Hi Takanori,
Great, "#SBATCH --open-mode=append" works - thanks very much!
Leonid
Prof. Leonid Sazanov
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria
Phone: +43 2243 9000 3026
E-mail: [log in to unmask]
On 04/10/18 11:57, Takanori Nakane wrote:
> Hi,
>
> If you don't submit to a queue, run.out and run.err are not
> overwritten but appended.
> RELION use ">> run.out 2>> run.err" not "> run.out 2> run.err".
>
> When you submit to a queue, the STDOUT and STDERR are handled by the queue
> system. The behaviour depends on the queue system.
> For example, SGE appends the logs. In SLURM,
> "#SBATCH --open-mode=append" might be necessary.
>
> Best regards,
>
> Takanori Nakane
>
>> Hi,
>> Currently when one starts a job by continuation in Relion GUI, any
>> existing run.out file in the job directory is overwritten, and so there is
>> no log file for the earlier parts of the job. This is especially
>> inconvenient for 3D classifications, where it would be great to see entire
>> log in GUI.
>>
>> It is of course possible to make a copy of earlier run.out file manually
>> each time before new job starts, but it should be easy to add an option in
>> relion, such that if it is a "continue" job and run.out file already
>> exists in the job directory, new run.out file does not overwrite it, but
>> is rather appended to it?
>>
>> Thanks!
>>
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