[slurm-users] "command not found"

[david vilanova]

Thanks manuel,
The shared folder between master and slave sounds like a good option. I’ll
go and try that one,
Thanks

El El vie, 15 dic 2017 a las 12:36, Manuel Rodríguez Pascual <
manuel.rodriguez.pascual at gmail.com> escribió:

> 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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