[Swift-devel] workflow hung?

[Veronika V. Nefedova]

/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
> >