Dear Benoist,

Alas, this is not so simple. When you click the Run button on the GUI,
directories are created and information is written to the
default_pipeline.star file with all expected input/output files, where
they came from etc.

Perhaps the following workaround is useful?

On the local computer where you do have X:

1. Make a standard job submission script, just like you were on your
cluster, and set it into the RELION GUI
(https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Download_%26_install#Set-up_queue_job_submission)

2. Set the queue submit command to the linux command 'cat'

3. For each job you want to submit:

 - 3a. fill in the GUI on your local computer

 - 3b. hit the Run button: the output directory gets created, and the
appropriate run_submit script will be in it (because of step 1)

 - 3c. rsync the whole projectdir to your cluster

 - 3d. (ON THE CLUSTER) submit the run_submit.script on the cluster, and
wait until it's finished

 - 3e. rsync the whole ProjectDir from the cluster back to your local
computer

For small jobs, you might just execute on the local computer of course,
just set Submit to Queue to No.


This is admittedly a bit complicated. The next version (RELION-3.0) will
have command-line capabilities to submit jobs into the pipeline. This
will make cluster submission without X a lot easier (and will allow much
easier automation too!)

HTH,

Sjors



On 02/15/2018 03:07 PM, Benoist LAURENT wrote:
> Dear Relion community,
>
> I need use relion on an HPC cluster.
>
> As most clusters I’ve been using in the past, there is no X-server on the cluster, so relion’s GUI is not available.
> So here is what I’ve done:
>
> 1. Move data on workdir@cluster,
> 2. Run the calculations using the command-line tools,
> 3. Get the output file back from the cluster onto my desktop machine,
> 4. Put those files in the project tree at appropriate places.
>
> Yet, the files do not appear when I launch the GUI.
>
> How do you guys are able to use the GUI on HPC clusters ?
>
> Thank you in advance for sharing.
> Cheers,
> Ben
>
> --
> Benoist Laurent, PhD
> Research Engineer CNRS
> Institut de Biologie Physico-Chimique - FRC 550
> 13, rue Pierre et Marie Curie - F-75005 Paris
> Tel. +33 [0]1 58 41 52 08

-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres