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Subject: Re: [OMPI devel] mpirun Produces Extraneous Output
From: Ralph Castain (rhc_at_[hidden])
Date: 2014-06-13 23:38:52


Hi Greg

I've been running your script over and over again with the current 1.8.2 and svn developer's trunk, and I cannot get a failure. It just merrily runs.

Could you tell me how you configured OMPI to get this behavior?

Thanks
Ralph

On Jun 10, 2014, at 11:59 AM, Ralph Castain <rhc_at_[hidden]> wrote:

> Ouch - I'll try to chase it down.I'm unaware of anyone passing a significant amount of data via stdin before, so it's quite possible this has been around for awhile. Normally one avoids that practice.
>
>
> On Jun 10, 2014, at 11:36 AM, Greg Thomsen <gthomsen_at_[hidden]> wrote:
>
>> All,
>>
>> I believe I've found a bug in the I/O forwarding portion of OpenMPI which occasionally causes mpirun to generate additional data on standard output that was not produced by the application being run.
>>
>> The application in question reads from standard input and writes to standard output only on the rank 0 process. All non-rank 0 processes only participate in computation and do not produce data on standard output. The application is used in standard Unix-like pipelines like so:
>>
>> A | mpirun -np 4 application | B
>>
>> Since B is looking for structured input, it is sensitive to additional data being generated.
>>
>> While chasing down the source of this problem, I've observed the following:
>>
>> * The problem is sensitive to timing. Using strace to figure out where
>> the problem lies can easily hide it. Either of the following would
>> change how the issue was expressed:
>>
>> A | mpirun -np 4 strace -o output.txt -e read,write application | B
>> A | strace -ff -o output.txt -e read,write mpirun -np 4 application
>> | B
>>
>> While harder to state definitively, redirecting in from file and out
>> to file, rather than through pipes, also appears to hide the problem.
>> Since the workflow in question has large volumes of data, using
>> file-based I/O isn't feasible and wasn't thoroughly explored during
>> testing.
>>
>> * It appears to be correlated to a short I/O operation. A short read
>> from application's standard output maps to the first byte of the
>> extraneous output sent to B. Looking at hex dumps indicates that the
>> contents of a recent buffer are inadvertently written to B.
>>
>> The attached text case can show this.
>>
>> * This also is an issue for forwarding standard error from the rank 0
>> process. Modifying application so that it only writes to standard
>> error, and then redirecting standard error to standard output in the
>> shell, will still cause the problem:
>>
>> A | mpirun -np 4 application 2>&1 | B
>>
>> * This seems to only occur at the end of the data stream. The pipeline
>> in question works through records and if it occurred earlier than the
>> last, it would be noticed. The conditions where it was seen
>> regularly always pointed to the end of the data stream.
>>
>> The attached shell script reproduces the problem in every version of OpenMPI tested (1.5.0, 1.6.3, 1.7.4, and 1.8.1). Without any arguments, it reads a fixed amount of data from /dev/zero and then compares the size of the output from the above pipeline. For versions exhibiting the bug, and the above conditions, the problem should be seen within the first ~20 attempts. For other conditions I've seen the script run for a week without problem.
>>
>> With an input path, it reads the first 1,000,000 bytes from the path supplied. With a fixed pattern in the data (see the compressed test input), it is easy to see that the extra data generated is a copy from earlier in the data stream.
>>
>> Hopefully this gets someone in the right section of the code. Let me know if additional information is needed.
>>
>> Thanks!
>>
>> Greg
>> <mpi_test_input.bz2><mpi-test.sh>_______________________________________________
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>> Link to this post: http://www.open-mpi.org/community/lists/devel/2014/06/14999.php
>