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https://github.com/mankoff/gdb_fortran_tools

Tools to help debug Fortran code with gdb - plotting, saving, and Numpy functions.
https://github.com/mankoff/gdb_fortran_tools

debug debugger debugging fortran gdb numpy python

Last synced: 11 days ago
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Tools to help debug Fortran code with gdb - plotting, saving, and Numpy functions.

Host: GitHub
URL: https://github.com/mankoff/gdb_fortran_tools
Owner: mankoff
License: mit
Created: 2024-07-04T14:51:21.000Z (5 months ago)
Default Branch: main
Last Pushed: 2024-10-24T05:49:14.000Z (24 days ago)
Last Synced: 2024-10-24T23:56:43.332Z (24 days ago)
Topics: debug, debugger, debugging, fortran, gdb, numpy, python
Language: Python
Homepage:
Size: 149 KB
Stars: 2
Watchers: 2
Forks: 0
Open Issues: 1
Metadata Files:
- Readme: README.org
- License: LICENSE

Awesome Lists containing this project

README

        
* gdb_fortran_tools

* Table of contents                               :toc_3:noexport:

:PROPERTIES:

:CUSTOM_ID: toc

:END:

- [[#gdb_fortran_tools][gdb_fortran_tools]]

- [[#introduction][Introduction]]

- [[#installation][Installation]]

- [[#usage-example][Usage example]]

- [[#commands][Commands]]

- [[#supported-types][Supported types]]

- [[#warnings][Warnings]]

  - [[#array-indexing][Array indexing]]

  - [[#allocatable-arrays][Allocatable arrays]]

- [[#additional-hints][Additional hints]]

- [[#requirements][Requirements]]

- [[#acknowledgements][Acknowledgements]]

* Introduction

:PROPERTIES:

:CUSTOM_ID: intro

:END:

Support more advanced =gdb= debugging of Fortran code

+ [X] Generic access to many basic numpy array operators: sum, min, max, log10, etc.

+ [X] Access to custom complex on-liners

+ [X] Graphics: plot, imshow, scatter

+ [X] Save data: pickle, CSV

* Installation

:PROPERTIES:

:CUSTOM_ID: install

:END:

#+BEGIN_SRC bash :exports both :results verbatim

git clone https://github.com/mankoff/gdb_fortran_tools

#+END_SRC

Set an environment variable to that location (perhaps in your =.bashrc= or other init script).

#+BEGIN_SRC bash :exports both :results verbatim

export GFT_DIR=/path/to/gdb_fortran_tools

#+END_SRC

Edit your =~/.gdbinit= file to load =gdb_fortran_tools=

#+BEGIN_SRC python

python

import os

import sys

if 'GFT_DIR' not in os.environ:

   print(f'WARNING: environmental var GFT_DIR not found')

else:

   sys.path.insert(0, os.path.expanduser(os.environ['GFT_DIR']))

   try:

      import gdb_fortran_tools

   except:

      print("WARNING: Could not import gdb_fortran_tools")

end

#+END_SRC

* Usage example

:PROPERTIES:

:CUSTOM_ID: example

:END:

With the following code in =example.F90=

#+BEGIN_SRC f90 :exports both :tangle example.F90

program main

  real, allocatable, DIMENSION(:) :: x, y

  real, allocatable, DIMENSION(:,:) :: xy

  INTEGER :: im, jm, i,j

  im = 4

  jm = 5

  

  allocate(x(im))

  allocate(y(jm))

  allocate(xy(im,jm))

  do i=1,im

     x(i) = i

     do j=1,jm

        y(j) = j

        xy(i,j) = x(i)*y(j)

     end do

  end do

  

  print *, x

  print *, y

  print *, xy

end program main

#+END_SRC

Compile it for debugging with

#+BEGIN_SRC bash :exports both :results verbatim

gfortran -g example.F90

#+END_SRC

Run gdb:

#+BEGIN_SRC bash :exports both :results verbatim

gdb ./a.out

start

break 21

continue

# traditional GDB commands

p x

ptype x

# Simple numpy accessors

np sum x

np max y

np log10 xy

# Plots

plot x

imshow xy

logshow xy

plot xy

plot x y(2:5)

scatter x y(2:5)

# arbitrary Python commands

pycmd xy print(_)

pycmd xy np.min(_[np.where(_ != 0)])

pycmd xy [item for item in _.flatten() if (item % 2) == 0]

# save to CSV

savecsv xy.csv xy

#+END_SRC

* Commands

+ Graphical

  + imshow :: Display 2D array using =matplotlib.pyplot.imshow=

  + imshow0 :: Same as =imshow= but set 0 to NaN (colorbar scaling)

  + logshow :: Same as =imshow= but display =np.log10()= of data

  + scatter :: Display scatter plot of two vectors

  + plot3d :: Display 3D plot of 2D array

  + scatter3d :: Display 3D scatter plot

  + hist :: Display histogram of vector

  + fft :: Display FFT of vector

+ Numerical

  + np   :: Call =np.function(variable)= for any numpy function

  + pycmd   :: Run any sequence of valid one-line Python =statements= on variable. Within =statement=, access variable via =_= (underscore)

+ I/O

  + savecsv   :: Save =variable= to =file.csv=

  + savepy   :: Save =variable= to =filename= in Python pickle format

  + save   :: Save =variable= to =file= using numpy =tofile= function

* Supported types

#+BEGIN_SRC f90 :exports both

real*{4,8}, dimension(:), dimension(:,:), dimension(:,:,:)

integer*{4,8}, dimension(:), dimension(:,:), dimension(:,:,:)

logical

#+END_SRC

* Warnings

:PROPERTIES:

:CUSTOM_ID: warn

:END:

** Array indexing

+ Fortran uses 1-based array indexing

+ Python uses 0-based array indexing

** Allocatable arrays

Note: If gdb reports

#+BEGIN_EXAMPLE

(gdb) ptype foo

type = real(kind=8), allocatable (72,0:47)

#+END_EXAMPLE

Then you need to use the syntax =imshow foo(:,:)=

* Additional hints

You can create custom =gdb= commands that build on commands provided here. For example to find the range of an array, add this to your =~/.gdbinit=

#+BEGIN_SRC bash :exports both :results verbatim

define mm

    np min $arg0

    np max $arg0

end            

document mm

    print min and max of an array or vector. Uses gdb_fortran_tools.

end	

#+END_SRC

* Requirements

:PROPERTIES:

:CUSTOM_ID: req

:END:

- GDB >= 7.0

- Python 3

- NumPy

- Matplotlib

* Acknowledgements

:PROPERTIES:

:CUSTOM_ID: ack

:END:

Thanks to [[https://github.com/X-Neon][X-Neon]] and [[https://github.com/X-Neon/gdbplotlib][gdbplotlib]].