Hi, Thanks for testing that. The optimisation failures are not failures of relax, but that it is a new platform where optimisation is a tiny bit different. I'm collecting all the information about these, and adding exceptions for each machine. I might have to turn this off though. You'll see that the optimised pararameters will be nevertheless very close to those in the test name 'test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149'. If you could email more of the information from the system test, this would be quite useful to make this test pass. There should be a long print out like:
-------------------------------------- System: Darwin Release: 9.8.0 Version: Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 Win32 version: Distribution: Architecture: 64bit Machine: i386 Processor: i386 Python version: 2.6.2 numpy version: 1.3.0 s2: 0.9699999999999785 te: 2047.9999999962433 rex: 0.14900000000039709 chi2: 5.2479491342506911e-24 iter: 162 f_count: 758 g_count: 169 h_count: 0 warning: None -------------------------------------- before the traceback message you posted. This is the information needed. But everything should be fine, just that you won't be able to run relaxation curve-fitting for the R1 and R2 until the module is compiled. The python version I compiled on (2.6.5) is similar enough to your 2.6.2 - this is not the issue. Maybe the numpy version is the problem - I compiled on 1.4.1 and you are using 1.2.1. They could have introduced an incompatibility. If you can install the numpy headers package and scons, you'll be able to compile without problem by typing 'scons'. Cheers, Edward On 27 January 2011 12:14, Tiago Pais <[email protected]> wrote: > Thank you Edward, > Renaming the relax_fit.so did the job! Nice catch! > > However, when running the test suite it is falling in the System/Functional > tests: > > Traceback (most recent call last): > File "/usr/local/relax-1.3.7/test_suite/system_tests/model_free.py", line > 677, in test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 > self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, > h_count, warning) > File "/usr/local/relax-1.3.7/test_suite/system_tests/model_free.py", line > 2051, in value_test > self.assert_(spin.f_count in f_count, msg=mesg) > AssertionError: Optimisation failure. > > > And this is the output information from relax --info (v1.3.8) > > Hardware information: > Machine: i686 > Processor: > > System information: > System: Linux > Release: 2.6.28-17-generic > Version: #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 > GNU/Linux version: Ubuntu 9.04 jaunty > Distribution: Ubuntu 9.04 jaunty > Full platform string: > Linux-2.6.28-17-generic-i686-with-Ubuntu-9.04-jaunty > > Software information: > Architecture: 32bit ELF > Python version: 2.6.2 > Python branch: branches/release26-maint > Python build: release26-maint, Apr 19 2009 01:56:41 > Python compiler: GCC 4.3.3 > Python implementation: CPython > Python revision: > Numpy version: 1.2.1 > Libc version: glibc 2.4 > > Python packages (most are optional): > > Package Installed Version Path > minfx True Unknown > /usr/local/relax-1.3.8/minfx > bmrblib False > numpy True 1.2.1 > /usr/lib/python2.6/dist-packages/numpy > ScientificPython True 2.4.11 > /usr/lib/python2.6/dist-packages/Scientific > wxPython False > mpi4py False > epydoc False > optparse True 1.5.3 > /usr/lib/python2.6/optparse.pyc > Numeric True 24.2 > /usr/lib/python2.6/dist-packages/Numeric/Numeric.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: False > > I have not tried the "scons" possibility that you suggested. > > Regards, > TiagoP > > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 26 de Janeiro de 2011 19:56 > To: Tiago Pais > Cc: [email protected] > Subject: Re: Segmentation Fault on Relax - 1.3.7 > > Hi, > > This is strange! Do the source code versions work ok? It could be > the a strange combination of python and numpy, together with relax's C > modules. You could possibly remove (or rename) the > maths_fns/relax_fit.so file and try again. It would be useful to have > information about the system to work out what is happening. You can > get all the relevant info by typing: > > $ relax --info > > This is assuming relax will run at all. Another option would be if > you have 'scons', 'numpy', and 'numpy-devel' (or something like that) > installed. You could then type: > > $ scons clean_all > > to remove the compiled C module, and > > $ scons > > to build it again. I hope this helps! > > Cheers, > > Edward > > > > On 26 January 2011 19:35, Tiago Pais <[email protected]> wrote: >> Dear all, >> Surely this should be a very silly mistake of mine but I can not manage to >> put to work any of the relax versions above 1.3.6. >> I just get the message "Segmentation fault" when I type "relax" >> >> Do I need to uninstall the previous 1.3.4 version? >> For now I would like to keep the old one since I have things analyzed on >> that one. >> >> Any help would be much appreciated. >> Cheers >> Tiago P >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 5821 (20110126) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-users >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 5822 (20110126) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 5823 (20110127) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
