[Swift-user] trying coasters and sites1.xml

[Michael Wilde]

Erin,

See pointers below.

- Mike


On 6/6/09 6:40 PM, Hodgess, Erin wrote:
> Dear Swift People:
> 
> I have a process, fun1.swift, which works just fine, as you can see:
> 
> [erin at tp-login2 bin]$ swift -tc.file tc.data fun1.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090606-1836-j7rc2402
> Progress:
> Progress:  Selecting site:8  Active:1  Checking status:1
> Progress:  Selecting site:6  Active:1  Checking status:1  Finished 
> successfully:2
> Progress:  Selecting site:4  Active:1  Checking status:1  Finished 
> successfully:4
> Progress:  Selecting site:2  Active:1  Checking status:1  Finished 
> successfully:6
> Progress:  Active:1  Checking status:1  Finished successfully:8
> Final status:  Finished successfully:10
> [erin at tp-login2 bin]$
> 
> 
> However, if I run with a sites file, I get:
> 
> [erin at tp-login2 bin]$ swift -tc.file tc.data -sites.file sites1.xml 
> fun1.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090606-1837-xu7t94t5
> Progress:
> Execution failed:
>         Could not find any valid host for task "Task(type=UNKNOWN, 
> identity=urn:cog-1244331435263)" with constraints {tr=RInvoke, 
> filenames=[Ljava.lang.String;@4b6218f9, trfqn=RInvoke, 
> filecache=org.griphyn.vdl.karajan.lib.cache.CacheMapAdapter at 1555aa19}
> [erin at tp-login2 bin]$
> 

That message means Swift is trying to run an application name RInvoke.

It looks through tc.data, and did not find it listed as installed on any 
of the sites in your sites.xml.

You need to replicate this line in your tc.data file:

localhost	RInvoke	/home/erin/R-2.9.0/bin/RInvoke.sh	INSTALLED 
INTEL32::LINUX	null

for the site "teraport", and for any other sites you want Swift to try 
to run it on. So add:

teraport	RInvoke	/home/erin/R-2.9.0/bin/RInvoke.sh	INSTALLED 
INTEL32::LINUX	null

(Teraport uses the same file server and path names to your CI home 
directory)

> here is the sites1 file:
> 
> [erin at tp-login2 bin]$ cat sites1.xml
> <config>
> 
> <pool handle="teraport" sysinfo="INTEL32::LINUX">
>    <profile namespace="globus" key="queue">fast</profile>
>    <profile namespace="globus"
> key="coasterWorkerMaxwalltime">00:30:00</profile>
>     <profile namespace="globus" key="coastersPerNode">2</profile>
>    <execution provider="coaster" url="none"  jobmanager="local:pbs" />
>    <gridftp url="local://localhost" />
>    <workdirectory >/home/erin/R-2.9.0/bin</workdirectory>
>  </pool>
> 
> [erin at tp-login2 bin]$
> 
> Now there is one other thing.  The fun1.swift calls a program called R, 
> which is not on all of the sites.  Could that be the problem, please?

You mean "RInvoke", not R, I think.  And yes, as above.

> Here is the fun1.swift file:
> [erin at tp-login2 bin]$ cat fun1.swift
> type file{}
> 
> (file rout) perm_r (file datfile, int pnum, file scriptname)
>         {
>         app
>                 {
>                 RInvoke @filename(scriptname) pnum @filename(datfile) ;
>                 }
>         }
> 
> 
> file r_script<single_file_mapper; file="ttest1.R">;
> 
> file perm_matrix<single_file_mapper; file="fun.dat">;
> 
> foreach i in [1:10]
>         {
>         file r_out <single_file_mapper; 
> file=@strcat("results/",i,".NG-S.out")>;
>         (r_out) = perm_r(perm_matrix, i, r_script);
>         }
> [erin at tp-login2 bin]$
> 
> 
> All of this stuff is in /home/erin/R-2.9.0/bin directory.
> 
> Thanks and keep warm!
> 
> Erin
> 
> 
> Erin M. Hodgess, PhD
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodgesse at uhd.edu
> 
> 
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