Re: [scipion-users] customizing hosts.conf to put .out and .err in the logs directory of each run

[Pablo C. <pc...@cn...>]

Thanks Gregory, I had a look too and that is the closest solution you 
can get now.

Just to be more precise.....

JOB_SCRIPT will have/?:

~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.job.out
~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.job.err

Haven't run it, just guessing from the code.


On 15/01/18 12:06, Gregory Sharov wrote:
> Hi Daniel,
>
> I believe you can achieve this by using "#SBATCH -o 
> %_(JOB_SCRIPT)s.out -e %_(JOB_SCRIPT)s.err"
>
>
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267542 <tel:+44%201223%20267542>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
> On Fri, Jan 12, 2018 at 8:39 AM, Daniel Larsson 
> <dan...@ic... <mailto:dan...@ic...>> wrote:
>
>     Hi,
>
>     I'm trying to customize my hosts.conf file for a SLURM batch
>     system. Currently, the .out and the .err files end up in the root
>     of my project directory e.g.
>     "~/ScipionUserData/projects/my_project/job7113248.out". I have the
>     SLURM variables set by: "#SBATCH -o job%%j.out -e job%%j.err".
>
>     Instead I'd prefer if the .out and .err could go into the 'logs'
>     directory for the specific run together with the rest of the log
>     files. E.g
>     "~/ScipionUserData/projects/my_project/Runs/000367_ProtRelionRefine3D/logs/job7113248.out".
>
>     Is there a way to achieve that?
>
>     Regards,
>     Daniel
>
>
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