User Tools

Site Tools


huibintemaspamfaq

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
Next revisionBoth sides next revision
huibintemaspamfaq [2019/01/10 10:35] – [Manual flagging] huibintemahuibintemaspamfaq [2019/09/10 06:36] – [SPAM crashes in screen session] huibintema
Line 2: Line 2:
 ===== 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]].
  
 ----- -----
Line 41: Line 41:
 </code> </code>
 This will report all libraries that are needed by Obit. If one is missing, the line will contain the text "=> not found". This will report all libraries that are needed by Obit. If one is missing, the line will contain the text "=> not found".
 +
 +-----
 +
 +==== libncurses.so.6 is missing ====
 +
 +Q: Why is libncurses.so.6 reported to be missing during the AIPS install?
 +
 +A: The AIPS install may fail because the libncurses.so.6 library cannot be found. This library is available in the lib subdirectory of the spam install directory. The library can be copied to one of the standard locations (e.g., /usr/lib) or the LD_LIBRARY_PATH environment variable can be modified to include the spam/lib directory before running AIPS install again. The latter can be done in bash:
 +<code bash>
 +export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${SPAM_PATH}/lib
 +</code>
 +Or in (t)csh:
 +<code bash>
 +setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${SPAM_PATH}/lib
 +</code>
  
 ----- -----
Line 129: Line 144:
  
 ----- -----
- 
  
 ==== Problems running SPAM on new Intel CPUs, possibly after Linux update ==== ==== Problems running SPAM on new Intel CPUs, possibly after Linux update ====
Line 135: Line 149:
 Q: Why doesn't the SPAM pipeline work (anymore), with AIPS generating NaNs in certain tasks? Q: Why doesn't the SPAM pipeline work (anymore), with AIPS generating NaNs in certain tasks?
  
-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://ftp.strw.leidenuniv.nl/pub/intema/spam/AIPS_31DEC13A.tgz|here]]. It may run a bit slower than the Intel compiled version.+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://ftp.strw.leidenuniv.nl/pub/intema/spam/AIPS_31DEC13_Gnu.tgz|here]]. It may run a bit slower than the Intel compiled version. 
 + 
 +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://ftp.strw.leidenuniv.nl/pub/intema/spam/AIPS_31DEC13_Gnu.tgz|here]]. It may run a bit slower than the Intel compiled version. 
 + 
 +(Kindly tested by Gerrit Schellenberger and Arnab Chakraborty) 
  
 ----- -----
Line 152: Line 173:
 ==== SPAM crashes in screen session ==== ==== SPAM crashes in screen session ====
  
-Q: Why does my SPAM pipeline run crash when the screen session in which I run SPAM is interrupted?+Q: Why does my SPAM pipeline run crash when the screen session in which I run SPAM is interrupted, or when I reconnect?
  
 A: As the SPAM pipeline can take several hours to days to run, it is useful to execute it in a screen session when working remotely. However, some users found that the SPAM pipeline crashed during a disconnect from the screen session with the error "Fatal IO error 11 (Resource temporarily unavailable) on X server localhost:1.0.", or something similar. This is likely due to the fact that the screen is started in an environment with the X server available that becomes unavailable after the disconnection, causing the crash of SPAM. A solution might be to use a "fake" X server, such as xvfb, in the screen session. Another solution is to run SPAM remotely via a VNC session. Note that checking the progress of the pipeline can also be done by checking the spam*.log in the datfil subdirectory. A: As the SPAM pipeline can take several hours to days to run, it is useful to execute it in a screen session when working remotely. However, some users found that the SPAM pipeline crashed during a disconnect from the screen session with the error "Fatal IO error 11 (Resource temporarily unavailable) on X server localhost:1.0.", or something similar. This is likely due to the fact that the screen is started in an environment with the X server available that becomes unavailable after the disconnection, causing the crash of SPAM. A solution might be to use a "fake" X server, such as xvfb, in the screen session. Another solution is to run SPAM remotely via a VNC session. Note that checking the progress of the pipeline can also be done by checking the spam*.log in the datfil subdirectory.
  
-(Kindly contributed by Andrea Botteon)+Another problem with using screen was found when reconnecting, leading to an "error: (4, 'Interrupted system call')". A fix has been added to ParselTongue which captures this exception without crashing the SPAM pipeline. 
 + 
 + 
 +(Kind contributions from Andrea Botteon and Błażej Nikiel-Wroczyński)
  
 ----- -----
Line 174: Line 198:
  
 (Kindly suggested by Chris Riseley) (Kindly suggested by Chris Riseley)
 +
 +-----
 +
 +==== Problems running SPAM on new Intel CPUs, possibly after Linux update ====
 +
 +Q: Why doesn't the SPAM pipeline work (anymore), with AIPS generating NaNs in certain tasks?
 +
 +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://ftp.strw.leidenuniv.nl/pub/intema/spam/AIPS_31DEC13_Gnu.tgz|here]]. It may run a bit slower than the Intel compiled version.
  
 ----- -----
huibintemaspamfaq.txt · Last modified: 2021/02/03 14:26 by huibintema

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki