[gridengine users] Effects of login_shells settings

Feng Zhang prod.feng at gmail.com
Wed Oct 31 20:14:16 UTC 2018


add an extra command line in job script:

unset module

may be helpful.

Best,

Feng
Best,

Feng


On Wed, Oct 31, 2018 at 2:48 PM Ilya M <4ilya.m+grid at gmail.com> wrote:
>
> 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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