Unable to access file --file is locked (SDDS_InitializeOutput)

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duanz
Posts: 50
Joined: 30 May 2009, 01:50

Unable to access file --file is locked (SDDS_InitializeOutput)

Post by duanz » 31 Jan 2021, 22:27

Hi Michael,

I'm using SLURM to submit elegant/Pelegant jobs on a cluster, inside the bash script there is a sddsprocess command that generate a new file out of an old file. But when the script is executed, sometimes( not always ) there is the following error message:

Error for sddsprocess:

Unable to access file "the filename" --file is locked (SDDS_InitializeOutput).

I wonder what is the cause for such an error, and what I could do to avoid it.


I just saw a possibly related question by Hexin "elegant file locked on centos7 server" , the following is the information of the file system I use, I installed elegant and sddstoolkit 2020.5.0 by compiling the source files.

(base) -bash-4.2$ mount | grep /sharefs | grep lustre
192.168.50.77@tcp:/sharefs on /sharefs type lustre (rw,flock,lazystatfs)


Thanks and best regards,

Zhe

soliday
Posts: 371
Joined: 28 May 2008, 09:15

Re: Unable to access file --file is locked (SDDS_InitializeOutput)

Post by soliday » 01 Feb 2021, 10:08

Are you sure that two jobs are not writing to the same file? Is there something in your bash script that would keep the output file names different from each other when you launch multiple jobs at the same time?

duanz
Posts: 50
Joined: 30 May 2009, 01:50

Re: Unable to access file --file is locked (SDDS_InitializeOutput)

Post by duanz » 01 Feb 2021, 16:51

Hi Soliday,

Thanks for your reply! I now put the sdds commands into a separate bash script, executed before the slurm script which only now submit the Pelegant job. In this way the above-mentioned issue is solved.

Best,

Zhe

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