huibintemaspamfaq
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huibintemaspamfaq [2017/12/13 01:42] – [Imaging with WSClean] huibintema | huibintemaspamfaq [2019/06/18 05:24] – huibintema | ||
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===== SPAM frequently asked questions ===== | ===== SPAM frequently asked questions ===== | ||
- | This ever-expanding section is based on user feedback. For questions on installing SPAM, see [[huibintemaspaminstall|this page]]. If you encounter a problem not listed below, please feel free to [[intema@strw.leidenuniv.nl|contact me]]. | + | This ever-expanding section is based on user feedback. For questions on installing SPAM, see [[huibintemaspaminstall|this page]]. If you encounter a problem not listed below, please feel free to [[huib.intema@curtin.edu.au|contact me]]. |
+ | |||
+ | ----- | ||
+ | |||
+ | ==== Obit is missing ==== | ||
+ | |||
+ | Q: Why is Obit reported to be missing during the ParselTongue install? | ||
+ | |||
+ | A: The ParselTongue configuration command may give you the following error message: | ||
+ | <code bash> | ||
+ | checking for Obit... missing | ||
+ | configure: error: Obit is not available | ||
+ | </ | ||
+ | This is likely to be caused by a missing python package or system library, not because Obit is missing (the script looks for Obit.so in the ${SPAM_PATH}/ | ||
+ | In bash: | ||
+ | <code bash> | ||
+ | . < | ||
+ | export PYTHONPATH=${SPAM_PATH}/ | ||
+ | export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}: | ||
+ | </ | ||
+ | Or in (t)csh: | ||
+ | <code bash> | ||
+ | source < | ||
+ | setenv PYTHONPATH ${SPAM_PATH}/ | ||
+ | setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}: | ||
+ | </ | ||
+ | Then | ||
+ | <code bash> | ||
+ | ${PYTHON} | ||
+ | </ | ||
+ | And in python: | ||
+ | <code python> | ||
+ | import OSystem, OErr | ||
+ | </ | ||
+ | Something will fail here, probably a missing python package or a missing library. Some of the missing libraries can be found [[ftp:// | ||
+ | <code bash> | ||
+ | ldd ${SPAM_PATH}/ | ||
+ | </ | ||
+ | This will report all libraries that are needed by Obit. If one is missing, the line will contain the text "=> not found". | ||
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+ | |||
==== Too many open files ==== | ==== Too many open files ==== | ||
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UPDATE: The latest ParselTongue distributed with SPAM has an improvement in place to reduce the occurence of this error. | UPDATE: The latest ParselTongue distributed with SPAM has an improvement in place to reduce the occurence of this error. | ||
+ | |||
+ | ----- | ||
+ | |||
+ | ==== Out of pty devices ==== | ||
+ | |||
+ | Q: SPAM crashes with a message about "pty devices" | ||
+ | |||
+ | A: Under certain circumstances, | ||
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wprojplanes = <some number, e.g. 128>, stokes = ' | wprojplanes = <some number, e.g. 128>, stokes = ' | ||
</ | </ | ||
+ | |||
+ | For more guidance on the options of CASA clean, go to the [[https:// | ||
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- | |||
==== Problems running SPAM on new Intel CPUs, possibly after Linux update ==== | ==== Problems running SPAM on new Intel CPUs, possibly after Linux update ==== | ||
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Q: Why doesn' | Q: Why doesn' | ||
- | A: Updates of the Linux operating system in 2017 has triggered floating point problems when running AIPS tasks on a new line of Intel Xeon E5-xxx CPUs. This is likely caused by an outdated Intel compiler used to build the AIPS binary install. A GNU compiled version of AIPS 31DEC13 fixes the problem and is available [[ftp:// | + | A: Updates of the Linux operating system in 2017 has triggered floating point problems when running AIPS tasks on a new line of Intel Xeon E5-xxx CPUs. This is likely caused by an outdated Intel compiler used to build the AIPS binary install. A GNU compiled version of AIPS 31DEC13 fixes the problem and is available [[ftp:// |
+ | |||
+ | Q: Why does the SPAM pipeline generate signal 11 errors in certain AIPS tasks? | ||
+ | |||
+ | A: What is causing this is not completely clear, but probably has to do with the newer Intel hardware and Linux installs. A work-around seems to be to use the GNU-compiled version of AIPS 31DEC13 available [[ftp:// | ||
+ | |||
+ | (Kindly tested by Gerrit Schellenberger and Arnab Chakraborty) | ||
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+ | |||
+ | ==== Manual flagging ==== | ||
+ | |||
+ | Q: Can I manually flag bad data in SPAM? | ||
+ | |||
+ | A: Manual flags can be inserted in both the // | ||
+ | <code python> | ||
+ | manual_flags = [ { ' | ||
+ | { ' | ||
+ | { ' | ||
+ | pre_calibrate_targets( uvfits_file_name, | ||
+ | </ | ||
+ | In this example, the antennas with AIPS indices 5 and 12 (corresponding to CASA indices 4 and 11) will be flagged completely (all times, both polarizations), | ||
+ | |||
+ | (Kindly suggested by Chris Riseley) | ||
+ | |||
+ | ----- | ||
+ | |||
+ | ==== Problems running SPAM on new Intel CPUs, possibly after Linux update ==== | ||
+ | |||
+ | Q: Why doesn' | ||
+ | |||
+ | A: Updates of the Linux operating system in 2017 has triggered floating point problems when running AIPS tasks on a new line of Intel Xeon E5-xxx CPUs. This is likely caused by an outdated Intel compiler used to build the AIPS binary install. A GNU compiled version of AIPS 31DEC13 fixes the problem and is available [[ftp:// | ||
+ | |||
+ | ----- | ||
+ | |||
+ | Feedback: [[huib.intema@curtin.edu.au|Click here]] | ||
huibintemaspamfaq.txt · Last modified: 2021/02/03 14:26 by huibintema