Sorry Edward, still not working...
The checked out revision of the repository relax version is number 12819
The errors appear to be exactly the same. What kind of values are you
getting for S2 and tauS? Here, I am getting 0 for all tauS and 0.06667 for
all S2.
$relax --info plots the following:
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2011 the relax development team
This is free software which you are welcome to modify and redistribute under
the conditions of the
GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
the prompt.
Hardware information:
Machine: i686
Processor:
System information:
System: Linux
Release: 2.6.31-23-generic
Version: #74-Ubuntu SMP Mon Feb 28 21:32:57 UTC 2011
GNU/Linux version: Ubuntu 9.10 karmic
Distribution: Ubuntu 9.10 karmic
Full platform string:
Linux-2.6.31-23-generic-i686-with-Ubuntu-9.10-karmic
Software information:
Architecture: 32bit ELF
Python version: 2.6.4
Python branch: tags/r264
Python build: r264:75706, Dec 7 2009 18:45:15
Python compiler: GCC 4.4.1
Python implementation: CPython
Python revision: 75706
Numpy version: 1.3.0
Libc version: glibc 2.4
Python packages (most are optional):
Package Installed Version Path
minfx True Unknown
/usr/local/relax-1.3/minfx
bmrblib False
numpy True 1.3.0
/usr/lib/python2.6/dist-packages/numpy
ScientificPython True 2.8
/usr/lib/python2.6/dist-packages/Scientific
wxPython False
mpi4py False
epydoc False
optparse True 1.5.3
/usr/lib/python2.6/optparse.pyc
readline True
/usr/lib/python2.6/lib-dynload/readline.so
profile True
/usr/lib/python2.6/profile.pyc
bz2 True
/usr/lib/python2.6/lib-dynload/bz2.so
gzip True
/usr/lib/python2.6/gzip.pyc
os.devnull True
/usr/lib/python2.6/os.pyc
Compiled relax C modules:
Relaxation curve fitting: True
Sorry for all the trouble.
Cheers
Tiago P
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: terça-feira, 12 de Abril de 2011 13:02
To: Tiago Pais
Cc: relax-devel@xxxxxxx
Subject: Re: [bug #18019] Gridsearch appears not to be working when
upper/lower bounds are set
Hi,
Where is the new one installed? Maybe relax is not using it. Are the
errors 100% the same? It's working for me perfectly with the
truncated data. I removed residue 37, and the grid search gives:
-----
relax> grid_search(lower=[0.111, 0, 0.0], upper=[0.111, 1.0,
2.0000000000000001e-10], inc=[1, 16, 16], constraints=True,
verbosity=1)
Over-fit spin deselection.
RelaxWarning: The spin '#snPHSinDiffFrame2CHnoHs_mol1:37&:L@506&@CD1'
has been deselected because of missing relaxation data.
Only the model-free parameters for single spins will be used.
Fitting to spin '#snPHSinDiffFrame2CHnoHs_mol1:14&:L@119&@CD1'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Grid search
~~~~~~~~~~~
Searching through 256 grid nodes.
k: 0 xk: [ 0.111, 0, 0] fk: 16513.3641708
k: 1 xk: [ 0.111, 0.066667, 0] fk: 10390.3333598
k: 2 xk: [ 0.111, 0, 13.333] fk: 7092.56902759
k: 3 xk: [ 0.111, 0.066667, 13.333] fk: 4780.221211
k: 5 xk: [ 0.111, 0.066667, 26.667] fk: 2820.12641286
k: 7 xk: [ 0.111, 0.066667, 40] fk: 2039.04303462
k: 9 xk: [ 0.111, 0.066667, 53.333] fk: 1700.9699681
k: 11 xk: [ 0.111, 0.066667, 66.667] fk: 1546.15216207
k: 13 xk: [ 0.111, 0.066667, 80] fk: 1476.32033148
k: 15 xk: [ 0.111, 0.066667, 93.333] fk: 1454.68522627
-----
Maybe you need to newest version of relax as well. Try:
$ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3
$ cd relax-1.3
$ svn co http://svn.gna.org/svn/minfx/trunk/minfx
$ cd ..
$ scons
and then see if things run?
Cheers,
Edward
On 12 April 2011 13:49, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
Hi,
I have deleted the previous minfx and installed the new one but It's still
not working. I also tried to increase the interval of S2f and put some
increments but the same error occurs.
Did you manage to do it with the truncated data?
TiagoP
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: terça-feira, 12 de Abril de 2011 10:27
To: Tiago Pais
Cc: relax-devel@xxxxxxx
Subject: Re: [bug #18019] Gridsearch appears not to be working when
upper/lower bounds are set
Hi,
I found the problem to be in minfx. Strangely, this used to work
before as I had performed grid searches with an increment of 1 in one
of the dimensions. The problem is that when there is an increment of
one, you need to pick a value between the lower and upper bound
values. Minfx is now taking the average value.
To use this, you can delete the minfx directory in the 1.3.8
installation, and get the new version of minfx by typing:
$ svn co http://svn.gna.org/svn/minfx/trunk/minfx
If you don't have access to svn, you might have to wait until I
release a new version of relax. However due to holidays, I will
unfortunately not be able to do this before mid May.
Regards,
Edward
On 12 April 2011 10:38, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
Hi Edward,
Yes I am sorry about the private label. I set it initially to private
because I was going to include the structure of the protein attached, but
then I realized that I didn't need to send the whole thing. Eventually I
forgot to set the label back to public. So, yes, you can use the info as
you
wish to try and solve the issue - including the test suite.
Hope to hear from you soon.
Cheers
TP
-----Original Message-----
From: Edward d'Auvergne [mailto:edward.dauvergne@xxxxxxxxx]
Sent: terça-feira, 12 de Abril de 2011 7:51
To: anonymous
Cc: Tiago Pais; relax-devel@xxxxxxx
Subject: Re: [bug #18019] Gridsearch appears not to be working when
upper/lower bounds are set
Hi,
Is there any reason this bug report has been made private? The data
is so truncated, there's nothing much anyone can do with it. The
privacy tag is usually reserved for security issues whereby it needs
to be kept private until a fix is found and released. Then the bug
can be made public. I'm looking into this now, but I'm not exactly
sure what is happening. Is it ok if I include this data, or part of
it, into the relax test suite? This will significantly help in the
debugging and will make sure this bug never returns!
Cheers,
Edward
On 11 April 2011 13:42, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx>
wrote:
URL:
<http://gna.org/bugs/?18019>
Summary: Gridsearch appears not to be working when
upper/lower bounds are set
Project: relax
Submitted by: None
Submitted on: Mon 11 Apr 2011 11:42:49 AM UTC
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Private
Assigned to: None
Originator Name: Tiago Pais
Originator Email: tpais@xxxxxxxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.8
Operating System: GNU/Linux
_______________________________________________________
Details:
My system is Ubuntu-9.04:
When I perform a gridsearch, exclusively for m5, with the lower and
upper
bounds set to: lower=[0.111, 0, -0.0], upper=[0.111, 1.00, 200] I keep
seeing
the following message during the calculations:
"Min f: 3474.82
k: 3860 xk: [ 0.111, 0.066667, -0] fk: nan
Increment: array([ 5, 16, 16])
Params: array([ 0.111, 1. , Inf])
Min params: array([ 0.111 , 0.06666667, -0. ])
f: nan
Min f: 3474.82
k: 3861 xk: [ 0.111, 0.066667, -0] fk: nan
Increment: array([ 6, 16, 16])
Params: array([ 0.111, 1. , Inf])
Min params: array([ 0.111 , 0.06666667, -0. ])
f: nan
"
And at the end the tauS is zero for all spins and the S2s is always
close
to
1.
Attached follows the script that I am using and a truncated sample of my
data
set (I hope it is not too truncated!) as well as the results that I am
getting.
If you need more info let me know.
Thanks
Regards
Tiago P
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Mon 11 Apr 2011 11:42:49 AM UTC Name: ErrorReportRelax.tar.gz
Size:
8kB By: None
<http://gna.org/bugs/download.php?file_id=12833>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?18019>
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RE: [bug #18019] Gridsearch appears not to be working when upper/lower bounds are set