<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Mike,<div><br></div><div>Thank you again for the detailed responses. I'm getting a better handle on what can be done and am trying to implement the workaround you suggested.</div><div>Speaking of which, is the reason that a shared directory location needs to be utilized because readData() does not know to look in the "app task directory" and defaults to the swift script launch directory?</div><div><br></div><div>Thanks again for the guidance,</div><div><br></div><div>Jonathan</div><div><br></div><div><div><div>On Mar 21, 2014, at 8:15 AM, Michael Wilde <<a href="mailto:wilde@anl.gov">wilde@anl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hi Jonathan,<br>
<br>
Thanks for bearing with us on this. I can see clearly where our
documentation is falling short of explaining this clearly.<br>
<br>
Ive got to work on some deadlines today, but I'll see if someone
else on the team can post a clarification with some examples.<br>
<br>
A brief response, below.<br>
<br>
<div class="moz-cite-prefix">On 3/20/14, 9:51 PM, Jonathan Ozik
wrote:<br>
</div>
<blockquote cite="mid:3FD5A438-74FE-418C-822D-229125EA6CDD@uchicago.edu" type="cite">
<pre wrap="">Hi Mike,
I've included my comments below. Also, please let me know if I should sign up for any mailing list in addition to swift-user, which I'm already signed up on.</pre>
</blockquote>
No, just swift-user. Ideally we should he started this discussion
there. I steered you to swift-devel because I thought the issue was
one of a new feature requirement, but I see its also one of
documentation and training.<br>
<br>
...<br>
<blockquote cite="mid:3FD5A438-74FE-418C-822D-229125EA6CDD@uchicago.edu" type="cite">
An app *can* return multiple files - even an array of files - but
not an array of files whose names and count is not known before
the app is launched.
<pre wrap="">This functionality would be exactly what I'd be looking for. If an app can return multiple files I'd just need to know where and how I'd have to specify the patterns for those files (or do I need to know the exact names?)</pre>
</blockquote>
Yes, that's the problem: you would need to know the exact names, in
the Swift script, before the app is called, so that you can *map*
all output file variables to the names that the app will be
*expected* to produce. I.e., current one needs a priori knowledge of
all output file names, and you need to map variable (which can
include array and structure members) to those names.<br>
<blockquote cite="mid:3FD5A438-74FE-418C-822D-229125EA6CDD@uchicago.edu" type="cite">
<pre wrap="">and how to make it so that the app returns those files. I've looked through the user guide and a few of the tutorials but I don't believe I've seen any example that fits this general functionality.
For example, if I have an executable "repast" that outputs files with patterns specified by globs, how do I make use of that knowledge to pick up those files and return them from an app?</pre>
</blockquote>
Thats the current language deficiency: you can not. We will explain
later today in more detail.<br>
<br>
The app is expected to produce all output files that any of its
output variables (or arrays or structures) are mapped to.<br>
<br>
For example, you can map an *ouput* array to the file names f1.out,
f2.out, and f3.out. Then the app will be expected to produce those
files. If it doesnt, Swift will raise a runtime error. So if you
know a prior (before the app is called) from context or from input
aregument values that these 3 files will be produced, you can use
one of the array mappers or the "ext" mapper to declare this
expectation.<br>
<br>
The best way to get past this obstacle (while we develop the desired
capability) is as follows. If you are running on a single machine,
you can write a wrapper shell script around the repast app that runs
repast and then returns a single file that contains a *list* of its
output files. But you need to place these output files in a known
shared directory, not in the current working directory in which
Swift will run the repast app (called the "job directory" at the
moment -- soon to be renamed the "app task directory"). Then you do
a readData() on this returned file to create an array of strings,
and use that array with the "array" mapper (explained in the User
Guide).<br>
<br>
We'll post to you a working example of as soon as possible - today,
if time permits. As well as an example of the proposed new feature.<br>
<br>
- Mike<br>
<blockquote cite="mid:3FD5A438-74FE-418C-822D-229125EA6CDD@uchicago.edu" type="cite">
<pre wrap="">
</pre>
<pre wrap="">I see, the one file per app invocation is probably not going to work for our use case, but I still think that I'm missing some crucial understandings of what conditions are required to point to and use generated or existing files within swift. That is, other than "stdout=@filename", how do I indicate that I'd like to return a file, say "myoutput.dat", from an app invocation? Apologies if this is too simple of a question but, like I said, I feel like I'm missing some crucial information...
</pre>
<blockquote type="cite">
<pre wrap="">What we do not have - but have long known that we need - is the ability to declare that all the files created by a *single* app invocation which match a specified pattern be returned as an array.
Mihael: is this something you could implement in the near future - after we agree on the semantics?
Justin, Tim, do you want to comment on this from a Swift/T perspective?
Thanks,
- Mike
</pre>
<blockquote type="cite">
<pre wrap="">I think I'm stumbling on the notion of what output, in terms of files, can be produced using an "app" element in a swift script. Most of the examples have stdout (or stderr) pointing to a file, but I'm not sure I've found an example where side effects (e.g., files produced by a process) can be retrieved. Is this possible?
Jonathan
On Mar 19, 2014, at 7:03 PM, Michael Wilde <a class="moz-txt-link-rfc2396E" href="mailto:wilde@anl.gov"><wilde@anl.gov></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Jonathan,
You are thinking about this exactly right, and have (quickly) hit one of our programmability weaknesses.
At the moment, there is no good way to do this. We have had much discussion on it, though, and plan to create such "collect files of this pattern into an array" semantics.
What we do for now is one of these two work-arounds:
- write a single tarfile as output (in a wrapper script for the app, which tars files of the appropriate pattern, like "*.simout"
- write the files directly to a specific (shared) directory instead of the Swift "app task directory" (called "job directory" in the current User Guide. Then return a single file with a list of these file names, and map that using an array_mapper if the results need to be passed to a next stage
We should see if we can get a prototype of such a feature to you in short order. But hopefully just to get things working, one of the above methods will suffice for you, for now.
Im cc'ing swift-devel to see what we can do.
Thanks for reminding us of this fairly common need!
- Mike
On 3/19/14, 5:57 PM, Jonathan Ozik wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Mike,
Perhaps I'm not thinking about this correctly, but I'm trying to figure out how to collect output files that are generated by a simulation run. The scenario is that the Repast executable is run and, after it is run, there are files that are output into some location. There can be an arbitrary number of such output files per simulation run but, if necessary, it would be possible to pre-specify which files to look for. Is there a simple way to indicate to swift that it should collect all the files matching a particular pattern within a directory? It looks like the mappers might work here but as far as I understand the mappers are defined prior to calls to executables. Again, I might just not be thinking about this in a "swift" enough way.
Jonathan
</pre>
</blockquote>
<pre wrap="">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
</pre>
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</blockquote>
<pre wrap="">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
</pre>
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<pre wrap=""></pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Michael Wilde
Mathematics and Computer Science Computation Institute
Argonne National Laboratory The University of Chicago
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