Miscellaneous Administrator Questions

This page is dedicated to miscellaneous problems that may arise during the course of ESTEST administration.

java.lang.OutOfMemoryError: Java heap space

This problem occurs when the eXist-db Jetty server runs out of heap space allocated to its process. The memory settings for eXist are discussed in Tuning the Database. Basically you must increase the available heap space by editing the setting in tools/wrapper/conf/wrapper.conf, change the lines

# Initial Java Heap Size (in MB)

# Maximum Java Heap Size (in MB)

to something like

# Initial Java Heap Size (in MB)

# Maximum Java Heap Size (in MB)

For MD simulations by Qbox you may have to go even more extreme in maxmemory, like 2048+.

PDOException: SQLSTATE[HY000]: General error: 1366

This error message occurs in Drupal powered-sites like ESTEST Discovery and is related to a bug in the Backup and Migrate module using a MySQL backend database and diacritical characters. See these threads for more info.

A simple PHP script will fix this issue

// your connection

// convert code
$res = mysql_query("SHOW TABLES");
while ($row = mysql_fetch_array($res))
    foreach ($row as $key => $table)
        mysql_query("ALTER TABLE " . $table . " CONVERT TO CHARACTER SET utf8 COLLATE utf8_unicode_ci");
        echo $key . " =&gt; " . $table . " CONVERTED<br />";

eXist-db depends on the local JAVA installation that can change when automatic system updates modify the path to the JRE library. To address this issue, one can create a soft link to the JRE location (something like /usr/lib/jvm/java-#-sun-#.#.#.#) that is kept up-to-date with other software updates. Then the soft link path needs to be set into the JAVA_HOME environment variable that is used by the eXist-db scripts located in /bin

Additionally, if you configured eXist-db to startup at boot using update-rc.d then you will need to change the configuration file tools/wrapper/conf/wrapper.conf

HTTP ERROR: 500 - An error occurred: Form too large

This occurs when the POST data limit in eXist-db (Jetty) is too small. To increase the POST data limit set the following definition in eXist-db ./tools/wrapper/conf/wrapper.conf.

Last modified 6 years ago Last modified on 07/16/12 10:55:22