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Hyrax 1.13.2

Submitted by ndp on Wed, 11/02/2016 - 17:10

Hyrax by OPeNDAP logoThe Hyrax-1.13.2 release is primarily a bug fix release that corrects two memory lifecycle problems. Highly recommended.

Server Documentation

1.13.2 release (7 Nov 2016)

Welcome to the Hyrax 1.13.2 release. This release contains fixes.

  • Fixed Hyrax-254. This bug caused random behavior when accessing aggregations (memory lifecycle issue).
  • Fixed a bug (Hyrax-282) in the netCDF Transmitter where subsets of Grid variables could result in a 500 error. Those now return the correct data values (memory lifecycle issue).
  • Changed BES timeout error from 418 (TeaPot) to 504 (Gateway Timeout).
  • Updated OLFS configuration defaults in viewers.xml file to reflect changes for ncWMS2 and Godiva3
  • Patched a problem with the way the XSL transforms are carried out that could have left the process running in an unexpected directory.
  • Added an in-memory cache for the handlers. Hyrax module developers can use this to speed response times when building metadata responses (e.g., DAS) is time-consuming.
  • Added a logrotate file to the rpm package. This helps keep the bes.log size manageable and provides better integration with Linux.
  • Added a Function Response Cache. Now function results are computed once and cached.Fixed a problem with ASCII responses when one or more dimensions of an N-dim array had only one element.
  • Fixes for the HDF5 handler:
    • HFVHANDLER-175: Make sure the lat/lon are checked under both /geolocation and / (root) groups.
    • HFVHANDLER-189: Handle the root attribute 
    • HFVHANDLER-191
    • HFVHANDLER-192: Handle _FilLValue and units for GPM
    • HFVHANDLER-194: New nlayer values for GPM level-3 4.0 data
    • HFVHANDLER-199: DAP4 memory cache
    • HFVHANDLER-198 and 184: DAP2 memory cache
  • Updated GDAL-based code to use GDAL 2.x
  • Fixed BES 'Transmitter' modules (modules that build non-DAP responses like netCDF, JSON, etc.) so that they work when constraint expressions contain function calls.
  • Updated the 'history' attribute in the netCDF Transmitter's responses so it's more precise about how the response was generated. The new value contains the date, time, server version and requesting URL, so it should be possible to recreate the response. The format of the attribute conforms to CF-1.6.
  • Changed the representation of Not-a-Number from 'nan' to 'NaN' in the ASCII response.
  • Fixed in libdap: an issue with DAP4 CE parsing, double quotes and %20 escape characters.

Required External Dependencies

In order to get Hyrax 1.13.2 running, you will need:

  • Java 1.7 or greater
  • Tomcat 7.x or 8.x
  • Note: On CentOS 6.6 use Java 7 + Tomcat 7 if you're using yum to install things.
  • Linux (We provide RPMs for CentOS 6.6 and 7.1; install them with yum); OSX source build using the optional hyrax-dependencies.tar sources or your own copies of HDF4, etc.

Software downloads for Hyrax 1.13.2

To run the Hyrax server, you will need to download and install the following (from source or binary):

  • OLFS (Java 1.7)
  • libdap
  • BES
  • ncWMS2 (optional)

Binaries for Hyrax 1.13.2

Java icon OLFS (Java-1.7)
  • OLFS 1.16.1 Web Archive File (gpg signature) Unpack using 'tar -xvf filename' and follow the instructions in the README file. (Requires Java 1.7 Built using Java 8 Tested against Tomcat 8.0.32).
  • CentOS 6.3 comes with Java 6; Oracle has stopped supporting that version of Java; update your machine if you haven't already. Use yum search java-1.7 to find the correct package. For our servlet you will only need the JRE - the Java Runtime Environment. You will also need to employ the "alternatives" tool to make java 7 JVM the preferred alternative.
  • Note: On CentOS 6.6 it's Java 7 + Tomcat 7 if you're using yum to install things. Tomcat 7 + Java 8 will not work!
Java icon ncWMS2 (Java-1.7)
Use the EDAL web page to locate the latest ncWMS2 "Servlet Container" software bundle as a WAR file. Install it into the same Tomcat instance as the OLFS. The configuration instructions may be found here.
Linux Tux Logo BES
Linux (CentOS 6.6) x86_64 RPMs - All of the RPMs we build, including the devel and debuginfo packages
  • libdap-3.18.2 (gpg signature)
  • bes-3.17.3-static (gpg signature) This RPM includes statically linked copies of all of the modules/handlers we support, including HDF4 & 5 with HDFEOS support. There is no need to install packages from EPEL with this RPM. Other sources of RPM packages will likely provide a bes RPM that uses handlers linked (dynamically) to dependencies from their distributions (CentOS, Fedora, etc.). RPMFind is a good tool to locate those RPMs.
Linux (CentOS 7.1) x86_64 RPMs - The RPM packages for CentOS 7/EL 7, otherwise, the same code as above.

Installing the binary distribution

  • Download the RPM packages above
  • Use yum to install the libdap and bes RPMs (sudo yum install libdap-3.18*.rpm bes-3.17.3*.rpm). Unless you're going to be building software from source for Hyrax, skip the *-devel and *-debuginfo RPMs.
  • At this point you can test the BES by typing the following into a terminal:
    • start it: sudo service besd start or use the script in /etc/init.d with sudo /etc/init.d/besd start
    • connect using a simple client: bescmdln
    • and get version information: show version;
    • exit from bescmdln
  • BES NOTE - If you are upgrading to Hyrax 1.13.2 from an existing installation older than 1.13.0
    In the bes.conf file the keys BES.CacheDir, BES.CacheSize, and BES.CachePrefix have been replaced with BES.UncompressCache.dir, BES.UncompressCache.size, and BES.UncompressCache.prefix respectively. Other changes include the gateway cache configuration (gateway.conf) which now uses the keys Gateway.Cache.dir, Gateway.Cache.size, and Gateway.Cache.prefix to configure its cache. Changing the names enabled the BES to use separate parameters for each of its several caches, which fixes the problem of 'cache collisions.'
  • Check the java version on your system: "java -version"
  • If you have earlier than 1.7.x then you'll need to install java 7:
    • yum install java-1.7.0
    • If you are on a modern-ish Linux system you may need to use the alternatives tool to make java 7 the current JVM. Run the command:
      "alternatives --config java"
      You'll get an interactive terminal application that will allow you to select your newly installed java 8 as the preferred alternative.
  • Use yum to install tomcat.noarch. Make the directory /etc/olfs, change its group to tomcat, and set it 'group writable' (mkdir /etc/olfs; chgrp tomcat /etc/olfs; chmod g+w /etc/olfs). Alternatively, get Apache Tomcat-7.x from the Apache Software Foundation and install it wherever you'd like (e.g., /usr/local/).
  • Download the OLFS Web ARchive (war) file (see above, by the Java logo) and put opendap.war in the tomcat webapps directory (cp opendap.war /usr/share/tomcat/webaps or, if you installed tomcat from the ASF distribution, its web application directory, e.g., /usr/local/apache-tomcat-7.0.59/webapps)
  • At this point you should be able to start tomcat (sudo service tomcat start or ./apache-tomcat-7.0.59/bin/ and test the server:
    • In a web browser, use http://localhost:8080/opendap/
    • Look at sample data files shipped with the server
  • If you are installing the OLFS in conjunction with ncWMS2 version 2.0 or higher: Copy both the opendap.war and the ncWMS2.war files into the Tomcat webapps directory. (Re)Start Tomcat. Go read about, and then configure ncWMS2 and the OLFS to work together.
  • From here, or if you are having problems, see our Hyrax documentation page
  • OLFS Note - If you are upgrading to Hyrax 1.13.2 from any previous installation older than 1.13.0
    The OLFS now has much better support for sites that use rpm to install Tomcat. To complement this, it has a new procedure for locating its configuration directory. During start up, the OLFS looks in two places for its configuration information. It checks the directory given by the environment variable OLFS_CONFIG_DIR first and then the directory /etc/olfs/, using the configuration information in the first place it is found. If either of those directories exist but are empty, the OLFS will unpack its default configuration information there. You can customize the configuration information using a text editor; the OLFS will not overwrite your changes. If neither OLFS_CONFIG_DIR nor /etc/olfs/ exist, the OLFS will fall back to its default configuration. Note that the OLFS_CONFIF_DIR or /etc/olfs must be writable by the tomcat user for this to work.
  • In order for the CatalogCache feature to be enabled you must update your olfs.xml file. Use the one located in $CATALINA_HOME/webapps/opendap/WEB-INF/conf as a template for your new one.

Source code for Hyrax 1.13.2

Source from GitHub

  • All of our source code is on GitHub. There you will find the hyrax repo, which is a meta-project that contains scripts to clone and build all of Hyrax. You will also see all of the repos that contain the Hyrax source code (libdap4, bes, and all of the handlers).
  • Directions on building Hyrax from GitHub are available at our documentation site.