[Swift-devel] wrong file staged in

[Veronika Nefedova]

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
>>
>> _______________________________________________
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>> Swift-devel at ci.uchicago.edu
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>>
>