Re: [bug #21959] cpmg_analysis -- May 02, 2014 - 11:09

Hi Mengjun,

If you have already downloaded the relax trunk source code, you can
update this to the latest version with the command:

$ svn up

You need to be in the base relax directory.  Then to run the
sample_scripts/relax_disp/cpmg_analysis.py script, you need to be in
the sample_scripts/relax_disp/ directory and type:

$ ..\..\relax cpmg_analysis.py

The reason for the change is the bug report and its fix at
https://gna.org/bugs/?22001.  If you haven't already downloaded the
latest code, then when you do you will need to run relax in this way.

Regards,

Edward


On 1 May 2014 21:11,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> Hi Edward,
>
> Thank you very much. I will try it as you suggested. I understand that the
> new version of Relax will solve such problem ? Thank you.
>
>
> Best regards,
>
> Mengjun
>
>
>
>
>
> Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
>
> > Hi Mengjun,
> >
> > To test this, if you have subversion installed on your computer you
> > can download the most recent relax code and test it yourself.  The
> > steps required are explained at
> > http://www.nmr-relax.com/download.html#Source_code_repository and at
> > http://www.nmr-relax.com/windows_devel.html#svn.  Don't worry about
> > the C module compilation as that is much more difficult under MS
> > Windows (http://www.nmr-relax.com/windows_devel.html).  It is quite
> > easy to obtain the latest code on MS Windows.
> >
> > Then once it is done, go into the relax-trunk directory and type:
> >
> > > .\relax sample_scripts/relax_disp/cpmg_analysis.py
> >
> >
> > Do not make any changes to the file.  This should then simply run.
> >
> > Regards,
> >
> > Edward
> >
> >
> > On 30 April 2014 15:39,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > Hi Edward,
> > >
> > > Thank you very much. Will the problem of bug be solved ? so I will be
> > > able
> > > to run cpmg_analysis.py on my computer?
> > >
> > >
> > > Best regards,
> > >
> > > Mengjun
> > >
> > >
> > >
> > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > >
> > > > Hi,
> > > >
> > > > You're right!  After looking at that for a while, I can see that that
> > > > feature is not working any more!  It used to be that the --log and
> > > > --tee options worked with all the other relax options, but somehow
> > > > they got mixed up (you can see the incorrect order in the run() method
> > > > of the relax.py file).  Thank you for reporting it, I've created a bug
> > > > report for this regression at https://gna.org/bugs/?21990, and fixed
> > > > the behaviour.
> > > >
> > > > Cheers,
> > > >
> > > > Edward
> > > >
> > > >
> > > >
> > > > On 24 April 2014 20:18,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > > > Hi Edward,
> > > > >
> > > > > I have ran in cmd:
> > > > >
> > > > >
> > > > > C:\relax-3.1.7> relax --tee log_new
> > > > > ...
> > > > > relax> print "Hello"
> > > > > relax> quit
> > > > > C:\relax-3.1.7>
> > > > >
> > > > > I can find the log_new file, please following:
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >                                   relax 3.1.7
> > > > >
> > > > >                     Molecular dynamics by NMR data analysis
> > > > >
> > > > >                    Copyright (C) 2001-2006 Edward d'Auvergne
> > > > >               Copyright (C) 2006-2014 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.
> > > > >
> > > > > Processor fabric:  Uni-processor.
> > > > >
> > > > > relax> Hello
> > > > > relax> Exiting the program.
> > > > >
> > > > >
> > > > > Then, when I run C:\relax-3.1.7> relax --info --log log_info, I can not
> > > > > find
> > > > > the file 'log_info' in C:\relax-3.1.7, I understand that this command
> > > > > line
> > > > > does not produce the log_info file, but there are some output in the
> > > > > cmd
> > > > > window:
> > > > >
> > > > >
> > > > >
> > > > > C:\relax-3.1.7>relax --info --log log_info
> > > > >
> > > > >
> > > > >
> > > > >                                   relax 3.1.7
> > > > >
> > > > >                     Molecular dynamics by NMR data analysis
> > > > >
> > > > >                    Copyright (C) 2001-2006 Edward d'Auvergne
> > > > >               Copyright (C) 2006-2014 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.
> > > > >
> > > > > Processor fabric:  Uni-processor.
> > > > >
> > > > >
> > > > > Hardware information:
> > > > >     Machine:                 x86
> > > > >     Processor:               x86 Family 6 Model 15 Stepping 13,
> > > > > GenuineIntel
> > > > >     Processor name:          x86 Family 6 Model 15 Stepping 13,
> > > > > GenuineIntel
> > > > >     Endianness:              little
> > > > >     Total RAM size:          3037.30078125 Mb
> > > > >     Total swap size:         2047.875 Mb
> > > > >
> > > > > Operating system information:
> > > > >     System:                  Windows
> > > > >     Release:                 7
> > > > >     Version:                 6.1.7601
> > > > >     Win32 version:           7 6.1.7601 SP1 Multiprocessor Free
> > > > >     Distribution:
> > > > >     Full platform string:    Windows-7-6.1.7601-SP1
> > > > >     Windows architecture:    x86
> > > > >
> > > > > Python information:
> > > > >     Architecture:            32bit WindowsPE
> > > > >     Python version:          2.7.6
> > > > >     Python branch:
> > > > >     Python build:            default, Nov 10 2013 19:24:18
> > > > >     Python compiler:         MSC v.1500 32 bit (Intel)
> > > > >     Libc version:
> > > > >     Python implementation:   CPython
> > > > >     Python revision:
> > > > >     Python executable:       C:\Python27\python.exe
> > > > >     Python flags:            sys.flags(debug=0, py3k_warning=0,
> > > > > division_warning
> > > > > =0, division_new=0, inspect=0, interactive=0, optimize=0,
> > > > > dont_write_bytecode=0,
> > > > >  no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0,
> > > > > verbose=0,
> > > > > unicode
> > > > > =0, bytes_warning=0, hash_randomization=0)
> > > > >     Python float info:
> > > > > sys.float_info(max=1.7976931348623157e+308,
> > > > > max_exp
> > > > > =1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
> > > > > min_10_exp=-3
> > > > > 07, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2,
> > > > > rounds=1)
> > > > >     Python module path:      ['', 'C:\\relax-3.1.7',
> > > > > 'C:\\Windows\\system32\\pyt
> > > > > hon27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib',
> > > > > 'C:\\Python27\\lib\\plat-
> > > > > win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
> > > > > 'C:\\Python27\\lib\\site-pack
> > > > > ages', 'C:\\Python27\\lib\\site-packages\\wx-3.0-msw']
> > > > >
> > > > > Python packages and modules (most are optional):
> > > > >
> > > > > Name               Installed    Version                  Path
> > > > >
> > > > > minfx              True         1.0.5
> > > > > C:\relax-3.1.7\minfx
> > > > >
> > > > > bmrblib            True         1.0.3
> > > > > C:\relax-3.1.7\bmrblib
> > > > >
> > > > > numpy              True         1.8.0
> > > > > C:\Python27\lib\site-pa
> > > > > ckages\numpy
> > > > > scipy              True         0.13.3
> > > > > C:\Python27\lib\site-pa
> > > > > ckages\scipy
> > > > > wxPython           True         3.0.0.0 msw (classic)
> > > > > C:\Python27\lib\site-pa
> > > > > ckages\wx-3.0-msw\wx
> > > > > mpi4py             False
> > > > >
> > > > > epydoc             False
> > > > >
> > > > > optparse           True         1.5.3
> > > > > C:\Python27\lib\optpars
> > > > > e.pyc
> > > > > readline           True
> > > > > C:\Python27\lib\site-pa
> > > > > ckages\readline.pyc
> > > > > profile            True
> > > > > C:\Python27\lib\profile
> > > > > .pyc
> > > > > bz2                True
> > > > > C:\Python27\DLLs\bz2.py
> > > > > d
> > > > > gzip               True
> > > > > C:\Python27\lib\gzip.py
> > > > > c
> > > > > io                 True
> > > > > C:\Python27\lib\io.pyc
> > > > >
> > > > > xml                True         0.8.4 (internal)
> > > > > C:\Python27\lib\xml\__i
> > > > > nit__.pyc
> > > > > xml.dom.minidom    True
> > > > > C:\Python27\lib\xml\dom
> > > > > \minidom.pyc
> > > > >
> > > > > relax information:
> > > > >     Version:                 3.1.7
> > > > >     Processor fabric:        Uni-processor.
> > > > >
> > > > > relax C modules:
> > > > >
> > > > > Module                        Compiled    File type    Path
> > > > >
> > > > > target_functions.relax_fit    True
> > > > > target_functions\relax_fi
> > > > > t.pyd
> > > > >
> > > > > Thank you.
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Mengjun
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Could you then run, in cmd:
> > > > > >
> > > > > > C:\relax-3.1.7> relax --tee log_new
> > > > > > ...
> > > > > > relax> print "Hello"
> > > > > > relax> quit
> > > > > > C:\relax-3.1.7>
> > > > > >
> > > > > > And then see if you have the 'log_new' file in that directory.  Also
> > > > > > run:
> > > > > >
> > > > > > C:\relax-3.1.7> relax --info --log log_info
> > > > > >
> > > > > > And search for the file 'log_info'.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 24 April 2014 18:57,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > > > > > Hi Edward,
> > > > > > >
> > > > > > > Yes, I see the file "C:\relax-3.1.7\test", please see the following
> > > > > > > information of the test file.
> > > > > > >
> > > > > > > Volume in drive C has no label.
> > > > > > >  Volume Serial Number is B035-71CF
> > > > > > >
> > > > > > >  Directory of C:\relax-3.1.7
> > > > > > >
> > > > > > > 04/24/2014  06:21 PM    <DIR>          .
> > > > > > > 04/24/2014  06:21 PM    <DIR>          ..
> > > > > > > 04/02/2014  01:15 PM           240,634 1L163_H.pdb
> > > > > > > 04/02/2014  01:06 PM               196 1L63.fasta.txt
> > > > > > > 04/02/2014  01:06 PM           158,517 1L63.pdb
> > > > > > > 04/24/2014  10:34 AM    <DIR>          auto_analyses
> > > > > > > 04/24/2014  10:34 AM    <DIR>          bmrblib
> > > > > > > 04/02/2014  10:16 PM             2,747 catia
> > > > > > > 03/17/2014  03:08 PM               593 catia.py
> > > > > > > 03/17/2014  03:29 PM            70,478 colour.py
> > > > > > > 04/01/2014  05:27 PM            53,638 colour.pyc
> > > > > > > 03/17/2014  03:29 PM            12,076 compat.py
> > > > > > > 04/01/2014  05:27 PM            10,048 compat.pyc
> > > > > > > 04/02/2014  10:29 PM            10,792 cpmg.log
> > > > > > > 04/02/2014  10:24 PM             2,838 cpmgfit.log
> > > > > > > 03/17/2014  03:09 PM               787 cpmgfit.py
> > > > > > > 04/24/2014  12:46 PM             9,445 cpmg_analysis.py
> > > > > > > 04/02/2014  10:16 PM               351 data_set_500.inp
> > > > > > > 04/02/2014  10:16 PM               351 data_set_800.inp
> > > > > > > 04/24/2014  10:34 AM    <DIR>          data_store
> > > > > > > 03/17/2014  03:22 PM            13,076 dauvergne_protocol.py
> > > > > > > 04/02/2014  02:47 PM            11,860 dauvergne_protocol_localtm.py
> > > > > > > 03/17/2014  03:29 PM             6,741 dep_check.py
> > > > > > > 04/01/2014  05:27 PM             4,204 dep_check.pyc
> > > > > > > 04/24/2014  10:34 AM    <DIR>          devel_scripts
> > > > > > > 04/24/2014  10:34 AM    <DIR>          docs
> > > > > > > 04/24/2014  10:35 AM    <DIR>          extern
> > > > > > > 04/02/2014  10:16 PM               420 Fit.catia
> > > > > > > 04/24/2014  10:35 AM    <DIR>          graphics
> > > > > > > 04/24/2014  10:35 AM    <DIR>          gui
> > > > > > > 03/17/2014  03:29 PM            60,273 info.py
> > > > > > > 04/01/2014  05:27 PM            49,941 info.pyc
> > > > > > > 04/24/2014  10:35 AM    <DIR>          input_r2eff
> > > > > > > 04/24/2014  10:35 AM    <DIR>          lib
> > > > > > > 04/24/2014  10:35 AM    <DIR>          lm63
> > > > > > > 04/24/2014  01:12 PM    <DIR>          local_tm
> > > > > > > 04/24/2014  03:32 PM                 0 logabs
> > > > > > > 04/23/2014  08:48 PM            12,450 log_debugb
> > > > > > > 04/24/2014  10:53 AM            12,390 log_debugd
> > > > > > > 04/24/2014  12:48 PM            11,945 log_debuge
> > > > > > > 04/24/2014  12:51 PM            11,856 log_debugf
> > > > > > > 04/03/2014  06:30 PM           115,686 log_full_test_suite.txt
> > > > > > > 04/24/2014  01:10 PM            11,747 mf_local_tm.py
> > > > > > > 04/24/2014  10:35 AM    <DIR>          minfx
> > > > > > > 04/24/2014  10:35 AM    <DIR>          multi
> > > > > > > 04/03/2014  06:29 PM                 0 New Text Document.txt
> > > > > > > 04/02/2014  02:37 PM            25,314 NOE_500.txt
> > > > > > > 04/02/2014  02:38 PM            25,314 NOE_700.txt
> > > > > > > 04/02/2014  10:16 PM    <DIR>          output
> > > > > > > 04/02/2014  10:16 PM                25 ParamGlobal.inp
> > > > > > > 04/02/2014  10:16 PM                58 ParamSet1.inp
> > > > > > > 04/24/2014  10:35 AM    <DIR>          pipe_control
> > > > > > > 04/24/2014  10:35 AM    <DIR>          prompt
> > > > > > > 04/02/2014  10:31 PM             9,166 R1rho_analyis.py
> > > > > > > 03/17/2014  03:22 PM             7,632 R1rho_analysis.py
> > > > > > > 03/17/2014  03:29 PM               119 README
> > > > > > > 03/17/2014  03:29 PM               112 relax
> > > > > > > 03/17/2014  03:29 PM               809 relax.bat
> > > > > > > 03/17/2014  03:29 PM            20,708 relax.py
> > > > > > > 04/01/2014  05:33 PM            12,333 relax.pyc
> > > > > > > 03/17/2014  03:29 PM               211 relax_gui_mode.py
> > > > > > > 04/02/2014  10:32 PM             5,416 return_offset_data.log
> > > > > > > 03/17/2014  03:22 PM             4,406 return_offset_data.py
> > > > > > > 04/24/2014  10:35 AM    <DIR>          sample_scripts
> > > > > > > 04/24/2014  10:35 AM    <DIR>          scons
> > > > > > > 03/17/2014  03:29 PM            25,339 sconstruct
> > > > > > > 03/17/2014  03:29 PM             8,349 setup.py
> > > > > > > 04/24/2014  10:35 AM    <DIR>          specific_analyses
> > > > > > > 03/17/2014  03:29 PM            18,788 status.py
> > > > > > > 04/01/2014  05:27 PM            13,867 status.pyc
> > > > > > > 04/02/2014  01:33 PM           140,114 T1_500.txt
> > > > > > > 04/02/2014  01:32 PM           146,472 T1_700.txt
> > > > > > > 04/09/2014  06:57 PM           123,131 T2_500.txt
> > > > > > > 04/02/2014  02:37 PM           122,337 T2_700.txt
> > > > > > > 04/24/2014  10:35 AM    <DIR>          target_functions
> > > > > > > 04/24/2014  06:24 PM                 0 test
> > > > > > > 04/24/2014  10:37 AM    <DIR>          test_suite
> > > > > > > 04/24/2014  10:37 AM    <DIR>          user_functions
> > > > > > > 03/17/2014  03:29 PM             4,437 version.py
> > > > > > > 04/01/2014  05:27 PM             2,567 version.pyc
> > > > > > >               55 File(s)      1,613,104 bytes
> > > > > > >               25 Dir(s)  130,722,390,016 bytes free
> > > > > > >
> > > > > > >
> > > > > > > Thank you.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > Mengjun
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > Do you then see the file "C:\relax-3.1.7\test"?  This must now
> > > > > > > > exist.
> > > > > > > >
> > > > > > > > Regards,
> > > > > > > >
> > > > > > > > Edward
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On 24 April 2014 18:26,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > > > > > > > Hi Edward,
> > > > > > > > >
> > > > > > > > > I tried the  C:\relax-3.1.7> dir > test, I did not see the text
> > > > > > > > > "Access
> > > > > > > > > is
> > > > > > > > > denied",
> > > > > > > > >
> > > > > > > > > please see the following output:
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Microsoft Windows [Version 6.1.7601]
> > > > > > > > > Copyright (c) 2009 Microsoft Corporation.  All rights reserved.
> > > > > > > > >
> > > > > > > > > C:\Users\xmj>cd..
> > > > > > > > >
> > > > > > > > > C:\Users>\cd..
> > > > > > > > > '\cd..' is not recognized as an internal or external command,
> > > > > > > > > operable program or batch file.
> > > > > > > > >
> > > > > > > > > C:\Users>cd..
> > > > > > > > >
> > > > > > > > > C:\>cd relax-3.1.7
> > > > > > > > >
> > > > > > > > > C:\relax-3.1.7>dir > test
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > C:\relax-3.1.7>
> > > > > > > > >
> > > > > > > > > Thank you.
> > > > > > > > >
> > > > > > > > > Best regards,
> > > > > > > > >
> > > > > > > > > Mengjun
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > >
> > > > > > > > > > Hi,
> > > > > > > > > >
> > > > > > > > > > Try the following then, in the Command Prompt window:
> > > > > > > > > >
> > > > > > > > > > C:\relax-3.1.7> dir > test
> > > > > > > > > >
> > > > > > > > > > I.e. run 'dir > test'.  If you see the text "Access is denied",
> > > > > > > > > > then
> > > > > > > > > > that means that you do not have permission to create files in that
> > > > > > > > > > directory.  Is this what you see?
> > > > > > > > > >
> > > > > > > > > > Regards,
> > > > > > > > > >
> > > > > > > > > > Edward
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On 24 April 2014 18:13,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > > > > > > > > > Hi Edward,
> > > > > > > > > > >
> > > > > > > > > > > I tried the 'relax -i --tee log' command, C:\relax-3.1.7\relax -i
> > > > > > > > > > > --tee
> > > > > > > > > > > log6, I entered the command line 'relax -i --tee log' under cmd,
> > > > > > > > > > > following
> > > > > > > > > > > output show up in the cmd window (I copied the output in cmd
> > > > > > > > > > > window
> > > > > > > > > > > using
> > > > > > > > > > > editor mode), but no log6 file is created in the C:\relax-3.1.7,
> > > > > > > > > > > I
> > > > > > > > > > > understand that the command line 'relax -i --tee log' will
> > > > > > > > > > > produce
> > > > > > > > > > > output
> > > > > > > > > > > in
> > > > > > > > > > > cmd window, but it does not produce the log file.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > C:\relax-3.1.7>relax -i --tee log6
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >                                   relax 3.1.7
> > > > > > > > > > >
> > > > > > > > > > >                     Molecular dynamics by NMR data analysis
> > > > > > > > > > >
> > > > > > > > > > >                    Copyright (C) 2001-2006 Edward d'Auvergne
> > > > > > > > > > >               Copyright (C) 2006-2014 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.
> > > > > > > > > > >
> > > > > > > > > > > Processor fabric:  Uni-processor.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Hardware information:
> > > > > > > > > > >     Machine:                 x86
> > > > > > > > > > >     Processor:               x86 Family 6 Model 15 Stepping 13,
> > > > > > > > > > > GenuineIntel
> > > > > > > > > > >     Processor name:          x86 Family 6 Model 15 Stepping 13,
> > > > > > > > > > > GenuineIntel
> > > > > > > > > > >     Endianness:              little
> > > > > > > > > > >     Total RAM size:          3037.30078125 Mb
> > > > > > > > > > >     Total swap size:         2047.875 Mb
> > > > > > > > > > >
> > > > > > > > > > > Operating system information:
> > > > > > > > > > >     System:                  Windows
> > > > > > > > > > >     Release:                 7
> > > > > > > > > > >     Version:                 6.1.7601
> > > > > > > > > > >     Win32 version:           7 6.1.7601 SP1 Multiprocessor Free
> > > > > > > > > > >     Distribution:
> > > > > > > > > > >     Full platform string:    Windows-7-6.1.7601-SP1
> > > > > > > > > > >     Windows architecture:    x86
> > > > > > > > > > >
> > > > > > > > > > > Python information:
> > > > > > > > > > >     Architecture:            32bit WindowsPE
> > > > > > > > > > >     Python version:          2.7.6
> > > > > > > > > > >     Python branch:
> > > > > > > > > > >     Python build:            default, Nov 10 2013 19:24:18
> > > > > > > > > > >     Python compiler:         MSC v.1500 32 bit (Intel)
> > > > > > > > > > >     Libc version:
> > > > > > > > > > >     Python implementation:   CPython
> > > > > > > > > > >     Python revision:
> > > > > > > > > > >     Python executable:       C:\Python27\python.exe
> > > > > > > > > > >     Python flags:            sys.flags(debug=0, py3k_warning=0,
> > > > > > > > > > > division_warning
> > > > > > > > > > > =0, division_new=0, inspect=0, interactive=0, optimize=0,
> > > > > > > > > > > dont_write_bytecode=0,
> > > > > > > > > > >  no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0,
> > > > > > > > > > > verbose=0,
> > > > > > > > > > > unicode
> > > > > > > > > > > =0, bytes_warning=0, hash_randomization=0)
> > > > > > > > > > >     Python float info:
> > > > > > > > > > > sys.float_info(max=1.7976931348623157e+308,
> > > > > > > > > > > max_exp
> > > > > > > > > > > =1024, max_10_exp=308, min=2.2250738585072014e-308,
> > > > > > > > > > > min_exp=-1021,
> > > > > > > > > > > min_10_exp=-3
> > > > > > > > > > > 07, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, radix=2,
> > > > > > > > > > > rounds=1)
> > > > > > > > > > >     Python module path:      ['', 'C:\\relax-3.1.7',
> > > > > > > > > > > 'C:\\Windows\\system32\\pyt
> > > > > > > > > > > hon27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib',
> > > > > > > > > > > 'C:\\Python27\\lib\\plat-
> > > > > > > > > > > win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
> > > > > > > > > > > 'C:\\Python27\\lib\\site-pack
> > > > > > > > > > > ages', 'C:\\Python27\\lib\\site-packages\\wx-3.0-msw']
> > > > > > > > > > >
> > > > > > > > > > > Python packages and modules (most are optional):
> > > > > > > > > > >
> > > > > > > > > > > Name               Installed    Version                  Path
> > > > > > > > > > >
> > > > > > > > > > > minfx              True         1.0.5
> > > > > > > > > > > C:\relax-3.1.7\minfx
> > > > > > > > > > >
> > > > > > > > > > > bmrblib            True         1.0.3
> > > > > > > > > > > C:\relax-3.1.7\bmrblib
> > > > > > > > > > >
> > > > > > > > > > > numpy              True         1.8.0
> > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > ckages\numpy
> > > > > > > > > > > scipy              True         0.13.3
> > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > ckages\scipy
> > > > > > > > > > > wxPython           True         3.0.0.0 msw (classic)
> > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > ckages\wx-3.0-msw\wx
> > > > > > > > > > > mpi4py             False
> > > > > > > > > > >
> > > > > > > > > > > epydoc             False
> > > > > > > > > > >
> > > > > > > > > > > optparse           True         1.5.3
> > > > > > > > > > > C:\Python27\lib\optpars
> > > > > > > > > > > e.pyc
> > > > > > > > > > > readline           True
> > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > ckages\readline.pyc
> > > > > > > > > > > profile            True
> > > > > > > > > > > C:\Python27\lib\profile
> > > > > > > > > > > .pyc
> > > > > > > > > > > bz2                True
> > > > > > > > > > > C:\Python27\DLLs\bz2.py
> > > > > > > > > > > d
> > > > > > > > > > > gzip               True
> > > > > > > > > > > C:\Python27\lib\gzip.py
> > > > > > > > > > > c
> > > > > > > > > > > io                 True
> > > > > > > > > > > C:\Python27\lib\io.pyc
> > > > > > > > > > >
> > > > > > > > > > > xml                True         0.8.4 (internal)
> > > > > > > > > > > C:\Python27\lib\xml\__i
> > > > > > > > > > > nit__.pyc
> > > > > > > > > > > xml.dom.minidom    True
> > > > > > > > > > > C:\Python27\lib\xml\dom
> > > > > > > > > > > \minidom.pyc
> > > > > > > > > > >
> > > > > > > > > > > relax information:
> > > > > > > > > > >     Version:                 3.1.7
> > > > > > > > > > >     Processor fabric:        Uni-processor.
> > > > > > > > > > >
> > > > > > > > > > > relax C modules:
> > > > > > > > > > >
> > > > > > > > > > > Module                        Compiled    File type    Path
> > > > > > > > > > >
> > > > > > > > > > > target_functions.relax_fit    True
> > > > > > > > > > > target_functions\relax_fi
> > > > > > > > > > > t.pyd
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > C:\relax-3.1.7>
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Thank you.
> > > > > > > > > > >
> > > > > > > > > > > Best regards,
> > > > > > > > > > >
> > > > > > > > > > > Mengjun
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Mengjun,
> > > > > > > > > > > >
> > > > > > > > > > > > When you run 'relax -i --tee log', there is no script being run.
> > > > > > > > > > > > Does
> > > > > > > > > > > > this still not produce the 'log' file from the directory you ran
> > > > > > > > > > > > it
> > > > > > > > > > > > from?  I'm deliberately ignoring the 'cpmg_analysis.py' script
> > > > > > > > > > > > right
> > > > > > > > > > > > now to try to understand and pinpoint where on earth this
> > > > > > > > > > > > strange
> > > > > > > > > > > > behaviour is located.  When trying to fix such a problem, you
> > > > > > > > > > > > need
> > > > > > > > > > > > to
> > > > > > > > > > > > identify the most basic factor which is at issue.  Here you are
> > > > > > > > > > > > running relax without a script, and it is failing.  Therefore I
> > > > > > > > > > > > can
> > > > > > > > > > > > only conclude that this is the failure point for everything.  If
> > > > > > > > > > > > we
> > > > > > > > > > > > can get 'relax -i --tee log' to run, then, and only then, will
> > > > > > > > > > > > it
> > > > > > > > > > > > be
> > > > > > > > > > > > possible to run the 'cpmg_analysis.py' script.  Because the
> > > > > > > > > > > > reason
> > > > > > > > > > > > for
> > > > > > > > > > > > not being able to produce the 'log' file is likely to the same
> > > > > > > > > > > > reason
> > > > > > > > > > > > why the script cannot be run.
> > > > > > > > > > > >
> > > > > > > > > > > > Regards,
> > > > > > > > > > > >
> > > > > > > > > > > > Edward
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > On 24 April 2014 17:22,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx>
> > > > > > > > > > > > wrote:
> > > > > > > > > > > > > Hi Edward,
> > > > > > > > > > > > >
> > > > > > > > > > > > > When I run relax -i --tee log, I rename log to log123 or
> > > > > > > > > > > > > loglog,
> > > > > > > > > > > > > which
> > > > > > > > > > > > > is
> > > > > > > > > > > > > new name, it should not be problem. For the permisions for the
> > > > > > > > > > > > > directory,
> > > > > > > > > > > > > I
> > > > > > > > > > > > > can get the log file when I run other script, for example, I
> > > > > > > > > > > > > have
> > > > > > > > > > > > > run
> > > > > > > > > > > > > dauvergne_protocol.py for the full model free analysis on my
> > > > > > > > > > > > > computer,
> > > > > > > > > > > > > it
> > > > > > > > > > > > > can create log file, dauvergne_protocol.py can run smoothly,
> > > > > > > > > > > > > but
> > > > > > > > > > > > > when
> > > > > > > > > > > > > I
> > > > > > > > > > > > > try
> > > > > > > > > > > > > to run cpmg_analysis.py, it does not work. So maybe my computer
> > > > > > > > > > > > > has
> > > > > > > > > > > > > some
> > > > > > > > > > > > > problems, I will ask some people to check my computer, at this
> > > > > > > > > > > > > moment
> > > > > > > > > > > > > it
> > > > > > > > > > > > > seems my computer can still work well, it can run relax
> > > > > > > > > > > > > scripts,
> > > > > > > > > > > > > dauvergne_protocol.py can run smoothly, but it can not run
> > > > > > > > > > > > > cpmg_analysis.py,
> > > > > > > > > > > > > if it is hard disk failture, it means the computer will have
> > > > > > > > > > > > > some
> > > > > > > > > > > > > strange
> > > > > > > > > > > > > noise? and can not start windows system easily?
> > > > > > > > > > > > >
> > > > > > > > > > > > >
> > > > > > > > > > > > > Thank you.
> > > > > > > > > > > > >
> > > > > > > > > > > > > Best regards,
> > > > > > > > > > > > >
> > > > > > > > > > > > > Mengjun
> > > > > > > > > > > > >
> > > > > > > > > > > > >
> > > > > > > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > > > > > >
> > > > > > > > > > > > > > Hi,
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > If the 'relax -i --tee log' command does not produce a 'log'
> > > > > > > > > > > > > > file
> > > > > > > > > > > > > > on
> > > > > > > > > > > > > > your computer, then that indicates where the problem is.
> > > > > > > > > > > > > > There
> > > > > > > > > > > > > > are
> > > > > > > > > > > > > > only two cases where this file cannot be produced:
> > > > > > > > > > > > > >
> > > > > > > > > > > > > >   - The 'log' file already exists.  The old file would
> > > > > > > > > > > > > > therefore
> > > > > > > > > > > > > > have
> > > > > > > > > > > > > > to be deleted, or run 'relax -i --tee log2'.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > >   - You do not have write permissions for the directory you
> > > > > > > > > > > > > > are
> > > > > > > > > > > > > > running the 'relax -i --tee log' command from.
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > If it is not one of these two cases, then there is something
> > > > > > > > > > > > > > seriously
> > > > > > > > > > > > > > sick with your computer!   For example your computer could be
> > > > > > > > > > > > > > currently suffering from a progressive hard disk failure.  In
> > > > > > > > > > > > > > any
> > > > > > > > > > > > > > case, this is not a problem due to relax but a general problem
> > > > > > > > > > > > > > with
> > > > > > > > > > > > > > your computer.  Do you have a system administrator at work who
> > > > > > > > > > > > > > can
> > > > > > > > > > > > > > look at this?
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Regards,
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > Edward
> > > > > > > > > > > > > >
> > > > > > > > > > > > > >
> > > > > > > > > > > > > >
> > > > > > > > > > > > > > On 24 April 2014 16:42,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx>
> > > > > > > > > > > > > > wrote:
> > > > > > > > > > > > > > > Hi Edward,
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > I have tried the 'relax -i --tee log' command, but it does
> > > > > > > > > > > > > > > not
> > > > > > > > > > > > > > > create
> > > > > > > > > > > > > > > log
> > > > > > > > > > > > > > > file on my computer, I just copy the output from cmd window
> > > > > > > > > > > > > > > using
> > > > > > > > > > > > > > > editor
> > > > > > > > > > > > > > > mode:
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >                                   relax 3.1.7
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >                     Molecular dynamics by NMR data analysis
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >                    Copyright (C) 2001-2006 Edward d'Auvergne
> > > > > > > > > > > > > > >               Copyright (C) 2006-2014 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.
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Processor fabric:  Uni-processor.
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Hardware information:
> > > > > > > > > > > > > > >     Machine:                 x86
> > > > > > > > > > > > > > >     Processor:               x86 Family 6 Model 15 Stepping
> > > > > > > > > > > > > > > 13,
> > > > > > > > > > > > > > > GenuineIntel
> > > > > > > > > > > > > > >     Processor name:          x86 Family 6 Model 15 Stepping
> > > > > > > > > > > > > > > 13,
> > > > > > > > > > > > > > > GenuineIntel
> > > > > > > > > > > > > > >     Endianness:              little
> > > > > > > > > > > > > > >     Total RAM size:          3037.30078125 Mb
> > > > > > > > > > > > > > >     Total swap size:         2047.875 Mb
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Operating system information:
> > > > > > > > > > > > > > >     System:                  Windows
> > > > > > > > > > > > > > >     Release:                 7
> > > > > > > > > > > > > > >     Version:                 6.1.7601
> > > > > > > > > > > > > > >     Win32 version:           7 6.1.7601 SP1 Multiprocessor
> > > > > > > > > > > > > > > Free
> > > > > > > > > > > > > > >     Distribution:
> > > > > > > > > > > > > > >     Full platform string:    Windows-7-6.1.7601-SP1
> > > > > > > > > > > > > > >     Windows architecture:    x86
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Python information:
> > > > > > > > > > > > > > >     Architecture:            32bit WindowsPE
> > > > > > > > > > > > > > >     Python version:          2.7.6
> > > > > > > > > > > > > > >     Python branch:
> > > > > > > > > > > > > > >     Python build:            default, Nov 10 2013 19:24:18
> > > > > > > > > > > > > > >     Python compiler:         MSC v.1500 32 bit (Intel)
> > > > > > > > > > > > > > >     Libc version:
> > > > > > > > > > > > > > >     Python implementation:   CPython
> > > > > > > > > > > > > > >     Python revision:
> > > > > > > > > > > > > > >     Python executable:       C:\Python27\python.exe
> > > > > > > > > > > > > > >     Python flags:            sys.flags(debug=0,
> > > > > > > > > > > > > > > py3k_warning=0,
> > > > > > > > > > > > > > > division_warning
> > > > > > > > > > > > > > > =0, division_new=0, inspect=0, interactive=0, optimize=0,
> > > > > > > > > > > > > > > dont_write_bytecode=0,
> > > > > > > > > > > > > > >  no_user_site=0, no_site=0, ignore_environment=0, tabcheck=0,
> > > > > > > > > > > > > > > verbose=0,
> > > > > > > > > > > > > > > unicode
> > > > > > > > > > > > > > > =0, bytes_warning=0, hash_randomization=0)
> > > > > > > > > > > > > > >     Python float info:
> > > > > > > > > > > > > > > sys.float_info(max=1.7976931348623157e+308,
> > > > > > > > > > > > > > > max_exp
> > > > > > > > > > > > > > > =1024, max_10_exp=308, min=2.2250738585072014e-308,
> > > > > > > > > > > > > > > min_exp=-1021,
> > > > > > > > > > > > > > > min_10_exp=-3
> > > > > > > > > > > > > > > 07, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
> > > > > > > > > > > > > > > radix=2,
> > > > > > > > > > > > > > > rounds=1)
> > > > > > > > > > > > > > >     Python module path:      ['', 'C:\\relax-3.1.7',
> > > > > > > > > > > > > > > 'C:\\Windows\\system32\\pyt
> > > > > > > > > > > > > > > hon27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib',
> > > > > > > > > > > > > > > 'C:\\Python27\\lib\\plat-
> > > > > > > > > > > > > > > win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27',
> > > > > > > > > > > > > > > 'C:\\Python27\\lib\\site-pack
> > > > > > > > > > > > > > > ages', 'C:\\Python27\\lib\\site-packages\\wx-3.0-msw']
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Python packages and modules (most are optional):
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Name               Installed    Version                  Path
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > minfx              True         1.0.5
> > > > > > > > > > > > > > > C:\relax-3.1.7\minfx
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > bmrblib            True         1.0.3
> > > > > > > > > > > > > > > C:\relax-3.1.7\bmrblib
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > numpy              True         1.8.0
> > > > > > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > > > > > ckages\numpy
> > > > > > > > > > > > > > > scipy              True         0.13.3
> > > > > > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > > > > > ckages\scipy
> > > > > > > > > > > > > > > wxPython           True         3.0.0.0 msw (classic)
> > > > > > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > > > > > ckages\wx-3.0-msw\wx
> > > > > > > > > > > > > > > mpi4py             False
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > epydoc             False
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > optparse           True         1.5.3
> > > > > > > > > > > > > > > C:\Python27\lib\optpars
> > > > > > > > > > > > > > > e.pyc
> > > > > > > > > > > > > > > readline           True
> > > > > > > > > > > > > > > C:\Python27\lib\site-pa
> > > > > > > > > > > > > > > ckages\readline.pyc
> > > > > > > > > > > > > > > profile            True
> > > > > > > > > > > > > > > C:\Python27\lib\profile
> > > > > > > > > > > > > > > .pyc
> > > > > > > > > > > > > > > bz2                True
> > > > > > > > > > > > > > > C:\Python27\DLLs\bz2.py
> > > > > > > > > > > > > > > d
> > > > > > > > > > > > > > > gzip               True
> > > > > > > > > > > > > > > C:\Python27\lib\gzip.py
> > > > > > > > > > > > > > > c
> > > > > > > > > > > > > > > io                 True
> > > > > > > > > > > > > > > C:\Python27\lib\io.pyc
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > xml                True         0.8.4 (internal)
> > > > > > > > > > > > > > > C:\Python27\lib\xml\__i
> > > > > > > > > > > > > > > nit__.pyc
> > > > > > > > > > > > > > > xml.dom.minidom    True
> > > > > > > > > > > > > > > C:\Python27\lib\xml\dom
> > > > > > > > > > > > > > > \minidom.pyc
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > relax information:
> > > > > > > > > > > > > > >     Version:                 3.1.7
> > > > > > > > > > > > > > >     Processor fabric:        Uni-processor.
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > relax C modules:
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Module                        Compiled    File type    Path
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > target_functions.relax_fit    True
> > > > > > > > > > > > > > > target_functions\relax_fi
> > > > > > > > > > > > > > > t.pyd
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Thank you.
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Best regards,
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Mengjun
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > Hi,
> > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > The command is correct, running 'relax -i --tee log' will
> > > > > > > > > > > > > > > > produce
> > > > > > > > > > > > > > > > the
> > > > > > > > > > > > > > > > 'log' text file which you can then open and copy and paste
> > > > > > > > > > > > > > > > the
> > > > > > > > > > > > > > > > contents of.
> > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > Regards,
> > > > > > > > > > > > > > > >
> > > > > > > > > > > > > > > > Edward