Hi Olena,
I will reply on the relax-devel mailing list, as it is a bit
ridiculous to have a long conversation on the bug tracker. I have
received your private messages with the Input_state.bz2,
analysis.log.bz2, and analysis.log.7z files. These are not attached,
so they will remain private. Please reply to this message rather than
continuing the conversation in the bug tracker.
I have now run the analysis up to round_2 of the spherical diffusion
tensor. I stopped here, as that is where the bug reports do not
match. The problem I saw previously in your log file 'analysis_first
part.txt' (at https://gna.org/support/download.php?file_id=22627) is
that the spherical diffusion tensor initial optimisation had been
executed 42085 times (https://gna.org/bugs/index.php?22730#comment9).
But in your new analysis.log file, this is not the case. It is only
executed once:
[edward@localhost bug_22730]$ grep -c "^Function value: 200507.263"
*.txt *.log
analysis_first part.txt:42085
analysis_last10000lines.log:70
analysis.log:1
So here we now have two completely unrelated problems! The first
problem reported (https://gna.org/support/download.php?file_id=22627)
is not replicated in your current log file or in my analysis attempt.
Do you know why? This massive repetition looks like what happens when
the 'mpirun' command line program is incorrectly used or incorrectly
set up. Could that be the cause? Can you replicate this
super-massive repetition problem? Or could it be that your 7z
compression software somehow corrupted the log file? Could this be a
simple mistake? This is where I am quite confused, as it should be
impossible with relax's source code for this infinite repetition to
occur. The only case is if there are strange things happening with
your file system so that relax cannot detect the file. That is why I
asked you if your home directory was NFS, SMB, or some other network
drive.
There is one other case I can think of here, and that is if your file
system no longer had any room. Then relax will not be able to save
the results file, hence it will not be able to detect it and then it
will repeat the last optimisation round forever. Did you have such a
problem? I have not written the dauvergne_protocol auto-analysis to
handle this situation, as I assumed that a Python Error would stop the
analysis. That may not be the case when running with OpenMPI.
I would like to solve this infinite repetition first, as that has
taken up a lot of my time already. This is an impasse which prevents
the rest of the analysis from ever occurring. I.e. you cannot get to
the prolate model. Then I'll look and see if there is another issue
affecting your data.
Cheers,
Edward
On 15 October 2014 10:34, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Follow-up Comment #12, bug #22730 (project relax):
Hi,
I have no idea why the information containing the data and its specification
is missing. I follow the protocol loading the DC files (after I load the H
and
N spins from the pdb file), specifying all the parameters (temperature
control
etc.). Then prior the execution, I save the input as input_state.bz2 as
recommended. Perhaps, last time I opened the input_state.bz2 file, which
perhaps did not load the data? But then why did it work?
Anyway, this time, I upgraded Relax version to 3.3.1 and load the files once
again from the scratch. I would appreciate if you have a look at the log
file
which, being compressed to 1.8 Mb, I uploaded here
https://mega.co.nz/#fm/HI4ShI7T
The Relax calculations are currently at the 'prolate' stage. But the last
file
was generated at 4 pm yesterday.
Should it be like that? If you think there could be a problem with the input
data, I can send it to you as well via private email.
Would appreciate if you help me to find and solve the problem.
Regards,
Olena
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Re: [bug #22730] Model-free auto-analysis - relax stops and quits at the polate step.