Hi,
On Wed, May 9, 2018 at 7:15 AM, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> What does make me a bit intrigued though is the fact that this error, in al my evaluations that show this error, always occur after processing 90% of the trajectories.
So this is actually due to how the different output streams, STDERR
(standard error, where cpptraj writes all error messages) and STDOUT
(standard output, where cpptraj writes everything else), are handled
by the underlying OS. As I understand it, usually STDOUT is buffered,
while STDERR is not. So what I think is happening here is the error
message is getting written before the STDOUT buffer is being flushed.
Due to the extreme delay between the messages I assume you're
redirecting output to a file - I think file redirects are fully
buffered, while TTY output is line buffered. So if you were to just
run the same script and watch the output, the error message should be
closer to where you expect (I think).
Hope this helps,
-Dan
>
> Here is where I get to thinking, is this error really reported just because there are no interactions detected? Because from my end, that is the explanation that seems most likely after checking every I/O file used for several of these analyses reporting an error. In that case, should this error not preferably occur after processing 100% of the trajectory data? Otherwise it seems odd to just ignore any data in the last 10%.
>
> Before bombarding you with a couple of thousands of lines of output, I’ll attach some select lines from one such run and my input, if you need more then let me know. In essence, what I am wondering is the following, is my conclusion regarding the lack of data being the root of this “error” correct. In that case, why is the error generated before processing all the trajectory data.
>
>
> Thank you for any input in advance
> Best regards
> // Gustaf
>
>
> My input:
>
> parm ../om1mtr.prmtop
> trajin ../nvt1ns.mdcrd
> …
> …
> trajin ../nvt100ns.mdcrd
> hbond S1 series out series_hb_BRT_O3_MO1_H.out \
> donormask :MO1.N donorhmask :MO1.H \
> acceptormask :BRT.O3 \
> avgout average_hb_BRT_O3_MO1_H.out nointramol
> run
> runanalysis lifetime S1[solutehb] out lifetime_hb_BRT_O3_MO1_H.out
>
>
> My logged run output:
>
> CPPTRAJ: Trajectory Analysis. V17.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 05/08/18 17:51:42
> | Available memory: 44.618 GB
>
> INPUT: Reading input from 'hb_brt_o3_mo1_h.ptraj'
> [parm ../om1mtr.prmtop]
> Reading '../om1mtr.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> [trajin ../nvt1ns.mdcrd]
> Reading '../nvt1ns.mdcrd' as Amber NetCDF
> …
> …
> [trajin ../nvt100ns.mdcrd]
> Reading '../nvt100ns.mdcrd' as Amber NetCDF
> [hbond S1 series out series_hb_BRT_O3_MO1_H.out donormask :MO1.N donorhmask :MO1.H acceptormask :BRT.O3 avgout average_hb_BRT_O3_MO1_H.out nointramol]
> HBOND: Donor mask is :MO1.N, Acceptor mask is :BRT.O3
> Separate donor H mask is :MO1.H
> Only looking for intermolecular hydrogen bonds.
> Distance cutoff = 3.000, Angle Cutoff = 135.000
> Writing # Hbond v time results to series_hb_BRT_O3_MO1_H.out
> Writing Hbond avgs to average_hb_BRT_O3_MO1_H.out
> Time series data for each hbond will be saved for analysis.
> [run]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: om1mtr.prmtop, 23712 atoms, 2166 res, box: Orthogonal, 2166 mol
>
> INPUT TRAJECTORIES (100 total):
> 0: 'nvt1ns.mdcrd' is a NetCDF AMBER trajectory, Parm om1mtr.prmtop (Orthogonal box) (reading 500 of 500)
> …
> …
> 99: 'nvt100ns.mdcrd' is a NetCDF AMBER trajectory, Parm om1mtr.prmtop (Orthogonal box) (reading 500 of 500)
> Coordinate processing will occur on 50000 frames.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'om1mtr.prmtop' (1 actions):
> 0: [hbond S1 series out series_hb_BRT_O3_MO1_H.out donormask :MO1.N donorhmask :MO1.H acceptormask :BRT.O3 avgout average_hb_BRT_O3_MO1_H.out nointramol]
> Set up 100 acceptors:
> Set up 306 donors:
> Imaging off.
> Estimated max potential memory usage: 6.123 GB
> ----- nvt1ns.mdcrd (1-500, 1) -----
> 0%
> ----- nvt2ns.mdcrd (1-500, 1) -----
>
> ----- nvt3ns.mdcrd (1-500, 1) -----
>
> ----- nvt4ns.mdcrd (1-500, 1) -----
>
> …
> …
>
> ----- nvt91ns.mdcrd (1-500, 1) -----
> 90% Error: No data sets selected.
> Error: lifetime: Could not add data sets.
> 1 errors encountered reading input.
> Error: Error(s) occurred during execution.
>
> ----- nvt92ns.mdcrd (1-500, 1) -----
>
> ----- nvt93ns.mdcrd (1-500, 1) -----
>
> ----- nvt94ns.mdcrd (1-500, 1) -----
>
> ----- nvt95ns.mdcrd (1-500, 1) -----
>
> ----- nvt96ns.mdcrd (1-500, 1) -----
>
> ----- nvt97ns.mdcrd (1-500, 1) -----
>
> ----- nvt98ns.mdcrd (1-500, 1) -----
>
> ----- nvt99ns.mdcrd (1-500, 1) -----
>
> ----- nvt100ns.mdcrd (1-500, 1) -----
> 100% Complete.
>
> Read 50000 frames and processed 50000 frames.
> TIME: Avg. throughput= 927.2248 frames / second.
>
> ACTION OUTPUT:
> HBOND: Actual memory usage is 0.000 kB
> 0 solute-solute hydrogen bonds.
>
> DATASETS (1 total):
> S1[UU] "S1[UU]" (integer), size is 50000
>
> DATAFILES (2 total):
> series_hb_BRT_O3_MO1_H.out (Standard Data File): S1[UU]
> average_hb_BRT_O3_MO1_H.out (Avg. solute-solute HBonds)
>
> RUN TIMING:
> TIME: Init : 0.0002 s ( 0.00%)
> TIME: Trajectory Process : 53.9244 s ( 99.92%)
> TIME: Action Post : 0.0007 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0430 s ( 0.08%)
> TIME: Other : 0.0000 s ( 0.00%)
> TIME: Run Total 53.9683 s
> ---------- RUN END ---------------------------------------------------
> [runanalysis lifetime S1[solutehb] out lifetime_hb_BRT_O3_MO1_H.out]
> Warning: 'S1[solutehb]' selects no data sets.
> TIME: Total analysis execution time: 0.0001 seconds.
> TIME: Total execution time: 54.4226 seconds.
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed May 09 2018 - 05:30:04 PDT
