[Numpy-discussion] f2py is not recognizing Absoft Fortran Compiler
I'm attempting to build an interface between a Fortran application I have and Python. The problem I'm having is that f2py is not recognizing my Absoft Fortran compiler. Details follow. I'm running on a iMacPro (2017) under Mac OS X Mojave (ver. 10.14.4). The version of the Absoft Compiler I'm running is 19.0.0. I'm using the Anaconda distribution of Python 3, version 3.6.8, where the version of NumPy used is ver. 1.16.3. The commands I'm using to build the Python interface function and there results are: f2py -m DIVA_EphGen_f77 -h DIVA_EphGen_f77.pyf DIVA_EphGen_f77.f --overwrite-signature (base) Samuels-Mac-Pro:2nd_ODE_auto_deriv_cleanup_Rev-07 user$ ./BuildMe_Part-1.sh Reading fortran codes... Reading file 'DIVA_EphGen_f77.f' (format:fix,strict) Post-processing... Block: DIVA_EphGen_f77 Block: diva_ephgen_f77 Post-processing (stage 2)... Saving signatures to file "./DIVA_EphGen_f77.pyf" (base) Samuels-Mac-Pro:2nd_ODE_auto_deriv_cleanup_Rev-07 user$ f2py -c --fcompiler=absoft DIVA_EphGen_f77.pyf DIVA_EphGen_f77.f \ --f77exec=/Applications/Absoft19.0/bin/af77 \ -L/Users/user/2nd_ODE_auto_deriv_cleanup_Rev-07/ -lDIVA_EphGen \ -L/Volumes/Development/AstrodynamicsLib/MacOSX.NAIF.Fortran.v65/toolkit-64-bit/lib/ -lspicelib \ -L/Volumes/Development/AstrodynamicsLib/MacOSX.NAIF.Fortran.v65/toolkit-64-bit/lib/ -lsupport \ -L/Application/Absoft19.0/lib64/ -lblas \ -L/Application/Absoft19.0/lib64/ -lAbsoftlapack \ --verbose (base) Samuels-Mac-Pro:2nd_ODE_auto_deriv_cleanup_Rev-07 user$ ./BuildMe_Part-2.sh running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "DIVA_EphGen_f77" sources creating /var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6 f2py options: [] f2py: DIVA_EphGen_f77.pyf Reading fortran codes... Reading file 'DIVA_EphGen_f77.pyf' (format:free) Post-processing... Block: DIVA_EphGen_f77 Block: diva_ephgen_f77 Post-processing (stage 2)... Building modules... Building module "DIVA_EphGen_f77"... Constructing wrapper function "diva_ephgen_f77"... diva_ephgen_f77(cmdline,scale_factor) Wrote C/API module "DIVA_EphGen_f77" to file "/var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6/DIVA_EphGen_f77module.c" adding '/var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6/fortranobject.c' to sources. adding '/var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6' to include_dirs. copying /Users/user/anaconda3/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.c -> /var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6 copying /Users/user/anaconda3/lib/python3.6/site-packages/numpy/f2py/src/fortranobject.h -> /var/folders/65/7cxpqns144q6wx5lyb7zcyh8gq/T/tmpkv4x9yg7/src.macosx-10.9-x86_64-3.6 build_src: building npy-pkg config files running build_ext new_compiler returns customize UnixCCompiler customize UnixCCompiler using build_ext preprocessor = ['x86_64-apple-darwin13.4.0-clang', '-E', '-D_FORTIFY_SOURCE=2', '-mmacosx-version-min=10.9'] compiler = ['x86_64-apple-darwin13.4.0-clang', '-DNDEBUG', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O2', '-pipe', '-D_FORTIFY_SOURCE=2', '-mmacosx-version-min=10.9'] compiler_so = ['x86_64-apple-darwin13.4.0-clang', '-DNDEBUG', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O2', '-pipe', '-D_FORTIFY_SOURCE=2', '-mmacosx-version-min=10.9'] compiler_cxx = ['x86_64-apple-darwin13.4.0-clang++'] linker_so = ['x86_64-apple-darwin13.4.0-clang', '-bundle', '-undefined', 'dynamic_lookup', '-Wl,-pie', '-Wl,-headerpad_max_install_names', '-Wl,-rpath,/Users/user/anaconda3/lib', '-L/Users/user/anaconda3/lib', '-Wl,-pie', '-Wl,-headerpad_max_install_names', '-Wl,-rpath,/Users/user/anaconda3/lib', '-L/Users/user/anaconda3/lib', '-Wl,-export_dynamic', '-Wl,-pie', '-Wl,-headerpad_max_install_names', '-Wl,-dead_strip_dylibs', '-march=core2', '-mtune=haswell', '-mssse3', '-ftree-vectorize', '-fPIC', '-fPIE', '-fstack-protector-strong', '-O2', '-pipe', '-D_FORTIFY_SOURCE=2', '-mmacosx-version-min=10.9'] linker_exe = ['x86_64-apple-darwin13.4.0-clang'] archiver = ['/Users/user/anaconda3/bin/x86_64-apple-darwin13.4.0-ar', 'rc'] ranlib = ['ranlib'] libraries = [] library_dirs = [] inclu
Re: [Numpy-discussion] f2py is not recognizing Absoft Fortran Compiler
On April/27/2019 21:59:37, Charles R Harris wrote: On Sat, Apr 27, 2019 at 7:40 PM Samuel Dupree <mailto:sdup...@speakeasy.net>> wrote: I'm attempting to build an interface between a Fortran application I have and Python. The problem I'm having is that f2py is not recognizing my Absoft Fortran compiler. Details follow. I'm running on a iMacPro (2017) under Mac OS X Mojave (ver. 10.14.4). The version of the Absoft Compiler I'm running is 19.0.0. I'm using the Anaconda distribution of Python 3, version 3.6.8, where the version of NumPy used is ver. 1.16.3. The commands I'm using to build the Python interface function and there results are: Can you run the compiler in the console and show the `-V` (version) output? The distutils absoft compiler code looks really old and many things could have changed. Chuck ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion Chuck, Thank you for replying to my post. Below is the result of running the Absoft Compiler with the -V option: (base) Samuels-Mac-Pro:2nd_ODE_auto_deriv_cleanup_Rev-07 user$ f77 -V Absoft Pro Fortran 19.0.0 ERROR: No input files. (base) Samuels-Mac-Pro:2nd_ODE_auto_deriv_cleanup_Rev-07 user$ Sam Dupree. ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Attempting to wrap a Fortran-77 subroutine using f2py but I haven't been able to understand what is causing the error
I'm attempting to wrap a Fortran-77 source member using f2py. I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro (2019) under Mac OS X Catalina (ver. 10.15.6). The version of NumPy I'm running is 1.18.3. I've attached a copy of the Fortran source code to this note (see rkfn78.for). The command I'm using to wrap this code is f2py3 -c rkfn78.for --fcompiler=gfortran --f77flags="-c -O -Wall" -m rkfn78 The output I get is captured in the file rkfn78_build_output.txt. I don't understand the cause behind the error message I get, so any advice would be welcomed. Sam Dupree. SUBROUTINE rkfn78( N, FCN, X, Y, YP, XEND, EPS, HMAX, H ) C -- C C RKFN78 ( N, FCN, X, Y, YP, XEND, EPS, HMAX, H ) C C Numerical solution of a system of second order C ordinary differential equations y"=f(x,y,dy) C This is an embedded nystroem method of order 7(8) C due to Fehlberg with stepsize control C C input parameters C C N dimension of the system (N.LE.51) C FCN name (external) of subroutine computing the C second derivative F(X,Y,DY): CSUBROUTINE FCN(X,Y,DY,F) CREAL*8 X,Y(N),DY(N),F(N) CF(1)=... ETC. C X initial x-value C XENDfinal x-value (XEND.GT.X) C Y(N)initial values for y C YP(N) initial values for y' C EPS local tolerance C HMAXmaximal stepsize C H initial stepsize guess C C output parameters C - C Y(N)solution at xend C YP(N) derivative of solution at xend C C COMMON STAT can be used for statistics CNFCN number of function evaluations CNSTEP number of computed steps CNACCPTnumber of accepted steps CNREJCTnumber of rejected steps C C Ref.: Erwin Fehlberg, Computing 14, p.371, 1975 C -- C23456789012345678901234567890123456789012345678901234567890123456789012 implicit none ! I/O list INTEGER*4 N REAL*8 X, Y(N), YP(N), XEND, EPS, HMAX, H ! method related constants INTEGER*4 N_STAGE, P PARAMETER ( N_STAGE=13, P=7 ) ! implementation dependant constants INTEGER*4 N_MAX, MAX_STEPS REAL*8 UROUND PARAMETER ( N_MAX=180, MAX_STEPS=2147483647, UROUND=1.1D-16 ) ! auxiliary variables REAL*8K ( 1:N_MAX, 0:N_STAGE ) REAL*8Y1 ( 1:N_MAX ), YP1 ( 1:N_MAX ), TE ( 1:N_MAX ) REAL*8POSNEG, HNEW, DENOM, ERR, FAC, H2, SUM, SUMP INTEGER I_STAGE, I, J, L LOGICAL REJECT ! coefficients REAL*8 ALPHA_(1:13), BETA_(1:13,0:12), GAMMA_(1:13,0:12) COMMON /CRKFN78/ ALPHA_, BETA_, GAMMA_ ! statistics INTEGER*4 NFCN,NSTEP,NACCPT,NREJCT COMMON/STAT/ NFCN,NSTEP,NACCPT,NREJCT Cf2py intent(in) N, FCN, X, XEND Cf2py intent(inout) Y, YP, HMAX, H, EPS Cf2py depend(in) Y, YP ! initial preparations IF (ALPHA_(13).NE.1.0D0) THEN CALL FN78INI END IF POSNEG = SIGN ( 1.0D0, XEND-X) HMAX = ABS(HMAX) H = MIN ( MAX(1.0D-8,ABS(H)) , HMAX ) H = SIGN ( H, POSNEG ) EPS= MAX ( EPS, 9.0*UROUND ) REJECT = .FALSE. NFCN = NFCN + 1 CALL FCN ( X, Y, YP, K(1,0) ) ! basic integration step DO WHILE ( POSNEG*(X-XEND)+UROUND .LE. 0.0 ) ! failure exit IF ( NSTEP.GT.MAX_STEPS .OR. X+0.05*H.EQ.X ) THEN WRITE (*,*) 'Exit of RKNF78 at x = ', X WRITE (*,*) 'NSTEP = ', NSTEP WRITE (*,*) 'MAX_STEPS = ', MAX_STEPS WRITE (*,*) 'H = ', H WRITE (*,*) 'X+0.05*H = ', X+0.05*H STOP END IF ! limit step size IF ( (X+H-XEND)*POSNEG .GT. 0.0 ) THEN H = XEND-X END IF H2= H**2 NSTEP = NSTEP+1 ! calculate K(*,1) .. K(*,N_STAGE) DO I_STAGE = 1,N_STAGE DO L=1,N SUM = 0.0 SUMP = 0.0 DO J=0,(I_STAGE-1) SUM = SUM + GAMMA_(I_STAGE,J)*K(L,J) SUMP = SUMP + BETA_ (I_STAGE,J)*K(L,J) END DO Y1(L) = Y(L) + ALPHA_(I_STAGE)*H*YP(L) + H2*SUM YP1(L) = YP(L) + H*SUMP END DO CALL FCN( X + ALPHA_(I_STAGE)*H, Y1, YP1, K(1,I_STAGE) ) END DO ! end of loop over stages NFCN = NFCN+N_STAGE ! error term and relative error estimation DO L=1,N TE(L) = GAMMA_(N_STAGE,N_STAGE-1) * H2 . * ( K(L,N_STAGE-1) - K(L,N_STAGE) ) END DO ERR = 0.0 DO L=1,N DENOM = MAX ( 1.0D-6, ABS(Y(L)), ABS(Y1(L)), 2.0*UROUND/EPS ) ERR = ERR + ( TE(L) / DE
Re: [Numpy-discussion] Attempting to wrap a Fortran-77 subroutine using f2py but I haven't been able to understand what is causing the error
Melissa, Thank you for answering my post. I made the changes you recommended and the code compiles successfully. But I do have one question. The arrays being passed in the CALL to FCN were treated as assumed shaped arrays in the called subroutine. Are assumed shaped arrays a problem for f2py? Sam Dupree. On October/19/2020 09:16:02, Melissa Mendonça wrote: Hello, Sam, sorry for taking so long to answer! The problem seems to be that you are using cf2py depend(in) Y, YP instead of cf2py depend(n) Y, YP <- (note that there was a spurious i in that depend expression) and that the callback FCN needs the dimension n as an argument. I was able to compile your code correctly after making these changes. If you have any further questions let me know, I hope this helps. Cheers, Melissa On Wed, Oct 14, 2020 at 4:03 AM Samuel Dupree <mailto:sdup...@speakeasy.net>> wrote: I'm attempting to wrap a Fortran-77 source member using f2py. I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro (2019) under Mac OS X Catalina (ver. 10.15.6). The version of NumPy I'm running is 1.18.3. I've attached a copy of the Fortran source code to this note (see rkfn78.for). The command I'm using to wrap this code is f2py3 -c rkfn78.for --fcompiler=gfortran --f77flags="-c -O -Wall" -m rkfn78 The output I get is captured in the file rkfn78_build_output.txt. I don't understand the cause behind the error message I get, so any advice would be welcomed. Sam Dupree. ___ NumPy-Discussion mailing list NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org> https://mail.python.org/mailman/listinfo/numpy-discussion <https://mail.python.org/mailman/listinfo/numpy-discussion> ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion -- mail-signature Samuel H. Dupree, jr.sdup...@speakeasy.net 10501 Rising Ridge Road Apartment 201 http://users.speakeasy.net/~sdupree/ Fredericksburg, VA 22407, USA HOME: 540-693-1240 iPhone: 215-530-8753 FAX: 866-514-9629 / "The Greatest Show on Earth" is not on Earth. It's in Space!/ ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Attempting to wrap a Fortran-77 subroutine using f2py but I haven't been able to understand what is causing the error
One more question. Where can I find a documentation on f2py that covers issues like assumed shaped arrays, and issues such as the one discussed in this post? Sam Dupree. On October/19/2020 13:01:13, Melissa Mendonça wrote: Sure, you can use assume-shape arrays, but if you generate a signature file using $ f2py rkfn78.for -m rkfn78 -h rkfn78.pyf you can see that f2py correctly determines n to be the length of the array Y, but since YP also depends on n, that's what generated the error you saw the first time. If you change the .pyf signature file to the one attached to this message, delete your original cf2py lines in the .for file and compile it all using $ f2py -c rkfn78.pyf rkfn78.for --fcompiler=gfortran --f77flags="-c -O -Wall" -m rkfn78 then you'll have no trouble with assumed-shape arrays. Cheers, Melissa On Mon, Oct 19, 2020 at 1:03 PM Samuel Dupree <mailto:sdup...@speakeasy.net>> wrote: > > Melissa, > > Thank you for answering my post. I made the changes you recommended and the code compiles successfully. But I do have one question. The arrays being passed in the CALL to FCN were treated as assumed shaped arrays in the called subroutine. Are assumed shaped arrays a problem for f2py? > > Sam Dupree. > > > On October/19/2020 09:16:02, Melissa Mendonça wrote: > > Hello, Sam, sorry for taking so long to answer! > > The problem seems to be that you are using > > cf2py depend(in) Y, YP > > instead of > > cf2py depend(n) Y, YP <- (note that there was a spurious i in that depend expression) > > and that the callback FCN needs the dimension n as an argument. I was able to compile your code correctly after making these changes. > > If you have any further questions let me know, I hope this helps. > > Cheers, > > Melissa > > > On Wed, Oct 14, 2020 at 4:03 AM Samuel Dupree <mailto:sdup...@speakeasy.net>> wrote: >> >> I'm attempting to wrap a Fortran-77 source member using f2py. I'm >> running he Anaconda distribution for Python 3.7.6 on a Mac Pro (2019) >> under Mac OS X Catalina (ver. 10.15.6). The version of NumPy I'm running >> is 1.18.3. >> >> I've attached a copy of the Fortran source code to this note (see >> rkfn78.for). The command I'm using to wrap this code is >> >> f2py3 -c rkfn78.for --fcompiler=gfortran --f77flags="-c -O -Wall" -m rkfn78 >> >> The output I get is captured in the file rkfn78_build_output.txt. >> >> I don't understand the cause behind the error message I get, so any >> advice would be welcomed. >> >> Sam Dupree. >> ___ >> NumPy-Discussion mailing list >> NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org> >> https://mail.python.org/mailman/listinfo/numpy-discussion <https://mail.python.org/mailman/listinfo/numpy-discussion> > > > ___ > NumPy-Discussion mailing list > NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org> > https://mail.python.org/mailman/listinfo/numpy-discussion <https://mail.python.org/mailman/listinfo/numpy-discussion> > ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Attempting to wrap a Fortran-77 subroutine using f2py but I haven't been able to understand what is causing the error
Melissa,
I've tried working with the documentation hosted at
https://numpy.org/doc/stable/f2py/ <https://numpy.org/doc/stable/f2py/>
and you're right, it is not very complete ;-). So on that front I wish
you the best. Once again, thank you very much for answering my post.
All the best.
Sam Dupree.
On October/19/2020 13:53:03, Melissa Mendonça wrote:
The documentation for f2py is not very complete, I'm afraid. I'll try
to work on that front in the next few months. For now, you can find it
here: https://numpy.org/doc/stable/f2py
<https://numpy.org/doc/stable/f2py>
Cheers,
Melissa
On Mon, Oct 19, 2020 at 2:35 PM Samuel Dupree <mailto:sdup...@speakeasy.net>> wrote:
One more question. Where can I find a documentation on f2py that
covers issues like assumed shaped arrays, and issues such as the
one discussed in this post?
Sam Dupree.
On October/19/2020 13:01:13, Melissa Mendonça wrote:
Sure, you can use assume-shape arrays, but if you generate a
signature file using
$ f2py rkfn78.for -m rkfn78 -h rkfn78.pyf
you can see that f2py correctly determines n to be the length of
the array Y, but since YP also depends on n, that's what
generated the error you saw the first time.
If you change the .pyf signature file to the one attached to this
message, delete your original cf2py lines in the .for file and
compile it all using
$ f2py -c rkfn78.pyf rkfn78.for --fcompiler=gfortran
--f77flags="-c -O -Wall" -m rkfn78
then you'll have no trouble with assumed-shape arrays.
Cheers,
Melissa
On Mon, Oct 19, 2020 at 1:03 PM Samuel Dupree
mailto:sdup...@speakeasy.net>> wrote:
>
> Melissa,
>
> Thank you for answering my post. I made the changes you
recommended and the code compiles successfully. But I do have one
question. The arrays being passed in the CALL to FCN were treated
as assumed shaped arrays in the called subroutine. Are assumed
shaped arrays a problem for f2py?
>
> Sam Dupree.
>
>
> On October/19/2020 09:16:02, Melissa Mendonça wrote:
>
> Hello, Sam, sorry for taking so long to answer!
>
> The problem seems to be that you are using
>
> cf2py depend(in) Y, YP
>
> instead of
>
> cf2py depend(n) Y, YP <- (note that there was a spurious i in
that depend expression)
>
> and that the callback FCN needs the dimension n as an argument.
I was able to compile your code correctly after making these changes.
>
> If you have any further questions let me know, I hope this helps.
>
> Cheers,
>
> Melissa
>
>
> On Wed, Oct 14, 2020 at 4:03 AM Samuel Dupree
mailto:sdup...@speakeasy.net>> wrote:
>>
>> I'm attempting to wrap a Fortran-77 source member using f2py. I'm
>> running he Anaconda distribution for Python 3.7.6 on a Mac Pro
(2019)
>> under Mac OS X Catalina (ver. 10.15.6). The version of NumPy
I'm running
>> is 1.18.3.
>>
>> I've attached a copy of the Fortran source code to this note (see
>> rkfn78.for). The command I'm using to wrap this code is
>>
>> f2py3 -c rkfn78.for --fcompiler=gfortran --f77flags="-c -O
-Wall" -m rkfn78
>>
>> The output I get is captured in the file rkfn78_build_output.txt.
>>
>> I don't understand the cause behind the error message I get,
so any
>> advice would be welcomed.
>>
>> Sam Dupree.
>> ___
>> NumPy-Discussion mailing list
>> NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org>
>> https://mail.python.org/mailman/listinfo/numpy-discussion
<https://mail.python.org/mailman/listinfo/numpy-discussion>
>
>
> ___
> NumPy-Discussion mailing list
> NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org>
> https://mail.python.org/mailman/listinfo/numpy-discussion
<https://mail.python.org/mailman/listinfo/numpy-discussion>
>
___
NumPy-Discussion mailing list
NumPy-Discussion@python.org
https://mail.python.org/mailman/listinfo/numpy-discussion
___
NumPy-Discussion mailing list
NumPy-Discussion@python.org
https://mail.python.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Do not understand what f2py is reporting
Andras, Thank you for respond to my post. I sincerely appreciate it. Following your advice, I replaced "integer * 4" with "integer" and I was able to generate the signature files for gravity_derivs.f. The problem now is generating the signature file for auto_deriv.f90. I agree that f2py has a problem with In: :auto_deriv:auto_deriv.f90:ad_auxiliary get_parameters: got "invalid syntax (, line 1)" on '(/((i,i=j,n), j=1,n)/)' I'm not sure I understand why f2py has a problem with this syntax. Is there documentation that talks to what Fortran77, Fortran 90/95 syntax f2py will and will not accept? Sam Dupree. On November/02/2020 07:22:06, Andras Deak wrote: On Sun, Nov 1, 2020 at 2:33 AM Samuel Dupree wrote: I'm attempting to build wrappers around two Fortran routines. One is a Fortran 77 subroutine (see file gravity_derivs.f) that calls a Fortran 90 package that performs automatic differentiation (see file auto_deriv.f90). I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro (2019) under Mac OS X Catalina (ver. 10.15.6). The version of NumPy I'm running is 1.18.3. The commands I used to attempt the build are contained in the file auto_deriv_build. The messages output by f2py are captured in the file auto_derivs_build_report.txt. I don't understand the cause behind the error messages I got, so any advice would be welcomed. Sam Dupree. Hi Sam, I've got a partial solution. I haven't used f2py yet but at least the error from your first `f2py` call seems straightforward. Near the top: Line #119 in gravity_derivs.f:" integer * 4degree" updatevars: no name pattern found for entity='*4degree'. Skipping. This shows that the fortran code gets parsed as `(integer) (*4degree)`. That can't be right. There might be a way to tell f2py to do this right, but anyway I could make your code compile by replacing every such declaration with `integer * 4 :: degree` etc (i.e. adding double colons everywhere). Once that's fixed your first f2py call raises another error: Fatal Error: Cannot open module file ‘deriv_class.mod’ for reading at (1): No such file or directory I could generate these mod files by manually running `gfortran -c auto_deriv.f90`. After that the .mod files appear and your first `f2py` call will succed. You can now `import gravity_derivs`, but of course this will lead to an error because `auto_deriv` is not available in python. Unfortunately your _second_` f2py` call also dies on `auto_deriv.f90`, with such offending lines: In: :auto_deriv:auto_deriv.f90:ad_auxiliary get_parameters: got "invalid syntax (, line 1)" on '(/((i, i=j,n), j=1,n)/)' I'm guessing that again f2py can't parse that syntax. My hunch is that if you can get f2py to work with `auto_deriv.f90` you should first run that. This should hopefully generate the .mod files after which the second call to `f2py` with `gravity_derivs.f` should work. If `f2py` doesn't generate the .mod files you could at worst run your fortran compiler yourself between the two calls to `f2py`. Cheers, András ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Compilation failures in f2py
Chris, Thank you for responding to my post. I uninstalled and then reinstalled CommandLineTools per your suggestion. I'm still getting the same error. It appears that gcc is not seeing any of the CommandLineTools directories. When I ran the command find /Library/Developer/CommandLineTools/ -name _stdio.h I got: (base) user@Mac-Pro ~ % find /Library/Developer/CommandLineTools/ -name _stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/_stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/xlocale/_stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX11.1.sdk/usr/include/secure/_stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/_stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/xlocale/_stdio.h /Library/Developer/CommandLineTools//SDKs/MacOSX10.15.sdk/usr/include/secure/_stdio.h Any suggestions? Sam Dupree. On January/12/2021 05:11:50, Christopher Albert wrote: Hi Sam, looks like the XCode command line tools containing standard headers are either not installed or updated. Try xcode-select --install or manually download them from https://developer.apple.com/download/more/ <https://developer.apple.com/download/more/> and maybe uninstall/reinstall them in case updates don't work. Check with find /Library/Developer/CommandLineTools/ -name _stdio.h which should give /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/_stdio.h (besides possible older versions of MacOSX) Best, Chris Am Sa., 9. Jan. 2021 um 03:02 Uhr schrieb Samuel Dupree mailto:sdup...@speakeasy.net>>: I'm attempting to wrap a Fortran-77 source member library using f2py. I'm running he Anaconda distribution for Python 3.7.6 on a Mac Pro (2019) under Mac OS X Big Sur (ver. 11.1). The version of Xcode.app I'm running is 12.3. The version of NumPy I'm running is 1.18.3. The errors I'm getting are from header files the compiler can't find as captured in the attached log file. A sample of the kind of errors I'm seeing are captured below. compile options: '-I/var/folders/2r/4bw6nw0x58z0_ybx632_h14mgq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7 -I/Users/user/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/Users/user/opt/anaconda3/include/python3.7m -c' gcc: /var/folders/2r/4bw6nw0x58z0_ybx632_h14mgq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c gcc: /var/folders/2r/4bw6nw0x58z0_ybx632_h14mgq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/fortranobject.c In file included from /opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/syslimits.h:7, from /opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:34, from /Users/user/opt/anaconda3/include/python3.7m/Python.h:11, from /var/folders/2r/4bw6nw0x58z0_ybx632_h14mgq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14: /opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/limits.h:195:61: error: no include path in which to search for limits.h 195 | #include_next /* recurse down to the real one */ | ^ In file included from /Users/user/opt/anaconda3/include/python3.7m/Python.h:25, from /var/folders/2r/4bw6nw0x58z0_ybx632_h14mgq/T/tmp5uemdb2k/src.macosx-10.9-x86_64-3.7/sofapymodule.c:14: /opt/local/lib/gcc10/gcc/x86_64-apple-darwin20/10.2.0/include-fixed/stdio.h:78:10: fatal error: _stdio.h: No such file or directory 78 | #include <_stdio.h> | ^~ compilation terminated. Any suggestions? Sam Dupree. ___ NumPy-Discussion mailing list NumPy-Discussion@python.org <mailto:NumPy-Discussion@python.org> https://mail.python.org/mailman/listinfo/numpy-discussion <https://mail.python.org/mailman/listinfo/numpy-discussion> ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Getting scipy.interpolate.pchip_interpolate to return the first derivative of a pchip interpolation
I'm running SciPy ver. 1.9.3 under Python ver. 3.9.15 on a Mac Pro
(2019) desktop running Mac OSX ver. 13.1 Ventura. The problem I'm having
is getting scipy.interpolate.pchip_interpolate to return the first
derivative of a pchip interpolation.
The test program I'm using is given below (and attached to this note).
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import pchip_interpolate
x_observed = np.linspace(0.0, 360.0, 51)
y_observed = np.sin(np.pi*x_observed/180)
dydx_observed = np.cos(np.pi*x_observed/180)
x = np.linspace(min(x_observed), max(x_observed), num=100)
y = pchip_interpolate(x_observed, y_observed, x, der=0, axis=0)
dydx = pchip_interpolate(x_observed, y_observed, x, der=1, axis=0)
plt.plot(x_observed, y_observed, "bo" , label="observation funct")
plt.plot(x_observed, dydx_observed, "rx" , label="observation deriv")
plt.plot(x , y , "c-", label="pchip interpolation funct")
plt.plot(x , dydx , "k-", label="pchip interpolation deriv")
plt.legend()
plt.savefig("pchip_example_01.png")
plt.show()
The program generates values of the sine function (y_observed) over the
range of 0 to 360 degrees. (x_observed). In a similar fashion, the
cosine function (first derivative of the sine function) is generated
over the same range (dydx_observed). pchip_interpolate is used to
perform the interpolation over a specified range for the function and
its first derivative. A composite plot is generated showing the points
for the function (the sine) and its first derivative (cosine). The
interpolated points overlay the function (sine) as expected. However,
the first derivative returned fails to overlay the cosine function. The
plot is attached to this note.
Any thoughts or suggestions?
Sam Dupree
#!/Users/user/opt/anaconda3/bin/python3
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import pchip_interpolate
x_observed = np.linspace(0.0, 360.0, 51)
y_observed = np.sin(np.pi*x_observed/180)
dydx_observed = np.cos(np.pi*x_observed/180)
x= np.linspace(min(x_observed), max(x_observed), num=100)
y= pchip_interpolate(x_observed, y_observed, x, der=0, axis=0)
dydx = pchip_interpolate(x_observed, y_observed, x, der=1, axis=0)
plt.plot(x_observed,y_observed, "bo" , label="observation funct")
plt.plot(x_observed, dydx_observed, "rx" , label="observation deriv")
plt.plot(x , y, "c-", label="pchip interpolation funct")
plt.plot(x , dydx , "k-", label="pchip interpolation deriv")
plt.legend()
plt.savefig("pchip_example_01.png")
plt.show()
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[Numpy-discussion] Re: Getting scipy.interpolate.pchip_interpolate to return the first derivative of a pchip interpolation
I believe I know what is going on, but I don't understand why.
The line for the first derivative that failed to coincide with the
points in the plot for the cosine is actually the interpolated first
derivative scaled by the factor pi/180. When I multiply the interpolated
values for the first derivative by 180/pi, the interpolated first
derivative coincides with the points for the cosine as expected.
What I don't understand is how the interpolator came up with the scale
factor it did and applied it using pure numbers.
Any thoughts?
Sam Dupree.
On 1/21/23 18:04, Samuel Dupree wrote:
I'm running SciPy ver. 1.9.3 under Python ver. 3.9.15 on a Mac Pro
(2019) desktop running Mac OSX ver. 13.1 Ventura. The problem I'm
having is getting scipy.interpolate.pchip_interpolate to return the
first derivative of a pchip interpolation.
The test program I'm using is given below (and attached to this note).
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import pchip_interpolate
x_observed = np.linspace(0.0, 360.0, 51)
y_observed = np.sin(np.pi*x_observed/180)
dydx_observed = np.cos(np.pi*x_observed/180)
x = np.linspace(min(x_observed), max(x_observed), num=100)
y = pchip_interpolate(x_observed, y_observed, x, der=0, axis=0)
dydx = pchip_interpolate(x_observed, y_observed, x, der=1, axis=0)
plt.plot(x_observed, y_observed, "bo" , label="observation funct")
plt.plot(x_observed, dydx_observed, "rx" , label="observation deriv")
plt.plot(x , y , "c-", label="pchip interpolation
funct")
plt.plot(x , dydx , "k-", label="pchip interpolation
deriv")
plt.legend()
plt.savefig("pchip_example_01.png")
plt.show()
The program generates values of the sine function (y_observed) over
the range of 0 to 360 degrees. (x_observed). In a similar fashion, the
cosine function (first derivative of the sine function) is generated
over the same range (dydx_observed). pchip_interpolate is used to
perform the interpolation over a specified range for the function and
its first derivative. A composite plot is generated showing the points
for the function (the sine) and its first derivative (cosine). The
interpolated points overlay the function (sine) as expected. However,
the first derivative returned fails to overlay the cosine function.
The plot is attached to this note.
Any thoughts or suggestions?
Sam Dupree
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