[Swift-devel] wrong file staged in

[Mihael Hategan]

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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