[gridengine users] Effects of login_shells settings

Ilya M 4ilya.m+grid at gmail.com
Wed Oct 31 18:47:32 UTC 2018


Hello,

I had an unexpected effect after adding bash to the login_shells list in
SGE 6.2.u5. Some array tasks started to get scheduled twice on the same
node (accounting info corroborates that) and 1-2 tasks in a job would not
produce any output at all, as if they did not run. This quickly became a
wide-spread problem in the cluster and I had to revert the change by
removing bash from the list.

I am trying to understand the cause of this behavior. I did not find
anything in the logs. The qmaster logs and accounting only showed that some
tasks were scheduled twice, running for the same number of seconds and both
times completing successfully. Was this an uncovered bug?

The rationale for adding bash to the list, were the errors some users
reported when trying to launch their jobs in bash:

/bin/bash: SPEcho: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPEcho'
> /bin/bash: SPCheckFile: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCheckFile'
> /bin/bash: SPNotify: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPNotify'
> /bin/bash: SPCheckFileNonEmpty: line 1: syntax error: unexpected end of
> file
> /bin/bash: error importing function definition for
> `BASH_FUNC_SPCheckFileNonEmpty'
> /bin/bash: SPCheckExec: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCheckExec'
> /bin/bash: SPLogError: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPLogError'
> /bin/bash: SPCkptDone: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCkptDone'
> /bin/bash: SPCheckFunc: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCheckFunc'
> /bin/bash: SPCkptShouldRun: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for
> `BASH_FUNC_SPCkptShouldRun'
> /bin/bash: SPCheckVar: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCheckVar'
> /bin/bash: SPCheckDir: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCheckDir'
> /bin/bash: SPLogInfo: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPLogInfo'
> /bin/bash: SPCleanDir: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPCleanDir'
> /bin/bash: SPLogWarning: line 1: syntax error: unexpected end of file
> /bin/bash: error importing function definition for `BASH_FUNC_SPLogWarning'
>

>
And the discussion here:
https://sourceforge.net/p/modules/mailman/message/28650889/, suggesting
that the cause might be absence of bash in the login_shells list.

Looking forward to some ideas and explanations.

Thank you,
Ilya.
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