If you have a look at the 'sconstruct' script, specifically in the relax_fit() method, you will also see that you can set the PYTHON_INCLUDE_DIR environmental variable to where ever the corresponding Python.h file is.
Regards, Edward On 26 August 2014 14:58, Edward d'Auvergne <[email protected]> wrote: > Hi, > > The problem is shown in the line: > > target_functions/relax_fit.c:21:20: error: Python.h: No such file or directory > > I.e. the Python headers cannot be found by the compiler. How do you > compile this? Do you use 'scons'? Have you compiled the module > before? Is the Python.h file in the directory > /sbinlab2/software/python-enthought-dis/canopy-1.4.0-full-rh5-64/Canopy_64bit/User/include/python2.7? > > Regards, > > Edward > > > On 26 August 2014 14:57, Troels Emtekær Linnet <[email protected]> wrote: >> 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
