[slurm-users] "command not found"

[Manuel Rodríguez Pascual]

Hi David,

The command to be executed must be present on the node where the script is
run.  When you submit a job in Slurm only the script is copied to the slave
node, so the data and binaries must be there prior to the script execution.

The are many alternatives to deal with this situation depending on the
system and software requirements. A common practice (as far as I know, I am
not an experienced sysadmin) is to install the software in a shared storage
and mount it both on the master node and in the slaves. This is analog to
what you are probably doing with the user $HOME.

Of course this cannot always be done, and sometimes the only solution is
install a particular library or application in every node. In this case
there are many solutions to automatice the process.

Cheers,

Manuel

2017-12-15 12:21 GMT+01:00 david <vilanew at gmail.com>:

> Hi,
>
> when running a sbatch script i get "command not found".
>
>
> The command is blast (quite used bioinformatics tool).
>
>
> The problem comes from the fact that the blast binary is installed in the
> master node  but not on the other nodes. When the job runs on another node
> the binary is not found.
>
>
> What would be way to deal with this situation ? what is common practice ?
>
>
> thanks,
>
> david
>
>
>
>
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