OMII-UK: Known Issues Dev Kit

Known Issues for the Development Kit version 3.4.2

The following list describes known issues with the operation of the Development Kit. The list is separated into issues relating to infrastructure and issues relating to the Software Components.

Infrastructure known issues

Sun Java JDK 1.5.0_10

It has been reported that the Server installation does not install correctly with using Sun Java JDK 1.5.0_10. The Server installation bails having failed to start Tomcat. This is not the case with other versions of the 1.5.0 JDK, namely 1.5.0_01 though _09 and _11 through _14. We recommend the use of one of these other JDKs.

OMII-UK known issue: B3820

IBM JDK Limitations

Although successful installation of the OMII-UK server can be achieved with an IBM JDK, failure may be experienced during the OMII-UK client installation and also when running software components, due to the version of WSS4J currently in use. It is recommended you use a Sun JDK instead.

OMII-UK known issue code: B2989, B3075

Certificate Revocation lists are ignored

The Web Services Security implementation included in OMII-UK release 3.4.0 has been upgraded to a version derived from Apache WSS4J 1.5.0.

The WS-Security implementation in earlier releases of the OMII-UK software included OMII-UK-customised support for Certificate Revocation Lists. This support has not yet been ported to the new implementation of WSS4J. Currently, Certificate Revocation lists are ignored.

This will not affect the behaviour of OMII-UK installations, except where servers or clients try to use revoked certificates. We plan to reinstate full CRL support in the next release of the OMII-UKsoftware.

OMII-UK known issue code: B2949

java.lang.NullPointerException (WebAppClassLoader)

In OMII-UK 3.0.0 various jar files commonly used by OMII-UKWeb services are made available in the Tomcat "shared/lib/" directory. This means that the classes in these jars can be used without placing an extra copy of the jar in the local "WEB-INF/lib/" directory of the Web application.

If a Web app makes use of the shared Axis library, you may have problems stopping and restarting it in a running container, for example using Tomcat Manager application. This is a consequence of static variables in Axis classes being shared by applications that load these classes off a common class loader.

After an attempted restart, a typical exception message related to this problem may look like this:

java.lang.NullPointerException org.apache.catalina.loader.WebappClassLoader.findResources(WebappClassLoader.java:956)

To work round this problem, restart Tomcat as a whole rather than restarting individual Web applications. This problem will be fixed in the next release of OMII-UK.

OMII-UK known issue code: B2415

Security problem with PostgreSQL database servers

There is a known security problem with PostgreSQL database servers, reported on the PostgreSQL website at http://www.postgresql.org/docs/techdocs.52. This OMII-UKserver release does include versions of the PostgreSQL server affected by this issue. However, we believe that with proper configuration, exposure can be kept to a minimum. The OMII-UKrelease uses md5 rather than trust level authentication for direct database connections, meaning that all accesses require a username and password. The PostgreSQL server is configured to only accept connections from the machine where the OMII-UK server is installed. Also opportunities where data used to generate SQL indirectly are protected under tomcat security on the server (username and password protection for HTTP accesses). For OMII-UK client installs, users can only access the server by way of using a certificate. For systems with public access, certificates stronger than the freely available OMII-UK demo certificates should be used. This means that only trusted parties can influence the SQL inserted into the PostgreSQL database. OMII-UK have every intention to update the versions of PostgreSQL used for the next release.

OMII-UK known issue code: B2476

Installation as root on a SuSE 10 machine

Depending on the setup of your SuSE 10 machine, you may see this error if you install OMII_3.0.0 as root, choose PostgreSQL 8.0.1 and libkrb5.so.17 cannot be found:

Which of the following database install options would you like to use? 1) RPM based Postgres 7.3.4 2) RPM based Postgres 8.0.1 > 2 Installing the following packages: libs postgres_rpms/suse/8.0.1/postgresql-libs-8.0.1-0.1.i586.rpm error: Failed dependencies: libkrb5.so.17 is needed by postgresql-libs-8.0.1-0.1 An error has occurred, uninstalling postgres (256) Failed to install postgres, cleaning up and exiting. Web Services Database setup failed, exiting. at ./OMIIstackInstall.pl line 138, <stdin> line 1. This issue will be fixed in the next release.

OMII-UK known issue code: B2131

Apple Mac requires databases to be on separate linux machine

If installing the OMII-UK Server on an Apple Mac, you need to ensure that all the OMII-UK supporting databases are installed on a separate Linux box - this is because the OMII-UK does not support the use of OMII-installed PostgreSQL on the Apple Mac platform at this time. You can however install your own PostgreSQL using instructions in: Installation & Setup Guide > Server Installer > Installing PostgreSQL on Mac OS X for use with a local OMII-UK Server

OMII-UK known issue code: B2386

Intermittent Tomcat shutdown issue with IBM JDK 1.4.2 - 1.4.2-1.0

The OMII-UK Web Services Container installer may fail to deploy the Integrated services in several instances that are under investigation. The reason appears to be that with these versions of the IBM JDK, Tomcat does not shutdown completely immediately following the execution of the shutdown script and this causes problems for the Server installer.

OMII-UK known issue code: B1297

Default garbage collection strategy in Sun Java 1.5.0_06

The default garbage collection strategy when using Sun Java 1.5.0_06 has shown to be insufficient for some applications of the OMII-UK server. In these cases the JVM can run out of heap memory when under sufficient load, causing the server to fail. In reality the server is not out of memory, only available memory at that time, and if the JVM's automatic garbage collection had been more aggressive, suitable resources would have been recovered, averting server failure.

OMII-UK known issue code: B2087

Strict umasks will not permit the WS container to install

umasks can be used in linux to withhold permissions upon file creation. Without a umask in effect, any file created will have 666 permissions (rw-rw-rw-) and any directory created will have 777 (rwxrwxrwx). A umask lists the permissions to withhold; hence a umask of 002 will result in files created with 664 permissions and directories with 775 (you subtract the umask from the permissions).

If you are a root user that habitually sets your umask to something more strict than 022 or 002 (eg. 007 or 027), then when you run the WS container installer for the first time, the install directory (among other things) will take its file permissions from the current umask and this makes it unsearchable by omii_tomcat_user and anyone else.

At present, you will need to relax your umask in order to run the OMII-UK Server installer.

OMII-UK known issue code: P424

Service response has not been verified but is provided here for information only, you must decide if you trust the content

At present, the OMII-UK uses a temporary certification authority located at 'security.omii.ac.uk'. If the UNIX clock on your own server is more than a few minutes behind the time of the certificate issuing server, a certificate will be generated that may not become valid until your server's clock passes the issuing time of the certificate.

OMII-UK known issue code: P178

Database details for server and database installs do not match

If you run the OMII-UK Server installer, install a database and state that the server is at a different IP address from the database. Then you rerun the Server installer and install the rest of Server and state that the database is local (which it is not), you do not get an error at this point even though the database details do not match.

OMII-UK known issue code: P1105

Parse and edit of existing Postgres pg_hba.conf

For root installations of the WS container when a PostgreSQL database is already on the target machine, the OMII-UK Server installer creates a new PostgreSQL pg_hba.conf file and leaves the permissions on this file in a non-editable state. Ideally what should be happening is that the existing .conf file should have the OMII-UK-related changes added to it so that the existing usage of the file is not affected. The original pg_hba.conf is backed up to pg_hda.conf.DATE. When installing the OMII-UK server as a normal user, there is a local PostgreSQL install which hence does not suffer from this problem.

OMII-UK known issue code: P600

File permissions being changed by Tomcat

After the Integrated Services are installed by a non-root user, the permission of file OMII_HOME/jakarta/conf/tomcat_users.xml is changed from -rw-r----- to -rw-r--r-- by Tomcat. This also happens every time Tomcat is started. This means that other users can read roles and passwords from the tomcat_users.xml file if you install the OMII-UK server as a non-root user in your own area. If the installation is executed as root, this problem does not occur.

OMII-UK known issue code: P1319

Departures from WS-I Basic Profile

The version of Axis packaged with OMII-UK is known to depart from WS-I Basic Profile at R2735: http://www.ws-i.org/Profiles/BasicProfile-1.1-2004-08-24.html#Part_Accessors

E.g. a SOAP request generated by the OMII-UK client:

<soapenv:Envelope ...> ... <soapenv:Body ...> <openAccount xmlns="http://www.it-innovation.soton.ac.uk/2004/grid/account"> <arg0 xsi:type="open-account-requestType"> ... </arg0> </openAccount> </soapenv:Body> </soapenv:Envelope>

The namespace declaration in the `<openAccount/>' element puts a default namespace into effect. The name of the `<arg0/>' accessor element is qualified by this default namespace. To our knowledge, this has not caused any problems in practise.

OMII-UK known issue code: P773

OMII-UK Client does not support install to Windows network references

The OMII-UK Client can be installed to mapped Windows network drives eg. H:\wip\OMIICLIENT but it does not support installation to network references eg.
machine-name.domain\directory\OMIICLIENT due to limitations in the underlying Windows operating system. OMII-UK known issue code: P393

WSS4J and custom server-config.wsdd files

If you are distributing a custom `server-config.wsdd' with your Web application, please ensure it sets `enableNameSpacePrefixOptimization' to false as shown below:

This ensures that WSS4J works reliably. If you are NOT distributing a custom `server-config.wsdd', any such file generated automatically by OMII-UK Axis (post version 2.3.1) will explicitly set this parameter to false.

OMII-UK known issue code: P1678, P1985

Updating certificate with a different distinguished name

When updating the certificate on the server to one with a different distinguished name, the account service database must be removed. This involves stopping the server, removing all the OMII/grid/account/grid-account* files, then restarting the server. Having done this, open the account service page in a web browser by visiting http://HOST:PORT/account and ensure that no errors are reported. Note that all previously opened accounts will be removed.

OMII-UK known issue code: P2312

RHEL 4 dependency on libstdc++.so.5

When using a non-root Client with IBM JDK 1.5.0 to open an account, this operation fails with:

$ ./omii_client.sh open test-services/test/Account-test.xml Grid Client Exception in thread "main" java.lang.UnsatisfiedLinkError: fontmanager (libstdc++.so.5: cannot open shared object file: No such file or directory) at java.lang.ClassLoader.loadLibraryWithPath(ClassLoader.java:896)

This is caused by IBM JDK 1.5.0 (non-root, tgz version) having a dependency on libstdc++.so.5 which is not supplied with RHEL 4.

OMII-UK known issue code: P2130

Software Component known issues

Errors when performing initial install of AHE server

You may see these errors when installing AHE for the first time on an OMII-UK server:

[sql] Failed to execute: DROP TABLE RAHWL_1_0_2_ServiceGroups [sql] org.postgresql.util.PSQLException: ERROR: table "rahwl_1_0_2_servicegroups" does not exist [sql] Failed to execute: DROP TABLE RAHWL_1_0_2_Applications [sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block

These errors can be safely ignored; they are caused by the OMII-UK Server Installer attempting to delete any existing AHE databases before it performs an install.

OMII-UK known issue code: B2820

BPEL 64-bit failures

The BPEL client will fail when using a 64-bit Sun JDK, due to BPEL's dependency on Eclipse. Using a 64-bit Eclipse Linux version is not recommended.

OMII-UK known issue code: B3110.

BPEL creates AeBpelEngine directory

When installing BPEL on the OMII-UK Server, a new directory, AeBpelEngine, is created in the user's home directory. It is harmless and can be ignored.

OMII-UK known issue code: B2847

Grimoires race condition

There is a known problem with the Grimoires service on the server. The problem can occur if there are 2 clients concurrently accessing the service, with one accessing some metadata and the other updating the same metadata. A race condition exists where the client looking up the data can find the data it requires, but then said data is deleted before it can be read. This is because the client updating the data performs a deletion and then an insertion operation concurrently with the read operation. This results in an exception, which is reported to the client. However the client currently masks this exception.

OMII-UK known issue code: B2475

OGM platform and JDK limitations

OGM has experienced test failures during manual testing with Windows Vista and MacOSX. It has also experienced failures with Java 6 on all platforms apart from RedHat Enterprise Linux 4.4 and Scientific Linux 4.4.

OMII-UK known issue code: B3215

BPEL 2.1.0 'Produce Deployment Archive' workaround

The BPEL tutorial in the OMII-UK Training Guide refers to this known issue because the process detailed in 'Produce Deployment Archive' is at fault. Using the suggested build.xml to produce the .bpr file does not work so you need to use a workaround as follows:

1. Follow the instructions in the 'Deploy Workflows with Eclipse Server Runtime' section of the 'Deploying Workflows' topic in the OMII-UK User Guide, which represents an alternative method.

2. Ensure your server is shutdown before you attempt to 'publish' the project.

3. Once you have generated the bpr file, go back and continue with the tutorial instructions from 'Deploy Workflow'.

OMII-UK known issue code: B2829

OGSA-DAI server installation takes 13 minutes

When installing the OMII-UK server on a SuSE 9.x platform, it has been observed that the OGSA-DAI component can take up to 13 minutes to initialise its example database. Normally this process only takes a few seconds up to a minute.

OMII-UK known issue code: B2060

Installing OGSA-DAI v2.2 on an OMII-UK Server

If you see warnings like those below during OGSA-DAI server-side installation, they can be ignored.

[copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.0} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.1} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.2} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.3} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.4} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.5} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.6} to copy. [copy] Warning: Could not find file /home/js/omii-server-3.0.0/managed_programme/ogsadai-wsi-2.2/dist/server/${dai.driver.jars.7} to copy.

OMII-UK known issue code: B2392

PlotWS initial web page may not be accurate

Some of the information on the initial web page for PlotWS may not be accurate and should be treated as such.

OMII-UK known issue code: B2006, 2079

Taverna includes only the windows version of GraphViz

Currently Taverna only includes the Windows version of GraphViz (Graph Visualisation Software), version 2.8.1. If installing on Linux you will need to download the correct version and install it separately. You can download the Linux version from http://www.graphviz.org/Download_linux.php

OMII-UK known issue code: B2596

Feedback for users when using Taverna securely

At present, users are not informed via the GUI (Graphical User Interface) as to whether they are currently using Taverna in a secure mode or not. This issue will be addressed in a future release.

OMII-UK known issue code: B2777

Interoperability of Taverna with other OMII-UK Software Component Services

For the OMII-UK_3.4.0 release, interoperability is limited to GridSAM, Grimoires and PlotWS.

OMII-UK known issue code: B2777

WSRF::Lite platform limitations

WSRF::Lite has experienced WSRF::Lite test failures on the NMI automated testbed for the following platforms: Debian 3.1 and MacOSX 10.4, and on RedHat Enterprise Linux 5 and CentOS 5 during manual testing. WSRF::Lite also does not support 64-bit architectures.

Manual tests on WSRF::Lite with Debian 4.0 and Ubuntu 6.0.6 have shown that "libdata-dumpxml-perl", "librpc-xml-perl", "libxml-parser-perl" and "slimserver" need to be installed before installing WSRF::Lite. This step is only for OMII-UK users who are familiar with Debian/Ubuntu.

OMII-UK known issue code: B2773

WSRF::Lite and Microsoft Windows

WSRF::Lite currently does not work on MS-Windows; it is Linux only in the OMII-UK_3.4.0 release.

OMII-UK known issue code: B2789

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« This page (revision-9) was last changed on 17-Aug-2009 15:26 by SimonHettrick