Hi Troels,
It is actually not so difficult to reconstruct this text file from the
OpenDX data files, if you know the parameter bounds used in the dx.map
user function call. However if you would like it automatically
created, then this must be as an option. The aim of the dx.map user
function is
Hi Edward.
I have created the map with inc=20 for each dimension.
The map takes up 280 kB.
The new file created takes up 1.1 MB.
I think it took between 1-2 Hours to make the map.
The new parameter + chi2 value files, gives a perfect insight into the chi2
values of the space.
It is also a
Hi Troels,
There are some analysis types in relax which are many, many orders of
magnitude faster than the relaxation dispersion analysis (and one that
is hundreds of orders slower). To generate this sized file for a
model-free analysis, for example, would be measured in seconds or
less. The
Follow-up Comment #6, bug #22730 (project relax):
Hi Edward,
I am back with some results from the calculations I began two weeks ago. Just
to remind, I am running the Model-free analysis on the 73 AA protein domain at
three magnetic fields. Relax is running using 7 slaves. However, the
Follow-up Comment #7, bug #22730 (project relax):
In this log file, I see two problems. The first is the incredibly high chi2
value. This is a clear indication that there is a problem with the input
data. The chi2 value should be in the thousands range, not 200507.26.
The second is that the
Update of bug #22772 (project relax):
Status: Need Info = Confirmed
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URL:
http://gna.org/bugs/?22798
Summary: Failure of relax to start due to an OrderedDict
ImportError on Python 2.6 and earlier.
Project: relax
Submitted by: bugman
Submitted on: Mon 13 Oct 2014 10:10:53 AM UTC
Category:
Update of bug #22798 (project relax):
Specific analysis category:None = All analyses
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Follow-up Comment #1, bug #22798 (project relax):
The standard way in Python to handle ordering for a dictionary is to create a
separate variable which is a Python list which contains the dictionary keys in
the desired order. This is probably what is inside the
collections.OrderedDict object
Follow-up Comment #2, bug #22798 (project relax):
According to the code at http://code.activestate.com/recipes/576693/, which
implements OrderedDict, the self.__root variable is the list which holds the
keys in the correct order.
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Follow-up Comment #3, bug #22798 (project relax):
The simplest (and laziest) solution would be to dump the code at
http://code.activestate.com/recipes/576693/ into the relax extern package and
use that instead. The MIT licence is compatible for this.
Follow-up Comment #8, bug #22730 (project relax):
The compressed bz2 log file is too big currently (around 3 Mb)so I took the
first part that would be compressed to around 1 Mb. I just decompressed the
bz2 file, cut the first part to zip within 1Mb.
Olena
(file #22627)
Follow-up Comment #9, bug #22730 (project relax):
With this new file, it is clear that something is terribly wrong. I can see
that the spherical diffusion tensor initial optimisation has been executed
42085 times in this first part of the log:
$ grep relax analysis_first\ part.txt | grep
Hi Troels,
For this change, you should also decrease the value of
uf.wizard_height_desc in the user_functions.dx module so that there is
more room for the arguments in the GUI. A value of 260 might work
well.
Cheers,
Edward
On 13 October 2014 10:47, tlin...@nmr-relax.com wrote:
Author:
Update of bug #22772 (project relax):
Assigned to:None = bugman
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Update of bug #22772 (project relax):
Summary: test suite failures = Test suite failures -
modelfree4 binary issue and the User_functions GUI tests with wxPython 2.9.
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Follow-up Comment #3:
For reference - the
Follow-up Comment #10, bug #22730 (project relax):
Thanks! I will upgrade the Relax version. Perhaps, it will solve the entire
problem.
Answering your questions, I use local harddisk. I ran Relax through a GUI
interface. I start with typing (in the defined directory):
mpirun -np 8
Follow-up Comment #11, bug #22730 (project relax):
The loading of the Dynamics Centre files is via the bruker.read user function,
but this is also absent from the log file. Would you know why? I also see no
user function calls for setting up the spin sequence information, or for
specifying the
Follow-up Comment #5, bug #22772 (project relax):
The problem with the Palmer.test_palmer_omp system test is because the 64-bit
Linux binary of Modelfree 4.20 was not properly detected.
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Update of bug #22772 (project relax):
Status: Confirmed = Fixed
Open/Closed:Open = Closed
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URL:
http://gna.org/bugs/?22801
Summary: Failure of the relax test suite on Python 2.5.
Project: relax
Submitted by: bugman
Submitted on: Mon 13 Oct 2014 02:28:30 PM UTC
Category: Test suite
Specific analysis category:
Hi Troels,
A nice code simplification here would be to not have the +\n code
until you are looping over these text elements and sending them to the
file. I.e. delete them then change the writing line to
plot_file.write(line+'\n'), so that '\n' only appears once in the
entire method.
Regards,
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