[Swift-devel] Problems Re: Example of wrapper staging?

[Michael Wilde]

As far as I can tell, when "sh" is the executable, the actual output 
file produced in the job dir is incorrect.

 From what I see so far, it looks like _swiftwrap.wrapperstaging may be 
forming a command line that doesnt work when the app is a "sh -c".

Still digging.

- Mike

On 11/9/14 2:25 PM, Michael Wilde wrote:
> Below is a simpler example of the failing case:
>
> $ hostname
> midway001
>
> # Works with echo as app and wrapperStaging:
>
> $ cat t03.swift
> type file;
>
> app (file o) echo () {
>       echo "hello" stdout=filename(o);
> }
>
> file o <"out.txt">;
>
> o = echo();
> $ cat swift.conf
> wrapperStagingLocalServer: "file://"
>
> app.sh { executable: /bin/sh, maxWallTime: "00:01:00" }
>
> site.local {
>       staging: "wrapper"
>       scratch: "/tmp/wilde/swiftest"
>       workDirectory: "/tmp/wilde/swiftwork"
> }
>
> lazyErrors: false
> executionRetries: 0
> keepSiteDir: true
> alwaysTransferWrapperLog: true
>
>
> $ rm out.txt
>
> # Fails with sh as app and wrapper staging:
>
> $ swift -config swift.conf t03.swift
> Swift trunk git-rev: 7a0c4927380514e4c7166dfd095fd0a4c6389b03
> heads/master 6172
> RunID: run011
> Progress: Sun, 09 Nov 2014 20:20:39+0000
> Final status:Sun, 09 Nov 2014 20:20:40+0000  Finished successfully:1
> $ cat out.txt
> hello
> $ cat t04.swift
> type file;
>
> app (file o) echo () {
>       sh "-c" "/bin/echo hello" stdout=filename(o);
> }
>
> file o <"out.txt">;
>
> o = echo();
> $ swift -config swift.conf t04.swift
> Swift trunk git-rev: 7a0c4927380514e4c7166dfd095fd0a4c6389b03
> heads/master 6172
> RunID: run012
> Progress: Sun, 09 Nov 2014 20:21:09+0000
> Final status:Sun, 09 Nov 2014 20:21:09+0000  Finished successfully:1
> $ cat out.txt
>
> $ ls -l out.txt
> -rw-rw-r-- 1 wilde wilde 1 Nov  9 14:21 out.txt
> $ od -x out.txt
> 0000000 000a
> 0000001
>
> # Works with sh as app and default staging:
>
> $ swift -config swift.conf.nows t04.swift
> Swift trunk git-rev: 7a0c4927380514e4c7166dfd095fd0a4c6389b03
> heads/master 6172
> RunID: run013
> Progress: Sun, 09 Nov 2014 20:21:59+0000
> Final status:Sun, 09 Nov 2014 20:21:59+0000  Finished successfully:1
> $ cat swift.conf.nows
> wrapperStagingLocalServer: "file://"
>
> app.sh { executable: /bin/sh, maxWallTime: "00:01:00" }
>
> lazyErrors: false
> executionRetries: 0
>
> $ cat out.txt
> hello
> $
>
> On 11/9/14 2:05 PM, Michael Wilde wrote:
>> Oddly, when I use "sh" -> /bin/sh for the app, this example fails.  The
>> swift run succeeds, but the returned file is zero-length (for the
>> example below) or contains a single newline (when I test a sh -c of a
>> simple echo).
>>
>> It *seems* that using cat as the app works while /bin/sh fails to return
>> output correctly.
>>
>> I'll need to debug further, but below are the working and then failing
>> swift scripts:
>>
>> # This works, c.txt comes back as 1M+12 bytes:
>>
>> $ cat wrapstage.swift
>> type file;
>>
>> app (file c) cat(file a, file b) {
>>        cat filename(a) filename(b) stdout=filename(c);
>> }
>>
>> file c <"c.txt">;
>> file a <"a.txt">;
>> file b <"http://mirror.internode.on.net/pub/test/1meg.test">;
>>
>> c = cat(a, b);
>>
>> # this fails: c.txt comes back as zero length:
>>
>> $ cat wrapstage2.swift
>> type file;
>>
>> app (file c) cat(file a, file b) {
>>        sh "-c" strcat("/bin/cat ", filename(a), " ", filename(b))
>> stdout=filename(c);
>> }
>>
>> file c <"c.txt">;
>> file a <"a.txt">;
>> file b <"http://mirror.internode.on.net/pub/test/1meg.test">;
>>
>> c = cat(a, b);
>> swift$
>>
>> A bug, or user error?
>>
>> - Mike
>>
>> On 11/8/14 5:32 PM, Michael Wilde wrote:
>>> Ok, that works great now, both with the conf you posted and with this one:
>>>
>>> wrapperStagingLocalServer: "file://"
>>>
>>> site.local {
>>>         staging: "wrapper"
>>>         scratch: "/tmp/wilde/swiftest"
>>> }
>>>
>>> Thanks,
>>>
>>> - Mike
>>>
>>> On 11/8/14 4:41 PM, Mihael Hategan wrote:
>>>> (solved on IM but replying here for reference).
>>>>
>>>> I made a mistake in the swift.conf I sent. wrapperStagingLocalServer is
>>>> a global option not a site option. However, it should work with the
>>>> vanilla swift.conf posted, which had the wrong option commented out.
>>>>
>>>> Mihael
>>>>
>>>>
>>>> On Sat, 2014-11-08 at 16:37 -0600, Michael Wilde wrote:
>>>>> I get this error:
>>>>>
>>>>> org.griphyn.vdl.util.SwiftConfigException: swift.conf:4 unexpected
>>>>> property 'site.local.wrapperStagingLocalServer'
>>>>>          at
>>>>> org.griphyn.vdl.util.SwiftConfigSchema.validate(SwiftConfigSchema.java:214)
>>>>>
>>>>> Ive tried spelling this property both as in your sample .conf and as in
>>>>> your text:
>>>>>
>>>>> wrapperStagingLocalServer and wrapperStageingLocalServer
>>>>>
>>>>> Neither is accepted.  Did a schema change not get committed?
>>>>>
>>>>> For general info: where is the json schema file that a user can check to
>>>>> find all valid conf parameters?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> - Mike
>>>>>
>>>>>
>>>>>
>>>>> On 11/8/14 4:13 PM, Mihael Hategan wrote:
>>>>>> type file;
>>>>>>
>>>>>> app (file c) cat(file a, file b) {
>>>>>> 	cat filename(a) filename(b) stdout=filename(c);
>>>>>> }
>>>>>>
>>>>>> file c <"c.txt">;
>>>>>> file a <"a.txt">;
>>>>>> file b <"http://mirror.internode.on.net/pub/test/1meg.test">;
>>>>>>
>>>>>> c = cat(a, b);
>>>>>> --------------------------------------------------------
>>>>>>
>>>>>> You would need a proper swift.conf. Here's an example of that:
>>>>>> --------------------------------------------------------
>>>>>> site.local {
>>>>>> 	staging: "wrapper"
>>>>>> 	scratch: "/some/scratch/dir"
>>>>>>              # *see email comments for details on the following option
>>>>>> 	# wrapperStagingLocalServer:"file://"
>>>>>> }
>>>>>> --------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> With a proper scratch dir there, this*should*  work for you without any
>>>>>> additional tweaking.
>>>>>>
>>>>>> Check _swiftwrap.wrapperstaging's stagein() and stageout() functions.
>>>>>> That's where you would add additional protocols.
>>>>>>
>>>>>> The wrapperStagingLocalServer sets the default staging location for
>>>>>> things that do not have an explicit scheme. In the case above, "c.txt"
>>>>>> and "a.txt" are staged in and out using"file://". If you wanted the
>>>>>> default to be some gridftp server, you would say something like
>>>>>> 'wrapperStageingLocalServer: "gsiftp://gridftp.server.org/"'. Of course,
>>>>>> _swiftwrap.wrapperstaging would need to know how to handle gsiftp URLs,
>>>>>> which it doesn't at the moment.
>>>>>>
>>>>>> Mihael

-- 
Michael Wilde
Mathematics and Computer Science          Computation Institute
Argonne National Laboratory               The University of Chicago