[Swift-devel] wrong file staged in

[Veronika Nefedova]

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