[Swift-devel] mapper problem or ...?
Veronika V. Nefedova
nefedova at mcs.anl.gov
Wed Mar 14 09:32:09 CDT 2007
Ok, now I think you hit the area in your explanations that I always had a
problem with. So here is my understanding of things:
if I have two apps that I need to chain together, I need to do this:
file a <"a.txt">;
file b <"b.txt">;
file c <"c.txt">;
a = APP1 (b);
c = APP2 (a);
I.e. the chaining of the programs happens on a 'logical' file level (a,b,c
rather then a.txt, b.txt, c.txt). Is that a correct understanding? I acted
on this understanding and my workflow has been working fine (till now --
but thats another story). Having create all this logical files was a *big*
pain (as I couldn't have the same logical names as physical filenames due
to a different file naming conventions in swift: no multiple ".", etc). It
really would've been much easier for my workflow to have just this:
a1.txt = APP1 (b.txt);
a2.txt = APP2 (b.txt);
c.txt = APP3 (a1.txt, a2.txt);
as my applications produce an enormous amount of intermediate files with
some specific naming conventions.
Now back to my original problem - constructing and passing to my next
application a collection of files. If I didn't have to do any mappers, it
would've been just as easy as (for example):
c.txt = APP3 (a*.txt);
Does it make sense at all ?
Thanks,
Nika
At 06:41 PM 3/13/2007, Mihael Hategan wrote:
>On Tue, 2007-03-13 at 18:28 -0500, Veronika V. Nefedova wrote:
> > Hmmm. So here is how my files are produced (inside double loop over $s and
> > $name):
> >
> > file $s9prt <"$name.prt">;
> > file $s9wham <"$s9.wham">;
> > file $s9crd <"$s9.crd">;
> > file $s9out <"$s9.out">;
> > file $s9done <"$s9donefile">;
> >
> > ($s9wham, $s9crd, $s9out, $s9done) = CHARMM3 (standn, gaff_prm, gaff_rft,
> > rtf_file_$s, prm_file_$s, psf_file_$s, crd_eq_file_$s, $s9prt, "$ss1",
> > "$s1", "$s2", "$s3", "$s4", "$s5", "$s7", "$s8", "$sprt", "$rcut1",
> "$rcut2");
> >
> > so if I change the mapping of the needed output file ($s9wham), everything
> > should work?
> >
> > file whamfiles_$s[$i] <"$s9.wham">;
>
>That one won't work.
>You need to let Swift map whamfiles_$s[] to what it wants. So you can't
>map individual items in an array differently.
>
>I believe that you rely on the fact that whamfiles_xzy maps to the same
>file names as some other variables. This won't work. You need to use the
>same variable. The file names are irrelevant if the program doesn't make
>sense for Swift.
>So think about it this way: mentally remove all the mapper declarations
>from the Swift program. If after that, the program makes sense, then you
>should be good to go. If it doesn't then it's likely it won't work.
>Remember, mapping is not something that can be used to hack things
>because the workflow structure has nothing to do with the mappers and
>Swift ignores mappers when figuring out the data flow.
>
>(dependent mappers notwithstanding)
>
> > i=`expr $i + 1`
> >
> > and call the function:
> > (whamfiles_$s[$i], $s9crd, $s9out, $s9done) = CHARMM3 (standn, gaff_prm,
> > gaff_rft, rtf_file_$s, prm_file_$s, psf_file_$s, crd_eq_file_$s, $s9prt,
> > "$ss1", "$s1", "$s2", "$s3", "$s4", "$s5", "$s7", "$s8", "$sprt",
> "$rcut1",
> > "$rcut2");
> >
> > Nika
> >
> > At 06:12 PM 3/13/2007, Mihael Hategan wrote:
> > >On Tue, 2007-03-13 at 18:07 -0500, Veronika V. Nefedova wrote:
> > > > ok, here is in short what I need to do:
> > > >
> > > > at some point in the workflow N files are produced (in my case its
> 68, but
> > > > it could be any number). These files produced each by a separate
> job (i.e.
> > > > N jobs produce N files).
> > > > The next job in the workflow needs to take those N files as an input.
> > > >
> > > > Question: how do I pass these unknown number of files as an input to an
> > > > application ? The array_mapper didn't work (or i didn't use it
> correctly).
> > >
> > >In this case you need some other kind of mapper that can deal with
> > >unknown numbers of items. The default mapper (i.e. specifying no mapper)
> > >should work.
> > >
> > >So you need to do:
> > >
> > >file whamfiles_002[];
> > >
> > >foreach v,k in someinput {
> > > whamfiles_002[k] = job(v);
> > >}
> > >
> > >... = GENERATOR(whamfiles_002);
> > >
> > > >
> > > > Thanks!
> > > >
> > > > Nika
> > > >
> > > > At 05:56 PM 3/13/2007, Mihael Hategan wrote:
> > > > >On a third thought. This looks like, eventually, you are trying to do
> > > > >the same thing that Yong did with the dependent mappers earlier. I
> think
> > > > >he would have more insight on the topic.
> > > > >
> > > > >On Tue, 2007-03-13 at 17:23 -0500, Veronika V. Nefedova wrote:
> > > > > > I think I am confused. Sorry!
> > > > > > 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
> > > > > > > >
> > > > > >
> > > > > >
> > > >
> > > >
> >
> >
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