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

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Ben Ward
Ben Ward on 24 Jul 2012
Edited: Walter Roberson on 29 Nov 2015
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
Ben Ward on 24 Jul 2012
Edited: Ben Ward on 24 Jul 2012
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
Ben Ward on 24 Jul 2012
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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Accepted Answer

Ben Ward
Ben Ward on 14 Aug 2012
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
Sönke on 18 Sep 2012
Edited: Sönke on 18 Sep 2012
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
Natalie on 11 Mar 2014
Edited: Natalie on 11 Mar 2014
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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More Answers (1)

Walter Roberson
Walter Roberson on 24 Jul 2012
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Ben Ward
Ben Ward on 24 Jul 2012
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
Walter Roberson on 24 Jul 2012
Interesting work-around.

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