[Swift-devel] workflow hung?

[Mihael Hategan]

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
> 
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