[Swift-devel] mapper problem or ...?

[Mihael Hategan]

On Tue, 2007-03-13 at 17:23 -0500, Veronika V. Nefedova wrote:
> I think I am confused. Sorry!

whamfiles_m002 is a file array
Swift will know how to break it into files and stage all of them in if
you pass it as an array to the atomic procedure.

@whamfiles_m002 is a string of space separated names. It gets passed to
the application as one single argument.

Mihael

> what will be the type of 'whamfiles' ? If its a string - will the swift 
> know to brake it down to filenames and stage them all in ?
> Also - is there a mapper (or whatever) that can map the list of *logical* 
> file names to an array ? (thats what I was trying to do).
> 
> Thanks!
> 
> Nika
> 
> 
> At 04:54 PM 3/13/2007, Mihael Hategan wrote:
> >Oh my :)
> >@whamfiles_m002 is known by the system at all times. That means
> >GENERATOR does not need to wait for the actual files to be there since
> >it knows very well what @whamfiles_m002 is (the list of names).
> >
> >You should try this instead:
> >...
> >... GENERATOR(whamfiles, str) {
> >    app {
> >      generator @whamfiles, str;
> >    }
> >}
> >
> >... = GENERATOR(whamfiles_m002, "m002")
> >
> >Mihael
> >
> >On Tue, 2007-03-13 at 16:46 -0500, Veronika V. Nefedova wrote:
> > > Hi,
> > >
> > > I have a question:
> > >
> > > I am using a fixed_array_mapper to pass some 68 files as an input to my
> > > application called GENERATOR. I need to use the mapper since the number of
> > > input files is unknown before the workflow starts. Here is how I use it:
> > > file whamfiles_m002[] <fixed_array_mapper;files=" solv_chg_a0_m002_wham,
> > > solv_chg_a1_m002_wham, solv_chg_a10_m002_wham, <snip -- many files, you 
> > get
> > > the idea>, solv_repu_0_0DOT2_b1_m002_wham">;
> > >
> > > These files are all generated by stage four of my workflow, each file is
> > > mapped to a physical filename, for example:
> > >
> > > file solv_chg_a0_m002_wham  <"solv_chg_a0_m002.wham">;
> > > and this particular file is produced this way:
> > > (solv_chg_a0_m002_wham, solv_chg_a0_m002_crd, solv_chg_a0_m002_out,
> > > solv_chg_a0_m002_done) = CHARMM2 (standn, gaff_prm, gaff_rft,
> > > rtf_file_m002, prm_file_m002, psf_file_m002, crd_eq_file_m002,
> > > solv_chg_a0_m002_prt, "prtfile:solv_chg_a0", "system:solv_m002",
> > > "stitle:m002", "rtffile:parm03_gaff_all.rtf",
> > > "paramfile:parm03_gaffnb_all.prm", "gaff:m002_am1", "stage:chg",
> > > "urandseed:5395098", "dirname:solv_chg_a0_m002");
> > >
> > > Then I call my application (the last stage of my workflow, stage five)
> > >
> > > (solv_chg_m002, solv_disp_m002, solv_repu_0DOT2_0DOT3_m002DOTwham,
> > > solv_repu_0DOT3_0DOT4_m002DOTwham, solv_repu_0DOT4_0DOT5_m002DOTwham,
> > > solv_repu_0DOT5_0DOT6_m002DOTwham, solv_repu_0DOT6_0DOT7_m002DOTwham,
> > > solv_repu_0DOT7_0DOT8_m002DOTwham, solv_repu_0DOT8_0DOT9_m002DOTwham,
> > > solv_repu_0DOT9_1_m002DOTwham, solv_repu_0_0DOT2_m002DOTwham ) = GENERATOR
> > > (@whamfiles_m002, "m002");
> > >
> > > And then when I start my workflow, the GENERATOR starts right away. I am
> > > not sure why. Does the mapper look for the physical files on the disk and
> > > when finds them - starts right away ? I do have the needed files in the
> > > directory from my previous runs. Or there is something else wrong here ?
> > >
> > > 109] wiggum /sandbox/ydeng/alamines > Swift V 0.0405
> > > RunID: b0n2liektep92
> > > pre_ch started              <---------- thats the first stage
> > > generator_cat started    <----------- not supposed to start now!
> > > generator_cat started
> > >
> > > My complete dtm file is in /home/nefedova/swift.dtm on
> > > terminable.ci.uchicago, but its pretty big...
> > >
> > > Thanks,
> > >
> > > Nika
> > >
> > >
> > > _______________________________________________
> > > Swift-devel mailing list
> > > Swift-devel at ci.uchicago.edu
> > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >
> 
>