Hi Stefano,
Unfortunately this is an difficult problem, in many cases being
impossible without hugely slowing down the calculations, that not many
other number crunching programs will handle. Depending on what you
exactly would like to do (log out, shut down, suspend, etc.), there
are different solutions. Maybe the nohup command is what you need
(https://en.wikipedia.org/wiki/Nohup) - this allows you to log out but
the calculation will keep running.
This may not be exactly what you would like but I have written the
dauvergne_protocol auto-analysis, which is the protocol behind the GUI
model-free analysis, to handle crashes or accidental shut downs. You
can see the protocol at:
http://www.nmr-relax.com/api/3.2/auto_analyses.dauvergne_protocol-module.html
http://www.nmr-relax.com/api/3.2/auto_analyses.dauvergne_protocol-pysrc.html
It is very important that you understand this protocol that I
developed. Or at least know what it is, why it exists, and that you
are using it.
For each stage of the protocol, results files are saved. When the
protocol is started, for each global diffusion model the
determine_rnd() method will find all previous results files and work
out which round of optimisation it is up to:
http://www.nmr-relax.com/api/3.2/auto_analyses.dauvergne_protocol-pysrc.html#dAuvergne_protocol.determine_rnd
Then the execute() method will load the diffusion tensor data from the
last result file and continue with the next round of optimisation. To
use this, it is best that you save the relax state before clicking on
the 'Execute' button. Then when you would like to halt the
calculation, simply close relax. All calculations for the current
round of optimisation will be lost, but all previous rounds will be
saved and safe. To restart, make sure you are in the same directory
as before, load the state you saved, then click on 'Execute'. I hope
this helps.
Regards,
Edward
On 28 May 2014 09:04, Stefano Luciano Ciurli <stefano.ciurli@xxxxxxxx> wrote:
Hi Edward et al.m
i there a way to halt a calculation and restart it later on?
Stefano
On May 27, 2014, at 5:32 PM, Edward d'Auvergne wrote:
Hi Stefano,
That is the correct procedure to set up the analysis. After loading
the relaxation data
(http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_loading_data.html),
in your case via the 'Add Bruker' button, you then need to:
- Set up your relaxation interactions via the 'Dipolar relaxation' and
'CSA relaxation' buttons
(http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_relaxation_interactions.html).
- Set the spin isotope information
(http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_spin_isotopes.html).
- Complete the rest of the setup
(http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_rest_setup.html).
This should be sufficient. As mentioned in the execution section of
the manual
(http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_execution.html),
after clicking on the 'Execute' button, you should very carefully
check all warnings in the relax controller window (or log file which
you should store for future reference, see the --log command line
option). You will also see in the manual that your calculation can
take up to a week
(http://www.nmr-relax.com/manual/new_protocol_in_GUI.html). This is
highly dependent on the dynamics of the protein system, the quality of
the input PDB file, the speed of your computer, and if you have used
Gary Thompson's multi-processor framework with OpenMPI
(http://www.nmr-relax.com/manual/multi_processor_framework.html).
Calculation times can range from less than 1 hour to 2 weeks or more.
Regards,
Edward
On 27 May 2014 17:10, Stefano Luciano Ciurli <stefano.ciurli@xxxxxxxx>
wrote:
As for this, I think I solved the problem myself: I only needed to work
through the dipolar relaxation, interatomic distance and CSA buttons.
Stefano
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Re: error message