[Swift-devel] workflow hung?

[Veronika V. Nefedova]

Right. But they are all different....

Ah, I see. If those 68 jobs were sequential - that wouldn't be a problems, 
correct ? But since they are all simultaneous - it hungs. Got it.

Thanks for spotting this one out!

Nika

At 02:26 PM 3/6/2007, Mihael Hategan wrote:
>There are multiple declarations of prt_file_m001.
>
>Mihael
>
>On Tue, 2007-03-06 at 14:23 -0600, Veronika V. Nefedova wrote:
> > v
> >
> > Registered futures:
> > file am1_file_m001  F/am1_file_m001 Closed
> > file rtf_file_m001  F/rtf_file_m001 Closed
> > file psf_file_m001  F/psf_file_m001 Closed
> > file prt_file_m001 - F/prt_file_m001 Open
> > ----
> >
> > At 02:19 PM 3/6/2007, Mihael Hategan wrote:
> > >Excellent! Quickly type "v", "Enter" and post the output :)
> > >
> > >On Tue, 2007-03-06 at 14:20 -0600, Veronika V. Nefedova wrote:
> > > > I haven't cancelled it -- it is still hanging out there (;
> > > >
> > > > Nika
> > > >
> > > > At 02:18 PM 3/6/2007, Veronika  V. Nefedova wrote:
> > > > >/sandbox/ydeng/alamines/swift-MolDyn-free-7bputznxmlga1.log
> > > > >
> > > > >on wiggum
> > > > >
> > > > >At 02:14 PM 3/6/2007, Mihael Hategan wrote:
> > > > >>What's the run id (or the log file)?
> > > > >>
> > > > >>Mihael
> > > > >>
> > > > >>On Tue, 2007-03-06 at 14:14 -0600, Veronika V. Nefedova wrote:
> > > > >> > Hi,
> > > > >> >
> > > > >> > I am testing an extend Molecular Dynamics workflow -- and it 
> seems
> > > to be
> > > > >> > hung after the first 3 steps of the workflow. The fourth step
> > > consists of
> > > > >> > 68 jobs that could/should be ran simultaneously. All these jobs
> > > have the
> > > > >> > same executable, but different command line parameters. Input
> > > files for
> > > > >> > these 68 jobs come from step 3 of the workflow (plus 2 additional
> > > files -
> > > > >> > one common to all jobs, and one unique for every job). I see 
> all these
> > > > >> > files on my localhost present.
> > > > >> > The log finishes with staging out of the results of step 3
> > > > >> (successful) and
> > > > >> > then nothing happens. No files are being staged in for step 4.
> > > > >> > This is the snapshot of the dtm file (CHARMM is step 3, 
> CHARMM2 is
> > > step 4)
> > > > >> > - the place where it all hung:
> > > > >> >
> > > > >> > (stdt_m001, psf_file_m001, crd_eq_file_m001, rst_file_m001,
> > > trj_file_m001,
> > > > >> > crd_min_f
> > > > >> > ile_m001) = CHARMM (gaff_rft, gaff_prm, stdn, rtf_file_m001,
> > > > >> prm_file_m001,
> > > > >> > crd_file
> > > > >> > _m001, water_file, "system:solv_m001", "stitle:m001",
> > > > >> > "rtffile:parm03_gaff_all.rtf",
> > > > >> >   "paramfile:parm03_gaffnb_all.prm", "gaff:m001_am1");
> > > > >> > file prt_file_m001 <"solv_chg_a0.prt">;
> > > > >> > file solv_chg_a0_m001_wham  <"solv_chg_a0_m001.wham">;
> > > > >> > file solv_chg_a0_m001_crd  <"solv_chg_a0_m001.crd">;
> > > > >> > file solv_chg_a0_m001_out <"solv_chg_a0_m001.out">;
> > > > >> > file solv_chg_a0_m001_done  <"solv_chg_a0_m001_done">;
> > > > >> >
> > > > >> > (solv_chg_a0_m001_wham, solv_chg_a0_m001_crd, 
> solv_chg_a0_m001_out,
> > > > >> > solv_chg_a0_m001
> > > > >> > _done) = CHARMM2 (standn, gaff_prm, gaff_rft, rtf_file_m001,
> > > > >> prm_file_m001,
> > > > >> > psf_file
> > > > >> > _m001, crd_eq_file_m001, prt_file_m001, 
> "dirname:solv_chg_a0_m001",
> > > > >> > "system:solv_m00
> > > > >> > 1", "stitle:m001", "rtffile:parm03_gaff_all.rtf",
> > > > >> > "paramfile:parm03_gaffnb_all.prm",
> > > > >> >   "gaff:m001_am1", "stage:chg", "urandseed:4880701");
> > > > >> >
> > > > >> > The complete dtm file is on wiggum in:
> > > > >> > /sandbox/ydeng/alamines/swift-MolDyn-free.dtm. I am probably 
> missing
> > > > >> > something here, but can't see what...
> > > > >> >
> > > > >> > Please let me know where to look for the errors,
> > > > >> >
> > > > >> > 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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> > > >
> > > >
> >
> >