[Swift-devel] Possible problem in coaster data transfer
Michael Wilde
wilde at mcs.anl.gov
Tue Apr 7 17:36:01 CDT 2009
It looks as if something in swift is garbling data files.
We see this when trying coaster data transfer to circumvent a problem
that the abe gridftp server was reporting (when using gridftp data
transfer).
The oops "pdt" file is the main output of the simulation (the
coordinates of each atom in the folded protein). These files should have
very regular multi-column lines, but in a few we see garbled lines.
This is in run: ci:/home/hockyg/oops/swift/output/abeoutdir.20
These file range from 1.5MB to 3MB in this test. There's one per job, 50
files in this run.
The lines on top are normal; the lines on the bottom are long due to
file corruption.
We've used coaster transfer off an on; we usually do gridftp transfer
and were using coaster transfer in this case while Mihael debugs a
problem thats manifesting as a gridftp error.
Glen suspected he saw such corruption earlier; this run seems to confirm it.
I'm not inclined to go deep into this at the moment, but rather to say
that we'll stick to gridftp transfer for the duration of this paper
writing effort.
- Mike
TOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
ATOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
ATOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
ATOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
ATOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
ATOM 337 N GLN 0 57 135 CA ALA 0 23 -17.316 8.147
0.047 1.00 0.00
com$
com$ awk 'length($0) > 150 {print $0}' `find | grep pdt`
com$ awk 'length($0) > 120 {print $0}' `find | grep pdt`
ATOM 335 C ASN 0 56 -34.964 1.477 15.043 1.00 0.00
0 13 -2.528 18.017 -1.927 1.00 0.00
ATOM 335 C ASN 0 56 -21.516 -6.860 -31.404 1.00 0.00
91 C ASN 0 32 -10.865 31.809 -15.581 1.00 0.00
ATOM 404 HN ALA 0 68 -10.285 -33.690 -26.233 1.00 0.00
135 CA ALA 0 23 12.808 -6.713 -11.148 1.00 0.00
ATOM 335 C ASN 0 56 0.510 -30.608 0.783 1.00 0.00
LEU 0 2 0.505 3.186 -1.484 1.00 0.00
ATOM 335 C ASN 0 56 -3.155 25.367 -4.095 1.00 83 C
ALA 0 64 5.541 11.559 -1.063 1.00 0.00
ATOM 404 HN ALA 0 68 66.525 32.704 -21.958 GLN 0 57
135 CA ALA 0 23 19.234 14.087 -7.779 1.00 0.00
ATOM 335 C ASN 0 56 16.926 -3.414 -5.774 1.00 0.00
EU 0 43 13.554 22.230 19.827 1.00 0.00
ATOM 335 C ASN 0 56 14.805 34.413 23.907 1.00 0.00
59 -18.300 2.743 -27.536 1.00 0.00
ATOM 335 C ASN 0 56 19.787 15.477 24.896 1.00 0.00
0 13 9.613 11.599 -1.295 1.00 0.00
ATOM 404 HN ALA 0 68 11.882 -14.3 337 N GLN 0 57
135 CA ALA 0 23 21.798 -14.600 -6.379 1.00 0.00
ATOM 112 HA2 GLY 0 19 3.632 -11.142 -24.657 1.00 0. 315
CA LEU 0 53 0.180 -22.479 -33.671 1.00 0.00
ATOM 335 C ASN 0 56 -3.145 -30.419 -39.260 1.00 E 0 66
-8.925 -40.775 -24.402 1.00 0.00
com$
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