! or system() or unix() - input redirection

Question

Ben Ward 2012-7-24

2
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/44388-or-system-or-unix-input-redirection

编辑： Walter Roberson 2015-11-29

I am trying to execute a system command from within Matlab (there is no input or output from/to Matlab, I just need it to call the program and wait).

./forward < input

This works fine in a bash terminal (MACI64), but not from Matlab. I have tried,

!./forward < input

system('./forward < input')

and

unix('./forward < input')

Each time, the input file is ignored.

(I also tried making a shell script containing the full command, but the extra input was still ignored. Also, if I change the name of the input file to one that doesn't exist (e.g. input_null, I get the following error: "/bin/bash: input_null: No such file or directory")

Is there any way to make this work?

thanks.

PS, simpler commands like

!grep -i string < input

work fine from Matlab

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Ben Ward 2012-7-24

编辑：Ben Ward 2012-7-24

It was: gfortran 4.8.0

BTW: to get it to just compile and run without the input file, I had to add to update the path in /Applications/MATLAB_R2012a.app/bin/matlab ...

export PATH=/Library:/opt/local/bin:/opt/local/sbin:$PATH

export PATH=$PATH:/usr/local/bin:/usr/X11/bin:/usr/texbin

and remove the default fortran libraries from /Applications/MATLAB_R2012a.app/sys/os/maci64/

Ben Ward 2012-7-24

在 MATLAB Online 中打开

Here is the file used to read the input file...

      module io_mod
      integer driver_ref,shift_obs
      contains
      subroutine driver_init
      use piped_mod
!-----------------------------------------------------------------------
      CHARACTER(LEN=255) :: message           ! use for I/O error messages
      integer, parameter :: stdin=5
!
      namelist /driver_io_nml/
     & site,
     & latitude,
     & physics_dir,
     & eco_dir,
     & physics_mod,
     & output_dir,
     & year1,
     & eval_input,
     & eval_output,
     & n_eval,
     & twin,
     & startelite
!
!-----------------------------------------------------------------------
!   default namelist settings
!-----------------------------------------------------------------------
      site        = 'BATS'
      latitude    = 32.1667
      physics_dir = '../../data/phys_data'
      eco_dir     = '../../data/eco_data'
      physics_mod = 'OCCAM'
      output_dir  = '../output'
      year1       = 1990
      eval_input  = 'hypercube.dat'
      eval_output = 'hypercost.dat'
      n_eval      = 1
      twin        = 0
      startelite  = 0
!
      read(unit=stdin, nml=driver_io_nml,iostat=ios,iomsg=message)
      if(iostat.ne.0)then
        write(*,*)'ERROR: ',ios
        write(*,*)message
      endif
!
      end subroutine driver_init
      end module io_mod

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Answer 1

Ben Ward 2012-8-14

4
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/44388-or-system-or-unix-input-redirection#answer_56185

在 MATLAB Online 中打开

Work-around from MathWorks...

Executing a GFORTRAN executable within a Apple terminal window is not equivalent to executing it within MATLAB. In particular, MATLAB will set various environment variables and this can have unexpected results which seems to be the case here.

To work around this issue you need to set your environment variables for the GFORTRAN-compiled programs correctly within MATLAB before you execute them. You can use the SETENV function for this purpose. Please execute your FORTRAN script as follows:

setenv(‘GFORTRAN_STDIN_UNIT’, ‘5’) 
setenv(‘GFORTRAN_STDOUT_UNIT’, ‘6’) 
setenv(‘GFORTRAN_STDERR_UNIT’, ‘0’)
!./forward < input 
setenv(‘GFORTRAN_STDIN_UNIT’, ‘-1’) 
setenv(‘GFORTRAN_STDOUT_UNIT’, ‘-1’) 
setenv(‘GFORTRAN_STDERR_UNIT’, ‘-1’)

Note that after executing the FORTRAN script, I set the environment variables back to their default values.

For more information on the SETENV function, please refer to the following link:

SETENV : http://www.mathworks.com/help/techdoc/ref/setenv.html

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Sönke 2012-9-18

编辑：Sönke 2012-9-18

There is yet another way to get fortran programs to work use the env command and undefine the variables this will kill your standard input and output but matlab restores them anyway, somehow.

env -u GFORTRAN_STDIN_UNIT -u GFORTRAN_STDOUT_UNIT -u GFORTRAN_STDERR_UNIT "command including pipes"

from a script

could work

but putting them into a shell file separately from "command including pipes" will somehow still restore the GFORTRAN_XXX_UNIT environment variables even from within the script ??

Natalie 2014-3-11

编辑：Natalie 2014-3-11

Thanks for the answer! This fixed a similar problem I was having trying to pipe a file into a fortran executable

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Answer 2

Walter Roberson 2012-7-24

0
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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/44388-or-system-or-unix-input-redirection#answer_54444

Please have a look at http://www.mathworks.co.uk/matlabcentral/answers/43640-a-peculiar-problem-when-using-system-command-to-run-a-c-shell-script-from-matlab and at http://www.mathworks.co.uk/matlabcentral/answers/38589-system-or-unix-command-run-compiled-fortran-binary-fails-but-it-runs-fine-from-a-terminal

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Ben Ward 2012-7-24

编辑：Walter Roberson 2015-11-29

在 MATLAB Online 中打开

Hi Walter,

thanks for the suggestions. I'll address the second one first...

I'm on a Mac, so to find the libraries for the executable, I used otool -L. This yielded identical output inside Matlab and the Terminal...

Matlab:

>> !otool -L forward
forward:
  /usr/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)
  /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
  /usr/local/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)

Terminal:

$ otool -L forward
forward:
  /usr/local/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)
  /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
  /usr/local/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)

using echo $DYLD_LIBRARY_PATH instead of echo $LD_LIBRARY_PATH yields nothing in the terminal, but the following in Matlab:

/Applications/MATLAB_R2012a.app/sys/os/maci64:/Applications/MATLAB_R2012a.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2012a.app/bin/maci64:/Applications/MATLAB_R2012a.app/extern/lib/maci64:/Applications/MATLAB_R2012a.app/runtime/maci64

I tried clearing this completely in Matlab, but it made no difference.

Regarding the first suggestion, I'm not sure I fully understand, but I don't think the input is going to STDERR? The read parameter is set to 5, which should equal standard input, but it is quite likely there is something I am missing here.

Ben Ward 2012-7-24

I can hack it to work by copying input to fort.5 before calling the executable. Thanks for the suggestions. If you have a more elegant solution, I would be very glad to hear it. cheers, Ben

Walter Roberson 2012-7-24

Interesting work-around.

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! or system() or unix() - input redirection

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