Cipres Science Gateway

XSEDE Symptoms/Warnings/Error Messages

• Cannot configure FileHandler!
• Error in command "Execute"
• Parsing error - poorly formed BEAST file, infile.xml:
• Cannot allocate memory
• The certificate has expired
• The provided RSL could not be properly parsed.

Wed Jun 16 07:36:09 PDT 2010 > INPUTSTAGING : ERROR : NGBW-JOB-MRBAYESHYBRID_ABE-E20EC65DC8CC4AC18553CD91447C09C8 : Cannot configure FileHandler!

This issue arises when a user is logged in to the application twice. The first login prevents the second login from configuring the file handler. The simplest thing is to log out from the first application. If you have closed that window already, just wait for the login to time out from inactivity. Any login will terminate after 20 min of inactivity, and then the error will go away.

Could not open file "infile.nex.run1.t"
AddTreeSamples error on at least one processor
Error in command "Mcmc"
There was an error on at least one processor
Error in command "Execute"

This error arises as the result of a file system read/write problem, and it is strictly due to an issue at SDSC as opposed to user error. Please report these issues to us via the bug tracker.

Parsing error - poorly formed BEAST file, infile.xml:
The '<TxTModel>' element with id, 'txt.tn93', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of name frequencies REQUIRED containing
Exactly one ELEMENT of type FrequencyModel REQUIRED

The CIPRES Science Gateway runs BEAST on BEAGLE by default. However, there are some kinds of BEAST files that, while perfectly legal, throw a parsing error message when run on BEAGLE. To fix this issue, just check the box that says "Do not use BEAGLE". The job will run slower, but it should run.

java.io.IOException: java.io.IOException: Cannot allocate memory

If you submit a job, and it immediately shows: "Vew Error" instead of "View Status", you might see this message when you click the "View Error" button:

Fri Feb 19 14:16:40 PST 2010 > INITIALIZE : SUCCESS : NGBW-JOB-MRBAYESHYBRID_ABE-2932F25FE6EC4021B62497DA3BCD0AEE : Task successfully initialized. Fri Feb 19 14:16:40 PST 2010 > INPUTCHECK : SUCCESS : NGBW-JOB-MRBAYESHYBRID_ABE-2932F25FE6EC4021B62497DA3BCD0AEE : Input data successfully checked, data valid. Fri Feb 19 14:16:40 PST 2010 > COMMANDRENDERING : ERROR : NGBW-JOB-MRBAYESHYBRID_ABE-2932F25FE6EC4021B62497DA3BCD0AEE : java.io.IOException: java.io.IOException: Cannot allocate memory

It indicates that there are so many jobs running at this time that the application cannot accept any more. Please be patient, and re-submit the job in a few hours using the "Clone" button on the task pane.

After 7 days, the connection between the XSEDE and CIPRES Science Gateway expires. There is no way to prevent this today. If you get this message, the connection expired. However, your job will complete, and we can recover your data. You just have to notify me via the bug tracker or at mmiller at sdsc dot edu. I will get your data to you.

E20EC65DC8CC4AC18553CD91447C09C8 : Command sucessfully processed.
Wed Jun 16 09:00:31 PDT 2010 > PROCESSING : ERROR : NGBW-JOB-MRBAYESHYBRID_ABE-E20EC65DC8CC4AC18553CD91447C09C8 : Error processing job: The provided RSL could not be properly parsed.

This error arises in MrBayes jobs when the command line is not formatted correctly. Please try reloading the job parameter interface and re-entering your configuration settings.