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HIPE archived known issues

These issues are resolved but are kept here to aid troubleshooting in case of regressions.

Installation and de-installation issues

Installer or start-up hang on Mac OSX and Java 1.6.0_51

Ticket number: HCSS-18288

    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."

When installing only HIFI or PACS modules in HIPE you cannot transfer products from HSA to HIPE

  • Versions affected: HIPE 11.
  • Workaround: The current workaround is to install all modules even if you are not going to use them.
  • Resolution: The resolution is not known but the problem is not currently reproducible in HIPE 11 or 12.

There is a known problem with the InstallAnywhere installer when the bash \u special character is present in some environment variables

Versions affected: HIPE 9, 10, 11.

Error message: Installation fails with any of the following errors:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"
An internal LaunchAnywhere application error has occured and this application cannot proceed. (LAX)

Stack Trace:
java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
at java.util.Properties.loadConvert(Unknown Source)
at java.util.Properties.load0(Unknown Source)
at java.util.Properties.load(Unknown Source)
at com.zerog.common.java.util.PropertiesUtil.loadProperties(Unknown Source)
at com.zerog.lax.LAX.<init>(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)

Workaround: Un-setting or substituting the /u bash special character (using instead $USER or $LOGNAME) in the PS1 environment variable solves the problem. To do that, you should edit the .bashrc file located at the home directory of the current user. In there, any occurrence of the \u special character should be replaced by $USER or $LOGNAME. Example:

PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
should be replaced by
PS1='${debian_chroot:+($debian_chroot)}$USER@\h:\w\$ '

Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941 See this page for current known issues on later HIPE versions.

Resolution: Newer versions of InstallAnywhere do not suffer from this problem.

Cannot install on Mac OS X 10.8 "Mountain Lion"

HIPE user installers (11.0.1 and earlier) do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
  • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
  • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.

Resolution: Installers from HIPE 11.1 are generated with a newer version of InstallAnywhere that supports Mac OS 10.8 or later. Since HIPE 11.1 is the preferred operational version, this issue is archived.

HIPE 13 Archived Known Issues

Cut levels in Display don't work properly for very small values in images

Ticket number: HCSS-19897

Versions affected: HIPE 13.0

Description: You cannot modify the cut levels of an image, loaded with the help of the Display class, that contains very small values (close to zero). For example, the image aa created by this script:

aa = Double2d(257,257)

width = 20.0
for i in range(257):
   for j in range(257):
      aa[i,j] = EXP(-(((j-128.)**2)+((i-128.)**2))/(2*width**2))

bb = aa + 0.001

On the other hand, the cut levels of image bb would be handled properly.

Workaround: Use an older version of HIPE to adjust cut levels in images.

SUSSEXtractor returns many more sources for SPIRE maps from version 12.66 onwards

Ticket number: HCSS-18988 (Fixed from version 13.0.4920)

Versions affected: All versions of HIPE from build 12.0.66 to 13.0.4919 (both included).

Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.0.66 to 13.0.4919 returns 3-4 times the number of sources it returned previously with the same parameters (except the PRF grid size, which has increased internally from 5x5 to 13x13 pixels). The fluxes of the detected sources are also different and generally higher by around 5 percent.

Workaround: You can force SUSSEXtractor to produce the original results by imposing a 5x5 PRF grid size, as tests have concluded that the photometry of the results of this task for the versions affected is worse than before. SUSSEXtractor has reverted to the original 5x5 PRF from HIPE builds later than 13.0.4919.

Example script:

myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([myImage.getWidth(),myImage.getHeight()],5.0)
sourceList = sourceExtractorSussextractor( \
    image = myImage,        # Image name \
    prf = myPrf,            # 5x5 PRF \

HIPE 12 Archived Known Issues

computeVelocityTask plots absorption profiles as emission

Ticket number: HCSS-19133

Versions affected: HIPE 12.

Description: The computeVelocityTask in the Cube Analysis Toolbox returns and plots a fittedLineCube. This plot displays absorption profiles as emission, even if isEmission=False. The data returned is correct, but this plot must be disregarded.

Workaround: Simply disregard the plot generated by the task and trust the data stored in the fittedLineCube.

Problem with doGridding in rotated maps with HIFI

Ticket number: HIFI-5716

Versions affected: HIPE 12.0

Description: for maps taken with a non-zero orientation on the sky, the HIFI pipeline will generate two cubes: one non-rotated cube projected onto the Equatorial frame (cubesContext) and one rotated by the scanning orientation angle (cubesContextRotated). In HIPE 12.0 a bug was introduced that generates both cubes in the rotated frame.

Workaround: In order to generate non-rotated cubes you can apply the doGridding task on the level 2 products with the option flyAngle=1e-5 (for example - it is just a matter of using a very small, non-strictly zero, angle). The problem will be solved in 12.1.

Java 7 issues

Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS X, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

Ticket: HCSS-18424

Configuration prone to cause the error

  • Operating system: Any version of Mac OS X.
  • Java version: any Java 7 version.

Usage prone to cause the error

  • Leave HIPE running unattended for several hours.
  • Return to work with HIPE and:
    • Switch applications.
    • Wake the computer/monitor from sleep.
    • Change the display resolution.
    • Send an application to another monitor in a multimonitor setup.

Error message

The crash displays a long error trace that begins with:

Thread 0 Crashed:: AppKit Thread  Dispatch queue: com.apple.main-thread
0   com.apple.CoreFoundation         0x00007fff8d7e2a1b CFRelease + 27
1   liblwawt.dylib                   0x000000011b557647 __Java_sun_lwawt_macosx_CWrapper_00024NSObject_release_block_invoke_1 + 91
2   JavaNativeFoundation             0x000000011a8ea5f5 +[JNFRunLoop _performCopiedBlock:] + 20
3   com.apple.CoreFoundation         0x00007fff8d8a7d9d +[NSObject performSelector:withObject:] + 61
4   com.apple.Foundation             0x00007fff85d9dd70 __NSThreadPerformPerform + 214
5   com.apple.CoreFoundation         0x00007fff8d7ec4f1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
6   com.apple.CoreFoundation         0x00007fff8d7ebd5d __CFRunLoopDoSources0 + 253
7   com.apple.CoreFoundation         0x00007fff8d812b49 __CFRunLoopRun + 905
8   com.apple.CoreFoundation         0x00007fff8d812486 CFRunLoopRunSpecific + 230
9   com.apple.HIToolbox              0x00007fff8acda2bf RunCurrentEventLoopInMode + 277

General information

If you are affected by this problem, it is useful to know that:

  • This is a Mac OS X problem, it does not affect any other operating system.
  • This is a Java 7 bug, being worked on by Oracle and set to be fixed in Java 8. More information can be found at http://bugs.java.com/view_bug.do?bug_id=8009012


From the information above, the only identified workarounds for those of you that run long sessions of HIPE are:

Cursor position in the editor view is inaccurate in high-DPI (Retina) displays using Java 7 version

Ticket number: HCSS-18698
Versions affected: HIPE 12 or older
Description: The cursor position appears inside characters instead of between them.


From Java 7 Update 55, Oracle has fixed the issue. As the bundled JRE for HIPE 12 or older is Java 7 Update 45, to be able to benefit from the patch you must change the script that launches HIPE and point it to the Java 7 Update 55 or later installed at system level. To do that, edit the file HIPE_DIR/bin/_launch.sh and edit or delete the line(s) that export the PATH variable:

export PATH

NOTE: You should only delete the lines if you are completely sure that the default version of the system is Update 55 or later. In order to check if that is the case, you can execute java -version or /usr/libexec/java_home -V on the Terminal and then, after confirming the default version, use that path to update the _launch.sh file.

New security requirement in Java 7 causes the Herschel Science Archive application to fail at launch

Description: If you have a recently patched Java 7 installation (update 40 or later), a new security requirement in Java 7 that requires the JAR file to have a Permissions attribute, is no longer reported only (note the information message with a yellow background) as it was in previous versions:


Now the Java runtime blocks the JAR file execution when you click the Run button.

Error message: The following error dialogs are displayed when trying to run the HSA application and clicking the Details button: Screen_Shot_2014-01-16_at_16.29.26.png

Workaround: Please follow the instructions provided by Oracle to run applications that lack the currently enforced security features.

Resolution: The required attribute was added to the JAR manifest and now the WebStart runs correctly for every HIPE version (they all point to the same .jnlp file in ESAC's servers).

Other issues

Jython bug when comparing NaN values with numbers

Jython behaves differently from Python when comparing NaN values with numbers.

In Python 2.4 or 2.5:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# False

In Jython 2.5.2:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# True

An issue has been opened on the Jython bug tracker.

Resolution: All operational HIPE versions now use Jython 2.5.3 which patched this bug (see the bug report above).

"Can't connect to X11" error when using the jylaunch command or the command-line mode of hipe

*Description:*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 or hipe -Djava.awt.headless=true instead of hipe.

Ticket number: HCSS-17846

Warning, important Jylaunch is a deprecated tool in HIPE 11 and is not present in HIPE 12. This advice should apply equally to its replacement: hipe main executable.

Resolution: The dependencies that caused this problem were removed in HIPE 11 build 2324. HIPE 11.0 or later should not be affected.

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Topic revision: r12 - 2015-04-07 - AlvarGarcia
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