cordex project:
$ ./esglist_datasets -i /esg/config/esgcet/esg.ini cordex
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| id | name | project | model | experiment | run_name | offline | master_gateway | domain | institute | publish_time | publish_status | parent | version | version_name | comment |
+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:21 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls.v1 | None |
| 2 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:25 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss.v1 | None |
| 3 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.huss | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:29 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.huss.v1 | None |
| 4 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.pr | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:33 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.pr.v1 | None |
| 5 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.prc | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:37 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.prc.v1 | None |
| 6 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.ps | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:40 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.ps.v1 | None |
| 7 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.rlds | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:44 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.rlds.v1 | None |
| 8 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.rsds | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:48 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.rsds.v1 | None |
| 9 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.sfcWind | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:52 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.sfcWind.v1 | None |
| 10 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.tas | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:42:56 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.tas.v1 | None |
| 11 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.mrros | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:00 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.mrros.v1 | None |
| 12 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.uas | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:06 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.uas.v1 | None |
| 13 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.vas | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:12 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.6hr.vas.v1 | None |
| 14 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.mrso | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:13 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.mrso.v1 | None |
| 15 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.pr | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:14 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.pr.v1 | None |
| 16 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.sfcWindmax | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:15 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.sfcWindmax.v1 | None |
| 17 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.tasmax | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:16 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.tasmax.v1 | None |
| 18 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.tasmin | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:18 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.day.tasmin.v1 | None |
| 19 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.mon.pr | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:18 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.mon.pr.v1 | None |
| 20 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.mon.tas | cordex | WRF331G | evaluation | None | False | None | EUR-22 | UCAN | 2013-11-18 19:43:19 | PUBLISH_DATASET | ROOT | 1 | cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.mon.tas.v1 | None |
+------------------------------------------------------------------------------------------------------------------------------------------------
In order undo the scan, run esgunpublish with the following flags:
$ ./esgunpublish -i /esg/config/esgcet/esg.ini --skip-gateway --skip-thredds --database-delete --map ~/cordex.txt
Generate a THREDDS catalog
You can generate the THREDDS catalog with :
$ sudo ./esgpublish -i /esg/config/esgcet/esg.ini --project cordex --map ~/cordex.txt --noscan --thredds
INFO 2013-11-19 19:46:30,642 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls.v1.xml
INFO 2013-11-19 19:46:30,837 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss.v1.xml
INFO 2013-11-19 19:46:31,019 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.huss.v1.xml
INFO 2013-11-19 19:46:31,198 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.pr.v1.xml
INFO 2013-11-19 19:46:31,536 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.prc.v1.xml
...............................................
In order to remove the catalogs from the THREDDS :
$ ./esgunpublish -i /esg/config/esgcet/esg.ini --map ~/cordex.txt --skip-gateway
idx notification
First, obtain a digital certificate from an ESGF trusted MyProxy server, and rename it to whatever path you have defined in esg.ini.
Remember, you have to log in a Federation to do it.
$ sudo /usr/local/globus/bin/myproxy-logon -s vesgint-idx.ipsl.jussieu.fr -l blancojc -o ~/.globus/certificate-file
Then you can publish the cordex catalog by executing :
$ sudo ./esgpublish -i /esg/config/esgcet/esg.ini --project cordex --map ~/cordex.txt --noscan --publish
INFO 2013-11-19 20:01:24,817 Publishing: cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls
INFO 2013-11-19 20:01:28,678 Result: SUCCESSFUL
INFO 2013-11-19 20:01:28,678 Publishing: cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss
INFO 2013-11-19 20:01:32,416 Result: SUCCESSFUL
INFO 2013-11-19 20:01:32,417 Publishing: cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.huss
INFO 2013-11-19 20:01:36,125 Result: SUCCESSFUL
INFO 2013-11-19 20:01:36,125 Publishing: cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.pr
INFO 2013-11-19 20:01:39,964 Result: SUCCESSFUL
INFO 2013-11-19 20:01:39,965 Publishing: cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.prc
Use esgunpublish to delete idx datasets:
$ ./esgpublish -i /esg/config/esgcet/esg.ini --map ~/cordex.txt --skip-thredds
Running all publication steps
For convenience, the full publication can be performed with one command. Also, if the arguments are directories rather than a mapfile, the directories will be scanned as if esgscan_directory were run:
$ sudo ./esgpublish -i /esg/config/esgcet/esg.ini --project cordex --map ~/cordex.txt --noscan --thredds
INFO 2013-11-19 19:46:30,642 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfls.v1.xml
INFO 2013-11-19 19:46:30,837 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.hfss.v1.xml
INFO 2013-11-19 19:46:31,019 Writing THREDDS catalog /esg/content/thredds/esgcet/1/cordex.EUR-22.UCAN.ECMWF-ERAINT.evaluation.r1i1p1.WRF331G_v02.3hr.huss.v1.xml
esgunpublish will remove the datasets from the idx, THREDDS, and node database in that order:
$ sudo ./esgpublish -i /esg/config/esgcet/esg.ini --database-delete --map ~/cordex.txt
Access files
Finally, in order to grant access to our files you need to add the line below :
<policy resource=".*CORDEX.*" attribute_type="ANY" attribute_value="" action="Read"/>
in your esgf_policies_local.xml file :
$ cat /usr/local/apache-tomcat-7.0.47/webapps/esg-orp/WEB-INF/classes/esg/orp/orp/config/esgf_policies_local.xml <?xml version="1.0" encoding="UTF-8" standalone="yes"?> <!-- This file is intended to be edited and maintained by the local Node admnistrators. It should contain only policies specific to data served by the local Node. It will not be overridden by a software update. --> <policies xmlns="http://www.esgf.org/security"> <policy resource=".*CORDEX.*" attribute_type="ANY" attribute_value="" action="Read"/> <!-- The following statements allow all members of group "CMIP5 Research" or "CMIP5 Commercial" to read any local URL that contains "cmip5". Note that the groups "CMIP5 Research" and "CMIP5 Commercial" are administered by PCMDI --> <!-- <policy resource=".*cmip5.*" attribute_type="CMIP5 Research" attribute_value="user" action="Read"/> --> <!-- <policy resource=".*cmip5.*" attribute_type="CMIP5 Commercial" attribute_value="user" action="Read"/> --> <!-- These statements provide CMIP5 Read access for members of the old gateways --> <!-- <policy resource=".*cmip5.*" attribute_type="CMIP5 Research" attribute_value="default" action="Read"/> --> <!-- <policy resource=".*cmip5.*" attribute_type="CMIP5 Commercial" attribute_value="default" action="Read"/> --> <!-- The following statement allows all members of group "MY GROUP" to read any local URL that contains "my_data" <policy resource=".*my_data.*" attribute_type="MY GROUP" attribute_value="user" action="Read"/> --> <!-- The following statement allows members of group "MY GROUP" with role="publisher" to publish local datasets with id containing "my_data" <policy resource=".*my_data.*" attribute_type="MY GROUP" attribute_value="publisher" action="Write"/> --> <!-- The following statements makes resources that contain '.*test.*' freely available for download --> <!-- <policy resource=".*test.*" attribute_type="ANY" attribute_value="" action="Read"/> --> <!-- The following statements makes all resources freely available for download --> <!-- <policy resource=".*" attribute_type="ANY" attribute_value="" action="Read"/> --> </policies>
<policy resource=".*CORDEX.*" attribute_type="ANY" attribute_value="" action="Read"/>
In production status, you will have to something like this:
<policy resource=".*CORDEX.*" attribute_type="CORDEX_Research" attribute_value="user" action="Read"/> <policy resource=".*CORDEX.*" attribute_type="CORDEX_Research" attribute_value="default" action="Read"/> <policy resource=".*CORDEX.*" attribute_type="CORDEX_Commercial" attribute_value="user" action="Read"/> <policy resource=".*CORDEX.*" attribute_type="CORDEX_Commercial" attribute_value="default" action="Read"/>
Attachments (8)
- esgcet_models_table.txt (424 bytes) - added by carlos 9 years ago.
- esg.ini (7.3 KB) - added by carlos 9 years ago.
- localopenssl.cnf (9.7 KB) - added by terryk 8 years ago.
- Datanodemgr-doc.pdf (213.7 KB) - added by terryk 8 years ago.
- chain.pem (4.7 KB) - added by terryk 8 years ago.
- ESGF_node_resource_estimate.pdf (446.3 KB) - added by antonio 8 years ago.
- geoiplookup0.2.sh (571 bytes) - added by terryk 8 years ago.
- is-enes2_statistics.txt (10.9 KB) - added by terryk 8 years ago.
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