[Swift-user] Re: [Swift-devel] trouble resuming

[skenny at uchicago.edu]

i think the main issue is that the rlog only contains
thread id's/mappings for files and not externals (even if
that's all you return). 

e.g. the rlog will contain something like: 

null.!unmapped
null.!unmapped
null.!unmapped
null.!unmapped
null.!unmapped

... 

if externals could be logged, i think the code below would
still need to have loop_query return its external in order for
that to work properly...regardless though, i don't *think*
jobs relying entirely on externals can be resumed in swift,
but maybe mihael will tell me i'm wrong and that there's a
magical solution ;)

~sk

---- Original message ----
>Date: Mon, 21 Sep 2009 16:28:28 -0500
>From: Michael Andric <andric at uchicago.edu>  
>Subject: [Swift-devel] trouble resuming  
>To: swift-user at ci.uchicago.edu, swift-devel at ci.uchicago.edu
>
>   I'm having trouble resuming swift-jobs.  When
>   resuming, it goes through 'Initializing' every
>   single job in the workflow and just finishes without
>   actually picking up where it left off.  Below is
>   the swift script. 
>   Thanks
>   Michael 
>   ## type declarations:
>   type file{}
>   type Rscript;
>   ## Mediator app declaration:
>   app (external turn) run_query (string med_args, file
>   config, Rscript code, file Annot){
>       Mediator med_args @filename(code)
>   @filename(Annot);
>   }
>   ## this process sets parameters and calls Mediator:
>   loop_query(int vert, string user, string db, string
>   host, string query_outline, Rscript code, file
>   config, string subject, string h, int beginTS, int
>   endTS, file Annot){
>       string outPrefix =
>   @strcat("gest_vs_nogest_vert",vert,h);
>       string med_args = @strcat("--user
>   ","andric"," --conf ", @filename(config)," --db ",
>   db," --host ", host,
>           " --vox ", vert," --subject ",
>   subject," --subquery tsTSVAR"," --begin_ts
>   ",beginTS," --end_ts ",endTS,
>           " --query ", query_outline,"
>   --r_swift_args ",outPrefix," ",vert," ",h,"
>   ",subject, " --outprefix ", "FAH_Q", " --r_script
>   ", at filename(code));
>       external turnpt = run_query(med_args, config,
>   code, Annot);
>   }
>   ## needed parameters to use Mediator:
>   string user = @arg("user");
>   string db = "HEL";
>   string host = "tp-neurodb.ci.uchicago.edu";
>   file config<single_file_mapper; file="user.config">;
>   ## mapping the R code:
>   Rscript code<single_file_mapper;
>   file="Rturning/turnchi_ss2.R">;
>   file Annot<single_file_mapper;
>   file="Rturning/resampled_coding_CarStory.txt">;
>   ## variables to move across in the foreach loops:
>   string declarelist[] = ["ss2"];
>   string hemilist[] = ["rh"];
>   int vertices[] = [1:155991:1];
>   #int vertices[] = [0:1:1];
>   foreach subject in declarelist{
>       foreach h in hemilist{
>           int beginTS = 0;
>           int endTS = 1254;
>           string query_outline = @strcat("SELECT
>   SUBQUERY FROM ",subject,"TS_data",h," WHERE subject
>   = '",subject,"' AND vertex=VOX");
>           foreach vert in vertices{
>               loop_query(vert, user, db, host,
>   query_outline, code, config, subject, h, beginTS,
>   endTS, Annot);
>           }
>       }
>   }
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