Using user defined type

[eogbe]

Hi

I am trying to generate a wrapper for my f90 code using f2py. It works for common types like int, real, etc but when i have user defined type I get the following error:

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 "mc79reorder" sources
creating /tmp/tmpDnh_3K/src.linux-x86_64-2.7
f2py options: []
f2py: mc79sign.pyf
Reading fortran codes...
Reading file 'mc79sign.pyf' (format:free)
Post-processing...
Block: mc79reorder
Block: hsl_mc79_integer
Block: unknown_type
Block: mc79_matching
Post-processing (stage 2)...
Block: mc79reorder
Block: unknown_interface
Block: hsl_mc79_integer
Block: unknown_type
Block: mc79_matching
Building modules...
Building module "mc79reorder"...
Constructing F90 module support for "hsl_mc79_integer"...
Skipping type unknown_type
Creating wrapper for Fortran subroutine "mc79_matching"("mc79_matching")...
Constructing wrapper function "hsl_mc79_integer.mc79_matching"...
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: No C-type found in "{'attrspec': [], 'typename': 'mc79_control', 'intent': ['in'], 'typespec': 'type'}", assuming void.
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).
getctype: No C-type found in "{'attrspec': [], 'typename': 'mc79_control', 'intent': ['in'], 'typespec': 'type'}", assuming void.
getctype: No C-type found in "{'attrspec': [], 'typename': 'mc79_control', 'intent': ['in'], 'typespec': 'type'}", assuming void.
Traceback (most recent call last):
File "/home/eogbe/anaconda2/bin/f2py", line 28, in
main()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 648, in main
run_compile()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 633, in run_compile
setup(ext_modules=[ext])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 327, in build_extension_sources
sources = self.f2py_sources(sources, ext)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 544, in f2py_sources
+ ['--build-dir', target_dir, source])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 440, in run_main
ret = buildmodules(postlist)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 384, in buildmodules
dict_append(ret[mnames[i]], rules.buildmodule(modules[i], um))
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/rules.py", line 1211, in buildmodule
mr, wrap = f90mod_rules.buildhooks(m)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f90mod_rules.py", line 202, in buildhooks
api, wrap = rules.buildapi(b)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/rules.py", line 1368, in buildapi
vrd = capi_maps.sign2map(a, var[a])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/capi_maps.py", line 603, in sign2map
ret['pydocsign'], ret['pydocsignout'] = getpydocsign(a, var)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/capi_maps.py", line 412, in getpydocsign
sig = '%s : %s %s%s' % (a, opt, c2py_map[ctype], init)
KeyError: 'void'

Is there any work around derived data types? I 'm using f2py with gfortran and python 2.7 on centOS.
Emmanuel

[pearu]

The solution is provided in
https://sysbio.ioc.ee/projects/f2py2e/FAQ.html#q-what-if-fortran-90-code-uses-type-spec-kind-kind

[mattip]

Maybe we could catch the KeyError and provide a more helpful error message?

[eogbe]

@pearu Could you please elaborate using the sample I have below?

MODULE example
  IMPLICIT NONE
  PRIVATE

! ---------------------------------------------------
! Derived type definitions
! ---------------------------------------------------
TYPE, PUBLIC :: userdefined
INTEGER :: lp = 6
INTEGER :: mp = 6
END TYPE mc79_control

  PUBLIC hsl
CONTAINS

  SUBROUTINE hsl(m,n,ptr,row,rowmatch,colmatch,control)
    INTEGER (userdefined), INTENT (IN) :: m
    INTEGER (userdefined), INTENT (IN) :: n
    INTEGER (userdefined), INTENT (IN) :: ptr(n+1)
    INTEGER (userdefined), INTENT (IN) :: row(:)
    INTEGER (userdefined), INTENT (OUT) :: rowmatch(m)
    INTEGER (userdefined), INTENT (OUT) :: colmatch(n)
    TYPE (userdefined), INTENT (IN) :: control
    lp = control%lp
    mp = control%mp
  END SUBROUTINE hsl
END MODULE example

How do I generate the fortran to c map for this?
Emmanuel

[pearu]

Try create a file
/home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap
with the following content:
{'integer':{'userdefined':'int'}}

Btw, shouldn't
END TYPE mc79_control
be
END TYPE userdefined
?

[eogbe]

Yes my bad. It is "end userdefined" in my code.

How do i call the code after creating .f2py_f2cmap? f2py -m mc79reorder -h hsl_79.pyf example.f90 .f2py_f2cmap didn't seem to work.

[pearu]

I used message

getctype: "integer(kind=myint_mc79)" is mapped to C "int" (to override define dict(integer = dict(myint_mc79="")) in /home/eogbe/Documents/solvers/hslcodes/hsl_mc79-1.1.0/src/test/newtest/.f2py_f2cmap file).

as a hint for the proper .f2py_f2cmap location.

When you created the .f2py_f2cmap, were there any effect? Were there any changes in error messages, for instance?

("Does not seem to work" is not really useful for giving useful feedback.)

[eogbe]

Running f2py -m mc79reorder -h hsl_79.pyf example.f90 .f2py_f2cmap I get the output:

Reading .f2py_f2cmap ...
Mapping "integer(kind=userdefined)" to "int"
Successfully applied user defined changes from .f2py_f2cmap
Reading fortran codes...
Reading file 'example.f90' (format:free)
Line #9 in example.f90:" TYPE, PUBLIC :: userdefined"
analyzeline: No name/args pattern found for line.
Reading file '.f2py_f2cmap' (format:free)
Post-processing...
Block: mc79reorder
Block: example
Block: unknown_type
Block: hsl
Post-processing (stage 2)...
Block: mc79reorder
Block: unknown_interface
Block: example
Block: unknown_type
Block: hsl
Saving signatures to file "./hsl_79.pyf"
{'attrspec': ['private', 'public']}
In: :mc79reorder:example.f90:example
vars2fortran: No typespec for argument "hsl".

It successfully applies the user defined changes but still reports "no typespec" for "hsl"
When i tried to create the .so file with the command "f2py -c --fcompiler=gnu95 hsl_79.pyf example.f90 .f2py_f2cmap" i get the "getctype: no c type found " error as before (without using .f2py_f2cmap):

Reading .f2py_f2cmap ...
Mapping "integer(kind=userdefined)" to "int"
Successfully applied user defined changes from .f2py_f2cmap
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 "mc79reorder" sources
creating /tmp/tmpTCBdVF/src.linux-x86_64-2.7
f2py options: []
f2py: hsl_79.pyf
Reading fortran codes...
Reading file 'hsl_79.pyf' (format:free)
Post-processing...
Block: mc79reorder
Block: example
Block: unknown_type
Block: hsl
Post-processing (stage 2)...
Block: mc79reorder
Block: unknown_interface
Block: example
Block: unknown_type
Block: hsl
Building modules...
Building module "mc79reorder"...
Constructing F90 module support for "example"...
Skipping type unknown_type
Creating wrapper for Fortran subroutine "hsl"("hsl")...
Constructing wrapper function "example.hsl"...
getctype: No C-type found in "{'attrspec': [], 'typename': 'userdefined', 'intent': ['in'], 'typespec': 'type'}", assuming void.
getctype: No C-type found in "{'attrspec': [], 'typename': 'userdefined', 'intent': ['in'], 'typespec': 'type'}", assuming void.
getctype: No C-type found in "{'attrspec': [], 'typename': 'userdefined', 'intent': ['in'], 'typespec': 'type'}", assuming void.
Traceback (most recent call last):
File "/home/eogbe/anaconda2/bin/f2py", line 28, in
main()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 648, in main
run_compile()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 633, in run_compile
setup(ext_modules=[ext])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build.py", line 47, in run
old_build.run(self)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/command/build.py", line 127, in run
self.run_command(cmd_name)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/eogbe/anaconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 148, in run
self.build_sources()
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 165, in build_sources
self.build_extension_sources(ext)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 327, in build_extension_sources
sources = self.f2py_sources(sources, ext)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/distutils/command/build_src.py", line 544, in f2py_sources
+ ['--build-dir', target_dir, source])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 440, in run_main
ret = buildmodules(postlist)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f2py2e.py", line 384, in buildmodules
dict_append(ret[mnames[i]], rules.buildmodule(modules[i], um))
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/rules.py", line 1211, in buildmodule
mr, wrap = f90mod_rules.buildhooks(m)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/f90mod_rules.py", line 202, in buildhooks
api, wrap = rules.buildapi(b)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/rules.py", line 1368, in buildapi
vrd = capi_maps.sign2map(a, var[a])
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/capi_maps.py", line 603, in sign2map
ret['pydocsign'], ret['pydocsignout'] = getpydocsign(a, var)
File "/home/eogbe/anaconda2/lib/python2.7/site-packages/numpy/f2py/capi_maps.py", line 412, in getpydocsign
sig = '%s : %s %s%s' % (a, opt, c2py_map[ctype], init)
KeyError: 'void'

There is something i am doing wrong i think.

[pearu]

The problems is in argument control:

TYPE (userdefined), INTENT (IN) :: control

f2py currently does not support wrapping functions with derived type arguments.

[eogbe]

That's what i initially thought. I was thinking there was a way around it or any suggestions to help me accomplish my task.

Thanks,
Emmanuel

[lamorton]

The solution is provided in
https://sysbio.ioc.ee/projects/f2py2e/FAQ.html#q-what-if-fortran-90-code-uses-type-spec-kind-kind

This link is dead.

[pearu]

The relevant piece of documentation can be found in github history, for instance:
https://github.com/numpy/numpy/blob/a859492c7b07dac0a56d9a08d6739e006a528f87/numpy/f2py/docs/FAQ.txt#L258

[cuijie-nano]

@pearu Could you please elaborate using the sample I have below?
`module example
implicit none

!----------------------------------
! type define
!----------------------------------

type array_car
    integer :: N1, N2, N3
    complex(kind=8), allocatable :: c_1d(:)
    real(kind=8), allocatable :: r_1d(:)
    integer,allocatable :: i_1d(:)
end type array_car

subroutine construct_qlist(e)
implicit none
type(array_car) :: out
real(kind=8) :: t(3,3),tt(3,3), q1(3), q2(3)
end subroutine hsl
end module example
`