[Swift-devel] workflow hung?

[Veronika V. Nefedova]

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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