Re: C modules not compiled
Hi. Try just write scons But this should only be for the source code. The packaged versions should already have the compiled C code in it. So this is weird. Can you run relax - d and post it here? Best Troels On 13 Nov 2014 22:34, "Maciejewski,Mark W." wrote: > Hello, > > I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine > except for the error: > "ImportError: relaxation curve fitting is unavailable, the corresponding C > modules have not been compiled." > > I installed relax using the command: > scons install > > I have searched the archives and see that others have had similar > problems, but cannot find a solution that works for me. > > Any suggestions on how to install or compile the C modules? > > Below is the output from "relax -info" > > Thanks, > Mark > > > [nmradmin@nmrbox_wisc ~]$ relax --info > > > > relax 3.2.3 > > 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. > > ImportError: relaxation curve fitting is unavailable, the corresponding C > modules have not been compiled. > > Processor fabric: Uni-processor. > > > Hardware information: > Machine: x86_64 > Processor: x86_64 > Processor name: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz > Endianness: little > Total RAM size: 3832 Mb > Total swap size: 3967 Mb > > Operating system information: > System: Linux > Release: 2.6.32-504.1.3.el6.x86_64 > Version: #1 SMP Tue Nov 11 17:57:25 UTC 2014 > GNU/Linux version: CentOS 6.6 Final > Distribution:centos 6.6 Final > Full platform string: > Linux-2.6.32-504.1.3.el6.x86_64-x86_64-with-centos-6.6-Final > > Python information: > Architecture:64bit ELF > Python version: 2.6.6 > Python branch: tags/r266 > Python build:r266:84292, Jan 22 2014 09:42:36 > Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-4) > Libc version:glibc 2.2.5 > Python implementation: CPython > Python revision: 84292 > Python executable: /usr/bin/python > 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.floatinfo(max=1.7976931348623157e+308, > max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021, > min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16, > radix=2, rounds=1) > Python module path: ['/usr/local/relax', > '/usr/lib/python2.6/site-packages/requests-2.4.3-py2.6.egg', > '/usr/lib/python2.6/site-packages/pip-1.5.6-py2.6.egg', > '/usr/lib/python2.6/site-packages/distribute-0.7.3-py2.6.egg', > '/usr/lib/python2.6/site-packages/setuptools-7.0-py2.6.egg', > '/home/nmradmin', '/usr/local/ccpnmr/ccpnmr2.4/python', > '/usr/lib64/python26.zip', '/usr/lib64/python2.6', > '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', > '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', > '/usr/lib64/python2.6/site-packages', > '/usr/lib64/python2.6/site-packages/PIL', > '/usr/lib64/python2.6/site-packages/gst-0.10', > '/usr/lib64/python2.6/site-packages/gtk-2.0', > '/usr/lib64/python2.6/site-packages/webkit-1.0', > '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode', > '/usr/lib/python2.6/site-packages', > '/usr/lib64/python2.6/site-packages/Scientific/linux2'] > > Python packages and modules (most are optional): > > Name InstalledVersionPath > minfx True 1.0.7 > /usr/local/relax/minfx > bmrblibTrue 1.0.3 > /usr/local/relax/bmrblib > numpy True 1.9.1 > /usr/lib64/python2.6/site-packages/numpy > scipy True 0.7.2 > /usr/lib64/python2.6/site-packages/scipy > wxPython True 2.8.12.0 (gtk2-unicode) > /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx > matplotlib True 0.99.1.1 > /usr/lib64/python2.6/site-packages/matplotlib > mpi4py False > epydoc True 3.0.1 > /usr/
Re: C modules not compiled
Hi Mark, Welcome to the relax mailing lists! The problem you see could be due to a number of factors. Firstly, could you check if you have the compiled file present on your system: $ ls -alh /usr/local/relax/target_functions/relax_fit.so $ file /usr/local/relax/target_functions/relax_fit.so If the file is there, then maybe you have a Python version problem. The C module was compiled using Python 2.7. Normally this will then work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4 that I regularly check this with). You can check this by running relax and typing: relax> import target_functions.relax_fit For example in Python 3, this gives the error: relax> import target_functions.relax_fit Traceback (most recent call last): File "", line 1, in ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so: undefined symbol: Py_InitModule4_64 Maybe you will see something similar. In any case you have two alternatives. The first is to upgrade Python, if the relax_fit.so file exists, though this can be a painful and dangerous task on Linux systems (you can change the base 'relax' file to point to a different alternative Python version if you wish). The second is as Troels suggests. Install the scons program, the Python headers, and then just run 'scons' as root in the /usr/local/relax directory to compile the module yourself. Note that you only need this C module for fitting exponential curves for the R1, R2, or relaxation dispersion analyses. Regards, Edward On 14 November 2014 01:05, Troels Emtekær Linnet wrote: > Hi. > > Try just write scons > > But this should only be for the source code. > > The packaged versions should already have the compiled C code in it. > > So this is weird. > > Can you run > relax - d > and post it here? > > Best > Troels > On 13 Nov 2014 22:34, "Maciejewski,Mark W." wrote: > >> Hello, >> >> I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine >> except for the error: >> "ImportError: relaxation curve fitting is unavailable, the corresponding C >> modules have not been compiled." >> >> I installed relax using the command: >> scons install >> >> I have searched the archives and see that others have had similar >> problems, but cannot find a solution that works for me. >> >> Any suggestions on how to install or compile the C modules? >> >> Below is the output from "relax -info" >> >> Thanks, >> Mark >> >> >> [nmradmin@nmrbox_wisc ~]$ relax --info >> >> >> >> relax 3.2.3 >> >> 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. >> >> ImportError: relaxation curve fitting is unavailable, the corresponding C >> modules have not been compiled. >> >> Processor fabric: Uni-processor. >> >> >> Hardware information: >> Machine: x86_64 >> Processor: x86_64 >> Processor name: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz >> Endianness: little >> Total RAM size: 3832 Mb >> Total swap size: 3967 Mb >> >> Operating system information: >> System: Linux >> Release: 2.6.32-504.1.3.el6.x86_64 >> Version: #1 SMP Tue Nov 11 17:57:25 UTC 2014 >> GNU/Linux version: CentOS 6.6 Final >> Distribution:centos 6.6 Final >> Full platform string: >> Linux-2.6.32-504.1.3.el6.x86_64-x86_64-with-centos-6.6-Final >> >> Python information: >> Architecture:64bit ELF >> Python version: 2.6.6 >> Python branch: tags/r266 >> Python build:r266:84292, Jan 22 2014 09:42:36 >> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-4) >> Libc version:glibc 2.2.5 >> Python implementation: CPython >> Python revision: 84292 >> Python executable: /usr/bin/python >> 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.floatinfo(max=1.7976931348623157e+308, >> max_exp=1024, max_10_exp=308, min=2.22507385
Re: C modules not compiled
Hi Mark, I would also recommend that you sign up for the relax-announce mailing list (https://mail.gna.org/listinfo/relax-announce/). This list only receives a few emails per year (see http://news.gmane.org/gmane.science.nmr.relax.announce), and it is used almost exclusively for announcing new relax versions, for example relax 3.3.2 which I am in the process of releasing now (see http://www.nmr-relax.com/download.html). Since relax 3.2.3, there have been the following releases: http://wiki.nmr-relax.com/Relax_3.3.0 http://wiki.nmr-relax.com/Relax_3.3.1 http://wiki.nmr-relax.com/Relax_3.3.2 That last link will appear later today. If you are performing either a model-free or relaxation dispersion analysis, I would highly recommend that you upgrade to relax 3.3.2 to obtain all the bug fixes and Troels' huge relaxation dispersion speed ups (http://wiki.nmr-relax.com/Relax_3.3.0). Regards, Edward On 14 November 2014 10:19, Edward d'Auvergne wrote: > Hi Mark, > > Welcome to the relax mailing lists! The problem you see could be due > to a number of factors. Firstly, could you check if you have the > compiled file present on your system: > > $ ls -alh /usr/local/relax/target_functions/relax_fit.so > $ file /usr/local/relax/target_functions/relax_fit.so > > > If the file is there, then maybe you have a Python version problem. > The C module was compiled using Python 2.7. Normally this will then > work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux > set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4 > that I regularly check this with). You can check this by running > relax and typing: > > relax> import target_functions.relax_fit > > > For example in Python 3, this gives the error: > > relax> import target_functions.relax_fit > Traceback (most recent call last): > File "", line 1, in > ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so: > undefined symbol: Py_InitModule4_64 > > > Maybe you will see something similar. In any case you have two > alternatives. The first is to upgrade Python, if the relax_fit.so > file exists, though this can be a painful and dangerous task on Linux > systems (you can change the base 'relax' file to point to a different > alternative Python version if you wish). The second is as Troels > suggests. Install the scons program, the Python headers, and then > just run 'scons' as root in the /usr/local/relax directory to compile > the module yourself. > > Note that you only need this C module for fitting exponential curves > for the R1, R2, or relaxation dispersion analyses. > > Regards, > > Edward > > > > > > On 14 November 2014 01:05, Troels Emtekær Linnet wrote: >> Hi. >> >> Try just write scons >> >> But this should only be for the source code. >> >> The packaged versions should already have the compiled C code in it. >> >> So this is weird. >> >> Can you run >> relax - d >> and post it here? >> >> Best >> Troels >> On 13 Nov 2014 22:34, "Maciejewski,Mark W." wrote: >> >>> Hello, >>> >>> I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine >>> except for the error: >>> "ImportError: relaxation curve fitting is unavailable, the corresponding C >>> modules have not been compiled." >>> >>> I installed relax using the command: >>> scons install >>> >>> I have searched the archives and see that others have had similar >>> problems, but cannot find a solution that works for me. >>> >>> Any suggestions on how to install or compile the C modules? >>> >>> Below is the output from "relax -info" >>> >>> Thanks, >>> Mark >>> >>> >>> [nmradmin@nmrbox_wisc ~]$ relax --info >>> >>> >>> >>> relax 3.2.3 >>> >>> 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. >>> >>> ImportError: relaxation curve fitting is unavailable, the corresponding C >>> modules have not been compiled. >>> >>> Processor fabric: Uni-processor. >>> >>> >>> Hardware information: >>> Machine: x86_64 >>> Processor: x86_64 >>> Processor name: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz >>> Endianness: little >>> Total RAM size: 3832 Mb >>> Total swap size: 3967 Mb >>> >>> Operating system information: >>> System: Linux >>> Release: 2.6.32-504.1.3.el6.x86_64
RE: C modules not compiled
Troels and Edward, Thanks for your assistance. Everything is working fine now. I was using the source code to install (relax-3.3.2.src) and the relax_fit.so file was not present causing the problem. From the base directory I typed "scons", which created the relax_fit.so file, and then "scons install " to install the program in /usr/local/relax and create the byte-compiled *.pyc files and everything was fine. I did not realize that I needed to perform the "scons" command first before the "scons install" command. I also downloaded the pre-build relax-3.3.2.GNU-Linux.x86_64 package and it ran fine as well. Thanks again, Mark -Original Message- From: edward.dauver...@gmail.com [mailto:edward.dauver...@gmail.com] On Behalf Of Edward d'Auvergne Sent: Friday, November 14, 2014 4:20 AM To: Troels Emtekær Linnet Cc: Maciejewski,Mark W.; relax-users@gna.org Subject: Re: C modules not compiled Hi Mark, Welcome to the relax mailing lists! The problem you see could be due to a number of factors. Firstly, could you check if you have the compiled file present on your system: $ ls -alh /usr/local/relax/target_functions/relax_fit.so $ file /usr/local/relax/target_functions/relax_fit.so If the file is there, then maybe you have a Python version problem. The C module was compiled using Python 2.7. Normally this will then work for Python 2.5, 2.6 and 2.7 but not Python >= 3.1 (I have a Linux set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4 that I regularly check this with). You can check this by running relax and typing: relax> import target_functions.relax_fit For example in Python 3, this gives the error: relax> import target_functions.relax_fit Traceback (most recent call last): File "", line 1, in ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so: undefined symbol: Py_InitModule4_64 Maybe you will see something similar. In any case you have two alternatives. The first is to upgrade Python, if the relax_fit.so file exists, though this can be a painful and dangerous task on Linux systems (you can change the base 'relax' file to point to a different alternative Python version if you wish). The second is as Troels suggests. Install the scons program, the Python headers, and then just run 'scons' as root in the /usr/local/relax directory to compile the module yourself. Note that you only need this C module for fitting exponential curves for the R1, R2, or relaxation dispersion analyses. Regards, Edward On 14 November 2014 01:05, Troels Emtekær Linnet wrote: > Hi. > > Try just write scons > > But this should only be for the source code. > > The packaged versions should already have the compiled C code in it. > > So this is weird. > > Can you run > relax - d > and post it here? > > Best > Troels > On 13 Nov 2014 22:34, "Maciejewski,Mark W." wrote: > >> Hello, >> >> I have installed relax 3.2.3 on CentOS release 6.6. The program runs >> fine except for the error: >> "ImportError: relaxation curve fitting is unavailable, the >> corresponding C modules have not been compiled." >> >> I installed relax using the command: >> scons install >> >> I have searched the archives and see that others have had similar >> problems, but cannot find a solution that works for me. >> >> Any suggestions on how to install or compile the C modules? >> >> Below is the output from "relax -info" >> >> Thanks, >> Mark >> >> >> [nmradmin@nmrbox_wisc ~]$ relax --info >> >> >> >> relax 3.2.3 >> >> 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. >> >> ImportError: relaxation curve fitting is unavailable, the >> corresponding C modules have not been compiled. >> >> Processor fabric: Uni-processor. >> >> >> Hardware information: >> Machine: x86_64 >> Processor: x86_64 >>
