system command in parfor loop

2022 1 17
1 个回答
更新时间：2022 1 26
7 次查看（30 天）

0 个投票

I am invoking a C++ executable from the Matlab command prompt.
Interactively, it goes like this:
>> [status,cmdout] = system('multi.exe','-echo')
Input unique file identifier. Ex: 2~04-13-013939 - 2~11-30-091444
And this works fine.
However, I need to invoke the C++ executable multiple times. So I created a parfor loop, like so:
parpool
tic
parfor i=1:nfiles
[status,cmdout] = system('multi.exe','-echo')
str3{i,1}
end
where str3 is a series of inputs:
str3 =
14×1 cell array
{'1~11-24-054646'}
{'1~11-24-095017'}
{'1~11-29-060908'}
{'1~11-29-101743'}
{'1~11-30-091225'}
{'2~11-24-055554'}
{'2~11-24-100903'}
{'2~11-29-060541'}
{'2~11-29-101814'}
{'2~11-30-091444'}
{'3~11-24-055933'}
{'3~11-29-101847'}
{'4~11-24-060505'}
{'4~11-29-101935'}
This ran for over 54 hours, but the task never completed, and I eventually hit Ctrl-C.
Any thoughts/ feedback?

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Mario Malic
Mario Malic 2022-1-17
Check this out. Parfor worked fine for me using Sysem.Diagnostics.Process.
https://www.mathworks.com/matlabcentral/answers/583955-get-the-status-using-system-command-when-program-has-been-closed#answer_485480
In order to relay the messages from workers in parpool, there are functions which I don't remember the name exactly. Check out this example https://www.mathworks.com/help/parallel-computing/parallel.pool.dataqueue.html
jessupj
jessupj 2022-1-17
编辑：jessupj 2022-1-17
just to play devil's advocate, i've approached a similar problem in the past by calling parallel instances of matlab from the shell. it was by no means the most I/O-efficient method and wasted a lot of time opening and closing matlab & pooling. the individual system jobs were geophysical models that took O(days) so the data importing and pool opening overhead was comparatively insignificant.

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回答（1 个）

Walter Roberson
Walter Roberson 2022-1-17

0 个投票

parpool
tic
parfor i=1:nfiles
cmd = sprintf('echo "%s" | multi.exe', str3{i,1});
[status,cmdout] = system(cmd, '-echo')
end

12 个评论
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Sujatha
Sujatha 2022-1-18
Sorry that didn't work. Please see attachment.
Sujatha
Sujatha 2022-1-18
This may be pertinent (please see enclosure). Thanks!
Sujatha
Sujatha 2022-1-19
I think I know what the issue is: In interactive mode, I type:
>> [status,cmdout] = system('multi.exe','-echo')
Matlab responds with:
Input unique file identifier. Ex: 2~04-13-013939 -
I then type:
2~11-30-091444 <Return> (Keyboard Return)
In the parfor loop, there is no <Return> (Keyboard Return) after the str3{i,1} input to the parallel processes!
Walter Roberson
Walter Roberson 2022-1-19
Perhaps you need
parpool
tic
parfor i=1:nfiles
cmd = sprintf('(echo "%s" & echo.) | multi.exe', str3{i,1});
[status,cmdout] = system(cmd, '-echo')
end
The period after the echo is important, and must be immediately after the echo with no space.
Sujatha
Sujatha 2022-1-19
No joy!
>> parfor i=1:4
cmd = sprintf('(echo "%s" & echo.) | multi.exe', str3{i,1});
[status,cmdout] = system(cmd, '-echo')
end
'multi.exe' is not recognized as an internal or external command,
operable program or batch file.
'multi.exe' is not recognized as an internal or external command,
operable program or batch file.
'multi.exe' is not recognized as an internal or external command,
operable program or batch file.
'multi.exe' is not recognized as an internal or external command,
operable program or batch file.
Sujatha
Sujatha 2022-1-19
What does:
(echo "4~11-24-060505" & echo.)
do?
Walter Roberson
Walter Roberson 2022-1-19
At the windows COMMAND level,
(echo "4~11-24-060505" & echo.) |
should create an output stream that contains
4~11-24-060505<NEWLINE><NEWLINE>
and make it available as input to the next program in sequence (which here would be multi.exe)
Could you confirm for me that if you hard-code
system('multi.exe', '-echo')
that the program multi runs, but that if you hard-code
system('(echo "4~11-24-060505" & echo.) | multi.exe', '-echo')
that it fails saying it does not know what multi.exe is ?
Sujatha
Sujatha 2022-1-20
Yes, that is true.
The program runs with:
system('multi.exe', '-echo')
The program fails with:
system('(echo "4~11-24-060505" & echo.) | multi.exe', '-echo')
and does not recognize "multi.exe".
Walter Roberson
Walter Roberson 2022-1-20
Well, there is another possibility.
parpool
tic
parfor i=1:nfiles
tname{i} = tempfile();
[fid, msg] = fopen(tname{i});
if fid < 0
error('iteration %d failed to create temporary file "%s" because "%s"', i, tname{i}, msg);
end
fprintf(fid, '%s\n\n', str3{i,1});
fclose(fid)
cmd = sprintf('multi.exe < "%s"', tname{i});
[status,cmdout] = system(cmd, '-echo')
end
Then once you are sure that all of the executables have finished, you can delete all of the files named in tname .
Sujatha
Sujatha 2022-1-26
An UndefinedFunction error was thrown on the workers for 'tempfile'. This might be because the
file containing 'tempfile' is not accessible on the workers. Use addAttachedFiles(pool, files)
to specify the required files to be attached. For more information, see the documentation for
'parallel.Pool/addAttachedFiles'.
Caused by:
Unrecognized function or variable 'tempfile'.
Sujatha
Sujatha 2022-1-26
addAttachedFiles(ans, tempfile), didn't help.
Walter Roberson
Walter Roberson 2022-1-26
parpool
tic
parfor i=1:nfiles
tname{i} = tempname();
[fid, msg] = fopen(tname{i});
if fid < 0
error('iteration %d failed to create temporary file "%s" because "%s"', i, tname{i}, msg);
end
fprintf(fid, '%s\n\n', str3{i,1});
fclose(fid)
cmd = sprintf('multi.exe < "%s"', tname{i});
[status,cmdout] = system(cmd, '-echo')
end

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