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Bug #273

trjcat -demux fails with fio range checking error

Added by Justin Lemkul over 10 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

When using trjcat -demux, the following error arises:

trjcat -f *.xtc -demux replica_index.xvg

Read 9 sets of 500 points, dt = 2

Reading frame 120 time 28.000
-------------------------------------------------------
Program trjcat, VERSION 4.0.2
Source code file: gmxfio.c, line: 938

Range checking error:
Variable fio has value -1073741821. It should have been within [ 0 .. 10 ]


Appending the -debug flag gives the following output in the .log file (attached as well):

t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
t=0, t0=0, b=0, e=0, dt=0: r=0
trx0.time = 0, time[k] = 0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
t=2, t0=0, b=0, e=0, dt=0: r=0
trx0.time = 2, time[k] = 0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
t=4, t0=0, b=0, e=0, dt=0: r=0
...

Trajectories, log files, index files, etc. can be supplied if they are necessary. The trajectory tarball is nearly 200 MB, but it can be posted if it would be useful.

trjcat.log (4.62 KB) trjcat.log The -debug log file. Justin Lemkul, 12/24/2008 06:03 PM
traj_short.tar.gz (8.01 MB) traj_short.tar.gz The shortened trajectories Justin Lemkul, 01/15/2009 12:31 PM
replica_index.xvg (26.4 KB) replica_index.xvg The replica_index.xvg file Justin Lemkul, 01/15/2009 12:32 PM

History

#1 Updated by Justin Lemkul over 10 years ago

Created an attachment (id=332)
The -debug log file.

#2 Updated by David van der Spoel over 10 years ago

Are you sure that all trajectory files are equally long (at least 28 ps)?

If so please post shorter versions of the trajectories (up to 30 ps should suffice) that reproduce the bug. It is not a problem to download some stuff either.

#3 Updated by Justin Lemkul over 10 years ago

(In reply to comment #2)

Are you sure that all trajectory files are equally long (at least 28 ps)?

If so please post shorter versions of the trajectories (up to 30 ps should
suffice) that reproduce the bug. It is not a problem to download some stuff
either.

I have uploaded 40-ps versions of each trajectory. These shorter trajectories do not give the same error, instead producing:

Reading frame 130 time 30.000
-------------------------------------------------------
Program trjcat_4.0.2_s, VERSION 4.0.2
Source code file: gmx_trjcat.c, line: 296

Fatal error:
Demuxing the same replica 4 twice at time 30.000002
-------------------------------------------------------

The original fio error occurs when I use the full-length trajectories. I have noticed, however, that the error only arises when the trajectories are one level above the working directory, i.e.:

trjcat -f ../*.xtc -demux ../replica_index.xvg

I get the "Demuxing the same replica" error if the trajectories are in the working directory, regardless of the length of the trajectory (30 ps or more).

#4 Updated by Justin Lemkul over 10 years ago

Created an attachment (id=336)
The shortened trajectories

#5 Updated by Justin Lemkul over 10 years ago

Created an attachment (id=337)
The replica_index.xvg file

#6 Updated by David van der Spoel over 10 years ago

This was a missing feature rather than a bug: you were expected to supply N output file names as well (and this will work in the current release). However now I added the feature that if you give a single output file name for N input files while demuxing you will get N output files prepended by a number, as in [kahlo:273/bla] % ls *xtc
0_trajout.xtc 2_trajout.xtc 4_trajout.xtc 6_trajout.xtc 8_trajout.xtc
1_trajout.xtc 3_trajout.xtc 5_trajout.xtc 7_trajout.xtc

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