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Troubleshooting

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jasercion edited this page Sep 21, 2020 · 51 revisions

Please check below for solutions to common problems and known bugs. We've tried to arrange them into logical categories.

You should also check that you have the latest release of the tools (you can do this by running conda list fermi). It's possible the problem may already have been fixed. See the Release Notes for the changes in each version.

If you still can't find a solution, please see Error Reporting.

Python Setup

  • Make sure that Anaconda or Miniconda Python is the python you are using (you can verify this via the which python command)/verify that your Anaconda or Miniconda installation is in your PATH.
  • In order to use Jupyter Notebooks you will need to install the nb_conda package via conda install, i.e., conda install nb_conda

Activating Conda

  • Activation using tcsh or csh fails with an error like "root: Command not found."
    You may need to downgrade conda or switch to the bash shell. Conda has poor support for csh/tcsh and has broken the activation script several times during upgrades, which causes problems because paths and other things not getting set correctly. For instance, the 4.6.14 version of conda made various changes to the activation script, especially for Windows, that broke the (t)csh activation. We can sometimes fix these issue in our activation script, so please report the issue. As a workaround and if you don't want to use the bash shell, you can also try downgrading conda:

    • Deactivate any conda environments.
    • Run conda install conda=4.6.12 (or whatever the latest version that worked).
    • Start a fresh shell or log back out and in again to make sure environment is reset.
    • Activate conda.

  • Activation fails with an error like :] Event not found."
    We have found that custom command prompts that contain terms like [\!] cause the activation to fail in the latest conda version (4.5), at least in csh. Escaping the final bracket, e.g., [\!\], seems to fix the problem. We have filed an error report with the Conda developers.

  • You receive a warning like:
    WARNING: You have LD_LIBRARY_PATH set. This might interfere with the correct functioning of conda and the Fermi ST
    or
    WARNING: You have PYTHONPATH set. This might interfere with the correct functioning of conda and the Fermi ST
    Having the PYTHONPATH or LD_LIBRARY_PATH set will likely not interfere with the tools. If you encounter a problem with the tools after seeing this warning on setup, try rerunning the problem command with these variables unset.

  • You receive the message cat: EOF: No such file or directory
    This message can happen when activating the tools in csh/tcsh environments. It is a known issue with the csh activation script of the tools and is currently being patched. This should not affect tool functionality.

Installation Issues

  • When attempting to install the tools dependency resolution seems stalled/never finishes.
    Try updating your version of conda and rerunning the installation. This tends to solve the problem.

Pulsar Tools

  • You get the message that the pulsar tools, like gtpsearch or gtpspec, are not found or installed. That is because many of the pulsar tools have been deprecated and removed from the Fermitools. They were not being used by the pulsar community and have not really had anyone to support them for a while. The pulsar community instead uses tools like tempo2 or PRESTO. Please look into using those tools for pulsar analysis.

ModelEditor

  • If ModelEditor fails to launch, make sure that you have the pyDS9 package installed via conda. For instructions on how to do this see the Additional Software section of the Installation Instructions.

gtburst

  • If gtburst is throwing the error OSError: [Errno 2] No such file or directory: '~/.gtburst/gtburstGUI.conf': Check the ~/.gtburst directory for a file named gtburstGUI.conf.db. Copying this file to ~/.gtburst/gtburstGUI.conf seems to fix the issue
  • If the gtburst GUI doesn't launch sometimes you need to manually perform an update. Do the following in python: 
       >>> from GtBurst import updater
   >>> updater.update()

Other Messages or Errors

Caught St13runtime_error at the top level: RoiCuts::sortCuts:

This error occurs when a tool such as gtexpmap finds duplicate DSS keywords in the FITS header, so you must delete one of the duplicated keywords. After that you must change the keyword NDSKEYS to reflect the surviving number of DSS keywords. You also must renumber the remaining keywords so that the numbering is consecutive and the max is the same as the total number, otherwise the tool will fail. You can use the FTOOL fv to accomplish this, but other FTOOLS such as fmodhead or fparkey should also work.

To avoid this error, when using gtselect be certain to match the following parameters to the exact values used when extracting the data from the LAT data server:

  • Minimum and maximum event energies
  • RA and DEC positions for the acceptance cone
  • Tmin and Tmax in MET

CALDB File Not Found Error

You may encounter the error Caught St13runtime_error at the top level: File not found: when running some tools, like gtexpcube2 or gtsuntemp. This error occurs when the irfs input parameter is set to CALDB, and the optional input counts map is set to none. The problem is that CALDB cannot find the EVENT_CLASS keyword in any of the input files and cannot determine the proper IRF to use. In these cases, you must explicitly set the IRF to use (e.g., P8R3_SOURCE_V2). Note the irfs parameter may be a hidden option on some tools. Future versions of the tools will make the error message more explicit.

CFITSIO library mismatch

You may see a message like WARNING: version mismatch between CFITSIO header (v3.43) and linked library (v3.41).

This warning occurs due to the fact that astropy carries a different version of CFITSIO than the version the FSSC builds the conda binaries against. This should not cause any issues with analysis.

External program cannot load shared library

If you are attempting to run an external program while the conda environment is activated and you are seeing a 'Cannot load shared library' error, prepend the location of the environment's libraries to the from of your $LD_LIBRARY_PATH:

bash: export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
(t)csh: setenv LD_LIBRARY_PATH $CONDA_PREFIX/lib:$LD_LIBRARY_PATH

Parameter not found (N5hoops10HexceptionE)

This can be caused by a corrupt or old parameter file, which specifies the input to a tool. Try removing the parameter file for the problem tool in your $HOME/pfiles directory (e.g., rm $HOME/pfiles/gtlike.par). When you run the tool again, it will install a fresh copy of the .par file into your pfiles directory.

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