HIPE known issues

Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to startup, help and other issues common to different HIPE versions.

This page is for known issues in the HIPE software. For known issues in data products see this page.

See this page for documentation errata and last-minute updates.

Known issues in HIPE 8.0

• Problem with NaN values with imageConvolution task. Starting from HIPE 7, the imageConvolution task works with images containing NaNs too. However, the results when NaNs are present (either in the map or around the coverage area) are not reliable. A fixed version of the task is scheduled for HIPE 9.

• Problem with correction of MADmap point-source artifacts. The PACS task photCorrMadmapArtifacts, used to correct point-source artifacts in MADmap produced Level 2.5 products, only works when the initial time-ordered data product (TOD) is created with scale factor of 1. All other values of scale factor may produce incorrect results. A fix, possibly distributed as a plug-in, will be available later.

• Problem with units in the Cube Spectrum Analysis Toolbox. This tool returns the wrong units of measurement with extraction plots and integrated maps. This issue has been detected with PACS data and is under investigation. Previous HIPE versions are not affected.

• User pool names (pool ID) restrictions: Old pools that do not follow the restrictions on the allowed names cannot be read in HIPE (eg a dot "." in the name is such a case). The user can safely rename the folder (found in the local store) following the rules: allowed characters in name: alphanumeric, dash ("-") and underscore ("_"), the name cannot start with a dash ("-") and cannot have "urn" as name. The pool ID is case-sensitive and must be with less than 255 characters.

• High memory usage with Mac OS 10.6 Snow Leopard. There are reports of HIPE 8.0.1 using all available memory and freezing while reprocessing observations under Mac OS 10.6 Snow Leopard. This problem does not seem to appear on other platforms, including other Mac OS versions. The problem is being investigated.

• Velocity Maps in the Cube Spectrum Analysis Toolbox. Fitting of faint lines (less than 2 sigma) or non-gaussian lines can result in incorrect velocities in the velocity map. It is advised to fit the velocity in a few positions manually in the spectrum explorer and verify the consistency with the calculated velocities at these positions in the velocity map in the cube explorer.

• Upgrade to Jython 2.5. Starting from version 8.0, HIPE will include a new version of Jython. You may have to adapt your scripts for them to work with the new version. See this page for the details.

• Links in the User's Reference Manual. Some hyperlinks in entries of the User's Reference Manual do not work, pointing instead to the top of the same page.

• Opening the HSA User Interface under Windows XP: If you open the HSA User Interface from HIPE while being logged in, the following error appears: JNLParseException[ Could not parse launch file. Error at line 0.]. The workaround is to log out in HIPE and start the HSA User Interface. If necessary, log in in the HSA User Interface and log back in in HIPE.

• Sending data from HIPE to DS9 under Mac OS: Using DS9 version 6.2, due to a problem with the DS9 application, HIPE fails to start DS9 automatically. Either use DS9 version 6.1 or start DS9 manually and re-send your image from HIPE. The DS9 team states that they plan on fixing this in the next release.

• Sending data from DS9 to HIPE under Windows. The following issues were reported when trying to send images via SAMP from DS9 to HIPE under Windows:
  • Windows 7: The option to send an image is sometimes disabled in DS9.
  • Windows XP: A SAMP message appears to be sent, but the image is not received by HIPE.
  • All Windows versions: At DS9 shutdown, the following Cygwin warning appears, even when data transfer works correctly, like in Windows Vista.

• Solved known issue with step by step execution. The known issue found in HIPE 7.0 with step by step execution has been solved. You can revert to the old behaviour by choosing Edit --> Preferences, going to Editors & Viewers --> Jython Editor and unticking the Use improved step by step execution checkbox.

• HIPE drops Versant database connection under Windows XP: A problem can occur if HIPE is run under Windows XP connected via WiFi to a Versant database server. If the connection is interrupted briefly, the HIPE session may fail with a "Network layer read error". Linux does not have this problem because it keeps retrying for several minutes.

• Garbled text after horizontal scrolling in Ubuntu 11.10. A problem on systems with NVidia cards and running Ubuntu 11.10 can cause text to appear garbled when scrolling horizontally, as shown by the figure below. To solve the problem, add the following property to the user.props file, located in the .hcss directory within your home directory. If there is no user.props file, create it.

java.vm.options = -Dsun.java2d.opengl=true

Known issues in HIPE 7.3

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.2

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.1

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.0

• Cannot download data from the Herschel Archive due to corrupted cache.

Error messages about product cache corruption may vary. One example is the following:

herschel.share.util.ConfigurationException: Failed to locate product in cache

To solve the problem, try one or more of the following:

• Choose Edit --> Preferences and go to Data Access --> Storages & Pools. Select a pool in the Pools pane and click the Clear cache button. Note that this button will not be available if there are no pools listed in the Pools pane.
• If the above does not work, clear the HSA cache manually by deleting the home/.hcss/pal_cache/hsa directory, where home is your home directory.
• If the above does not work, clear all caches manually by deleting the home/.hcss/pal_cache directory.

• High disk activity with many local pools

If you have a high number of local pools on your disk (of the order of hundreds or more) you may experience noticeably high disk activity at HIPE startup.

• Step by step execution sometimes runs two statements at once

This happens when executing a compound statement, such as a for loop. The first command after the compound statement will be executed in the same step as the compound statement. Consider for example the following script:

for i in range(3):
  print i
print "Finished"

The line by line execution will run the for loop and the print "Finished' statement in the same step. A workaround for this behaviour is to add a pass command after the end of the compound statement. The pass command will be executed in the same step as the for loop, but without any effect:

for i in range(3):
  print i
pass
print "Finished"

Older HIPE versions

Known issues for older HIPE versions are listed in a separate page.

General HIPE startup issues

HIPE does not start at all, without giving error messages. What's wrong?

This can happen for different reasons, that are explored in the next entries. When you start HIPE by clicking on its icon and a problem occurs, you may only see a terminal/command window appear for a fraction of a second, leaving you without information on the error.

To obtain more information about the error, try invoking HIPE directly from a terminal/command window ([installation_dir]/apps/hipe) and examine the text output. Note that the output from some errors can be quite lengthy, so you may need to scroll up to discover the root cause.

The next entries list some common problems that prevent HIPE from starting.

HIPE cannot start: the JVM cannot reserve enough memory

This only applies if you installed HIPE using the installer, and not downloading a developer build from the Continuous Integration System.

The cause is that the Java virtual machine is unable to start with the designated amount of memory.

The terminal/command window from which you invoke HIPE shows the following error message that indicates insufficient memory:

Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.

To fix this error you have to modify two properties in the installed.properties file within your HIPE installation directory. There is no need to reinstall HIPE.

The properties you need to modify are the following. You have to lower the amount of allocated memory:

java.vm.memory.max
java.vm.options=-XX:PermSize

Possible values are the following:

java.vm.memory.max=1024m
java.vm.options=-XX:PermSize=128m

Try running HIPE after modifying the values until it successfully starts.

You may have the same properties defined in a hipe.props or user.props file, located in the .hcss directory within your home directory. In this case, any values set in hipe.props override those in user.props, which override those in installed.properties. Make sure to edit the properties in the file with highest proprity for your changes to take effect. See this page for more information on property files and their precedence order.

HIPE cannot start: SAXNotRecognizedException

The terminal/command window from which you invoke HIPE shows a SAXNotRecognizedException.

To solve this issue, add the following line to the installed.properties file in your HIPE installation directory:

java.vm.options = -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl

HIPE cannot start: exception access violation.

The terminal/command window from which you invoke HIPE shows an EXCEPTION_ACCESS_VIOLATION error related to a class in org.apache.xerces.

Restart HIPE to resolve the issue.

This error is probably due to a bug in the Java Virtual Machine, and has so far been found only on Windows XP 32 bit.

General Help System issues

The help does not work anymore! What's wrong?

First, check if your issue is that described below, in Why is the HIPE Help System suddenly unable to connect to any help page? If not, you have probably encountered a bug. The following are known issues that can prevent you from viewing the documentation, resulting either in a blank page or an error message:

• A caching bug in Safari 4.0 can be solved by clearing the browser cache. Alternatively, open the help page with another web browser: copy and paste the address (something like http://127.0.0.1:8082/index.jsp?mark=null) to the address bar of the other browser.
• A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. Rebooting the computer solves the issue.
• Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the Help in URM menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
• In general, when you encounter a problem with the Help System you should follow these steps:
  • See if the help works with another browser. If possible, upgrade your browser to the latest version.
  • Clear the browser cache
  • Delete the browser cookies
  • Reboot the computer

If none of the above works, please raise a ticket with the Helpdesk.

Is there a way to open the HIPE Help System without starting HIPE?

Yes, via the hipe_help command, which resides in the apps folder in your HIPE installation. The hipe_help command will start a standalone Help System in a window called Yet Another JAva Help System. Press the Display button to open the Help initial page in your default browser.

Why does searching the documentation take such a long time?

When you execute the first search with a new HIPE version, HIPE has to index the contents of the documentation. This can take up to several minutes, depending on the performance of your system. Indexing of the documentation is only done for the first search. Subsequent searches will be much faster.

We are investigating ways to include pre-built indexes in the documentation shipped with HIPE, so you will not have to wait for the results of your first search.

The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

No, the Help System resides on your computer and does not need Internet connection, except for the What's New document, which is hosted on the Herschel Wiki website.

Why is the HIPE Help System suddenly unable to connect to any help page?

The Help System relies on a local web server to display help pages. If you close the application that started the web server, the server will shut down as well:

• If you started the Help System from HIPE, quitting HIPE will stop the Help System.
• If you started the Help System with the show_help command, closing the Yet Another JAva Help System window will stop the Help System.

Note that when the Help System stops, any browser window or tab showing help pages will remain open, but links on them will not work anymore.

Why are some code examples slightly different in the PDF and HTML versions of the documentation?

Code examples and commands in the PDF versions of the manuals sometimes have extra dashes added (for instance, -XX:MaxPermSize=256m becomes --XX:MaxPermSize=256m). If an example or a command does not work as expected, try checking the HTML version of the documentation, which is not affected by this bug.

Why are several important packages missing from the Javadoc?

You are probably looking at the static Javadoc located in the doc/api/ folder of your HIPE installation. The complete Javadoc can now be accessed from the HIPE Help System by clicking on HCSS Developer's Reference Manual (API) in the Developer Reference section. The plan is to remove the static version of the Javadoc completely.

Is it possible to have the traditional, frame-based Javadoc layout?

Javadoc pages appear within the HIPE Help System frame structure. If you click on the FRAME link on any Javadoc page, you will obtain the traditional Javadoc layout. To go back to the HIPE Help System layout you will have to use the Back button of your browser (clicking on the NO FRAMES link will not work). To avoid losing the HIPE Help System layout, you may want to right-click on the FRAMES link to open the traditional Javadoc layout into a new tab of your web browser.

How can I provide feedback/requests regarding HIPE documentation?

For informal feedback, click on the envelope icon on the top toolbar of any help page. This opens a new message in your email client, where you can add your feedback. If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.

Other issues

"Can't connect to X11" error when using the jylaunch command

Executing a script outside HIPE with the jylaunch command may fail with a java.lang.InternalError: Can't connect to X11 window server error. This may happen even if the script does not open any graphical window, since it may indirectly call components that require an X11 server. The workaround is to run the script with the command jylaunch -Djava.awt.headless=true instead of just jylaunch.

Problems saving observations to NFS-mounted disks and FAT32 disks

When saving observation to your computer, you may experience problems in the following cases:

• When saving data to NFS-mounted disks (you may get an IllegalMonitorStateException).
• When saving data to a FAT32 filesystem from a Mac (you may get an OverlappingFileLockException).

Both problems are solved by setting the following property:

hcss.ia.pal.pool.lstore.lock = simple

See the HIPE Owner's Guide for information on how to set properties.

Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

You probably retrieved the observation without having the corresponding instrument software installed (for instance, you retrieved a PACS observation without having the PACS modules in HIPE).

To solve this problem follow these steps:

1. Reinstall HIPE, including the software of the desired instrument.
2. Delete the following directories (home being your home directory):
   • home/.hcss/lstore/hsa_cache
   • home/.hcss/pal_cache/hsa
3. Retrieve the observation again.