[Swift-devel] wrong file staged in

[Veronika Nefedova]

I put the dtm file on terminable in ~nefedova/MolDyn.dtm

I see a few more directories with wrong files staged in, but I didn't  
check them all (130+ of them). I saw at least one with the correct  
files staged in.

Nika

On Jul 6, 2007, at 4:39 PM, Mihael Hategan wrote:

> Consistent or intermittent behavior?
>
> Also, can you attach the swift source?
>
> On Fri, 2007-07-06 at 16:37 -0500, Veronika Nefedova wrote:
>> Nope... I checked with grep:
>>
>> nefedova at viper:~/alamines> grep solv_repu_0DOT9_1_b1_prt MolDyn.dtm
>> file solv_repu_0DOT9_1_b1_prt <"solv_repu_0.9_1_b1.prt">;
>> (whamfiles[67] , solv_repu_0DOT9_1_b1_crd, solv_repu_0DOT9_1_b1_out,
>> solv_repu_0DOT9_1_b1_done) = CHARMM3 (standn, gaff_prm, gaff_rft,
>> rtf_file, prm_file, psf_file, crd_eq_file, solv_repu_0DOT9_1_b1_prt,
>> ss1, s1, s2, s3, s4, s5, s7, "urandseed:5964163", sprt, "rcut1:0.9",
>> "rcut2:1");
>> nefedova at viper:~/alamines>
>>
>> On Jul 6, 2007, at 4:31 PM, Mihael Hategan wrote:
>>
>>> Wonder if there is another declaration of the same variable  
>>> mapped to
>>> the wrong file.
>>>
>>> On Fri, 2007-07-06 at 16:03 -0500, Veronika Nefedova wrote:
>>>> The wrong file was staged in during the 4th stage of the  
>>>> workflow...
>>>>
>>>> I have this inside my foreach loop:
>>>> <snip>
>>>> file solv_repu_0DOT9_1_b1_prt <"solv_repu_0.9_1_b1.prt">;
>>>> file solv_repu_0DOT9_1_b1_crd  <"solv_repu_0.9_1_b1.crd">;
>>>> file solv_repu_0DOT9_1_b1_out <"solv_repu_0.9_1_b1.out">;
>>>> file solv_repu_0DOT9_1_b1_done  <"solv_repu_0.9_1_b1_done">;
>>>>
>>>> (whamfiles[67] , solv_repu_0DOT9_1_b1_crd,  
>>>> solv_repu_0DOT9_1_b1_out,
>>>> solv_repu_0DO\
>>>> T9_1_b1_done) = CHARMM3 (standn, gaff_prm, gaff_rft, rtf_file,
>>>> prm_file, psf_file,\
>>>> crd_eq_file, solv_repu_0DOT9_1_b1_prt, ss1, s1, s2, s3, s4, s5, s7,
>>>> "urandseed:59\
>>>> 64163", sprt, "rcut1:0.9", "rcut2:1");
>>>> <snip>
>>>>
>>>>
>>>> The first  file (with DOT) is an input files for CHARMM3 and three
>>>> last declared files (out, crd and done) are output files.
>>>>
>>>> When I check my remote directory during execution, I see that the
>>>> wrong files were staged in. In particular, the wrong prt file was
>>>> staged in:
>>>>
>>>> solv_disp_a3.prt instead of solv_repu_0.9_1_b1.prt  (aka
>>>> solv_repu_0DOT9_1_b1_prt)
>>>>
>>>> The solv_repu_0.9_1_b1.prt file is not produced by a previous  
>>>> stage,
>>>> its being/supposed to be/ staged in from the submit host.
>>>>
>>>> The above declaration is the only place where the file
>>>> solv_repu_0DOT9_1_b1_prt is being declared in swift file (I did  
>>>> grep
>>>> to check it). kml file also looks ok.
>>>>
>>>> I am not sure why it has happened -- this piece of code has not  
>>>> been
>>>> changed from the previous version...
>>>>
>>>>
>>>> This is the work directory for this job (CHARMM3) on TG-UC:
>>>>
>>>> nefedova at tg-login1:/disks/scratchgpfs1/iraicu/MolDyn-zvlc1f9c03pf0/
>>>> chrm_long-p2v28ydi> ls
>>>> m001_am1.prm           solv.inp          solv_m001_eq.crd
>>>> stderr.txt
>>>> m001_am1.rtf           solv_disp_a3.out  solv_repu_0.9_1_b1.rst
>>>> parm03_gaff_all.rtf    solv_disp_a3.prt  solv_repu_0.9_1_b1.trj
>>>> parm03_gaffnb_all.prm  solv_m001.psf     solv_repu_0.9_1_b1.wham
>>>> nefedova at tg-login1:/disks/scratchgpfs1/iraicu/MolDyn-zvlc1f9c03pf0/
>>>> chrm_long-p2v28ydi>
>>>>
>>>> as you can see 2 files have the wrong names (solv_disp_a3  
>>>> instead of
>>>> solv_repu_0.9_1_b1 ) and execution is screwed up since the wrong
>>>> parameter file (prt) was staged in...
>>>>
>>>>
>>>> I checked whether that file was even staged in to the remote  
>>>> host --
>>>> in fact it was:
>>>>
>>>> nefedova at tg-login1:/disks/scratchgpfs1/iraicu/MolDyn-zvlc1f9c03pf0>
>>>> find */ -name solv_repu_0.9_1_b1.prt -print
>>>> shared/solv_repu_0.9_1_b1.prt
>>>> But it never went to the right working directory...
>>>>
>>>> Any idea what is going on here?
>>>>
>>>> Thanks,
>>>>
>>>> Nika
>>>>
>>>> _______________________________________________
>>>> Swift-devel mailing list
>>>> Swift-devel at ci.uchicago.edu
>>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>>>
>>>
>>
>