[Swift-devel] Possible problem in coaster data transfer

[Michael Wilde]

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 $0}' `find | grep pdt`
ATOM    335  C   ASN 0  56     -34.964   1.477  15.043  1.00  0.00 
   0  13      -2.528  18.017  -1.927  1.00  0.00
ATOM    335  C   ASN 0  56     -21.516  -6.860 -31.404  1.00  0.00 
   91  C   ASN 0  32     -10.865  31.809 -15.581  1.00  0.00
ATOM    404  HN  ALA 0  68     -10.285 -33.690 -26.233  1.00  0.00 
135  CA  ALA 0  23      12.808  -6.713 -11.148  1.00  0.00
ATOM    335  C   ASN 0  56       0.510 -30.608   0.783  1.00  0.00 
   LEU 0   2       0.505   3.186  -1.484  1.00  0.00
ATOM    335  C   ASN 0  56      -3.155  25.367  -4.095  1.00  83  C 
ALA 0  64       5.541  11.559  -1.063  1.00  0.00
ATOM    404  HN  ALA 0  68      66.525  32.704 -21.958   GLN 0  57 
135  CA  ALA 0  23      19.234  14.087  -7.779  1.00  0.00
ATOM    335  C   ASN 0  56      16.926  -3.414  -5.774  1.00  0.00 
   EU 0  43      13.554  22.230  19.827  1.00  0.00
ATOM    335  C   ASN 0  56      14.805  34.413  23.907  1.00  0.00 
   59     -18.300   2.743 -27.536  1.00  0.00
ATOM    335  C   ASN 0  56      19.787  15.477  24.896  1.00  0.00 
   0  13       9.613  11.599  -1.295  1.00  0.00
ATOM    404  HN  ALA 0  68      11.882 -14.3    337  N   GLN 0  57 
135  CA  ALA 0  23      21.798 -14.600  -6.379  1.00  0.00
ATOM    112  HA2 GLY 0  19       3.632 -11.142 -24.657  1.00  0.   315 
CA  LEU 0  53       0.180 -22.479 -33.671  1.00  0.00
ATOM    335  C   ASN 0  56      -3.145 -30.419 -39.260  1.00  E 0  66 
    -8.925 -40.775 -24.402  1.00  0.00
com$