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.pyDo 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