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+g...@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. > _______________________________________________ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
