#656 Error attempting to parse qstat output as xml

[Andrei Akhmetzhanov]

I have got a strange error message on http://lalashan.mcmaster.ca/theobio/evolCancer/index.php/Special:GetProjectFile?project=Tumor_progression_modeling%2FEmergence%2FMortality%2FVariant_2&filename=chi2fit-UK.R

I don't know actually what it means

[Lee Worden]

This comes from a problem listing the background jobs on the cluster, fyi.
I'll try to look into it, if it's persisting.

[Lee Worden]

Here's what I get when I emulate what WW is trying to do on the cluster.

wonder@yushan-n02:~$ sudo -u apache -i
[sudo] password for wonder:
apache@yushan-n02:~$ . /usr/local/sge/default/common/settings.sh
apache@yushan-n02:~$ qstat -f -xml
error: commlib error: got select error (Connection refused)
error: unable to send message to qmaster using port 6444 on host "jdserv": got send error
apache@yushan-n02:~$

JD: maybe you and Todd can look into what's up with the grid engine? I'll try to improve WW's error reporting for this case.

[Lee Worden]

I have improved reporting of qstat error output. WW now outputs:

Error: ProjectEngine: Error attempting to parse qstat output as xml: String could not be parsed as XML
qstat output is:
error: commlib error: got select error (Connection refused)
error: unable to send message to qmaster using port 6444 on host "jdserv": got send error

[Andrei Akhmetzhanov]

Hi Lee, thanks for checking! Jonathan emailed me that Todd took a look at that problem.