I get this when I try to compile: gcc -o target_functions/c_chi2.os -c -I/sbinlab2/software/python- enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/include/python2.7 -fPIC target_functions/c_chi2.c gcc -o target_functions/exponential.os -c -I/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/include/python2.7 -fPIC target_functions/exponential.c gcc -o target_functions/relax_fit.os -c -I/sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/include/python2.7 -fPIC target_functions/relax_fit.c target_functions/relax_fit.c:21:20: error: Python.h: No such file or directory target_functions/relax_fit.c:31: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:80: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:118: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:168: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:179: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:196: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token target_functions/relax_fit.c:244: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'relax_fit_methods' target_functions/relax_fit.c: In function 'initrelax_fit': target_functions/relax_fit.c:305: error: 'relax_fit_methods' undeclared (first use in this function) target_functions/relax_fit.c:305: error: (Each undeclared identifier is reported only once target_functions/relax_fit.c:305: error: for each function it appears in.) scons: *** [target_functions/relax_fit.os] Error 1 scons: building terminated because of errors.
2014-08-26 13:30 GMT+02:00 Edward d'Auvergne <[email protected]>: > The minfx equivalent algorithms as scipy.optimize.fmin_cg() and > scipy.optimize.fmin_ncg(), as well as the other scipy.optimize > functions are now working with the exponential curve-fitting in relax > as the gradient is now implemented. None of the Scipy algorithms > require the Hessian. They really need to implement the Newton > optimisation technique to be taken seriously. This is quite different > to NCG: > > http://home.gna.org/minfx/minfx.ncg-module.html > http://home.gna.org/minfx/minfx.newton-module.html > > Regards, > > Edward > > > On 26 August 2014 13:23, <[email protected]> wrote: >> Author: tlinnet >> Date: Tue Aug 26 13:23:47 2014 >> New Revision: 25287 >> >> URL: http://svn.gna.org/viewcvs/relax?rev=25287&view=rev >> Log: >> Removed all code regarding scipy.optimize fmin_cg and fmin_ncg. >> >> This problem should soon be able to be solved with minfx. >> >> task #7822(https://gna.org/task/index.php?7822): Implement user function to >> estimate R2eff and associated errors for exponential curve fitting. >> >> Modified: >> trunk/specific_analyses/relax_disp/estimate_r2eff.py >> >> Modified: trunk/specific_analyses/relax_disp/estimate_r2eff.py >> URL: >> http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/estimate_r2eff.py?rev=25287&r1=25286&r2=25287&view=diff >> ============================================================================== >> --- trunk/specific_analyses/relax_disp/estimate_r2eff.py (original) >> +++ trunk/specific_analyses/relax_disp/estimate_r2eff.py Tue Aug 26 >> 13:23:47 2014 >> @@ -45,7 +45,7 @@ >> # Scipy installed. >> if scipy_module: >> # Import leastsq. >> - from scipy.optimize import fmin_cg, fmin_ncg, leastsq >> + from scipy.optimize import leastsq >> >> >> class Exp: >> @@ -424,7 +424,6 @@ >> >> # 'minfx' >> # 'scipy.optimize.leastsq' >> -# 'scipy.optimize.fmin_cg' >> def estimate_r2eff(spin_id=None, ftol=1e-15, xtol=1e-15, maxfev=10000000, >> factor=100.0, method='minfx', verbosity=1): >> """Estimate r2eff and errors by exponential curve fitting with >> scipy.optimize.leastsq. >> >> @@ -540,10 +539,6 @@ >> # Acquire results. >> results = minimise_leastsq(E=E) >> >> - elif method == 'scipy.optimize.fmin_cg': >> - # Acquire results. >> - results = minimise_fmin_cg(E=E) >> - >> elif method == 'minfx': >> # Acquire results. >> results = minimise_minfx(E=E) >> @@ -715,46 +710,6 @@ >> return results >> >> >> -def minimise_fmin_cg(E=None): >> - """Estimate r2eff and errors by exponential curve fitting with >> scipy.optimize.fmin_cg. >> - >> - Unconstrained minimization of a function using the Newton-CG method. >> - >> - @keyword E: The Exponential function class, which contain data and >> functions. >> - @type E: class >> - @return: Packed list with optimised parameter, estimated >> parameter error, chi2, iter_count, f_count, g_count, h_count, warning >> - @rtype: list >> - """ >> - >> - # Check that scipy.optimize.leastsq is available. >> - if not scipy_module: >> - raise RelaxError("scipy module is not available.") >> - >> - # Initial guess for minimisation. Solved by linear least squares. >> - x0 = E.estimate_x0_exp() >> - >> - # Define function to minimise. Use errors as weights in the >> minimisation. >> - use_weights = True >> - >> - if use_weights: >> - func = E.func_exp_weighted_general >> - dfunc = E.func_exp_weighted_grad >> - d2func = E.func_exp_weighted_hess >> - >> - # There are no args to the function, since values and times are stored >> in the class. >> - args=() >> - >> - gfk = dfunc(x0) >> - deltak = numpy.dot(gfk, gfk) >> - >> - # Cannot get this to work. >> - >> - #xopt, fopt, fcalls, gcalls, hcalls, warnflag = fmin_ncg(f=func, x0=x0, >> fprime=dfunc, fhess=None, args=args, avextol=1e-05, >> epsilon=1.4901161193847656e-08, maxiter=maxfev, full_output=1, disp=1, >> retall=0, callback=None) >> - #test = fmin_ncg(f=func, x0=x0, fprime=dfunc, fhess=d2func, args=args, >> avextol=1e-05, epsilon=1.4901161193847656e-08, maxiter=maxfev) >> - #fmin_cg(f, x0, fprime=None, args=(), gtol=1e-5, norm=Inf, >> epsilon=_epsilon, maxiter=None, full_output=0, disp=1, retall=0, >> callback=None): >> - #fmin_cg(f=func, x0=x0, fprime=dfunc, args=args, gtol=1e-5) >> - >> - >> def minimise_minfx(E=None): >> """Estimate r2eff and errors by minimising with minfx. >> >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-commits 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-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel 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-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel 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-devel
