Le 14/03/13 16:31, Miguel Ortiz Lombardía a écrit :
> Hi all,
>
> I have a weird problem with ptraj (not cpptraj). I am trying to analyse
> hydrogen bonds and water bridges on a trajectory comprising 2500 frames
> over 25 files (100 frames per file). I have carried out this analysis on
> two computers:
>
> 1. OS: OSX 10.6.8 (Snow Leopard Server) 64-bit
> Compilers: intel 12.1.6 (gcc version 4.2.1 compatibility)
> Amber 12 (patch level 15)
> AmberTools 12 (patch level 35)
> Configure: configure -macAccelerate (-mpi) intel
>
> 2. OS: Linux 2.6.32-220 (RHE Server 6.2) 64-bit
> Compilers: GNU 4.4.6 20110731 (Red Hat 4.4.6-3)
> Amber 12 (patch level 15)
> AmberTools 12 (patch level 35)
> Configure: configure -noX11 (-mpi) gnu
>
> In the first computer the analysis takes some time but all the frames
> are processed. On the second computer the trajectory files are
> apparently read and found to have 100 frames, but only one frame ('set')
> is treated.
>
> This is from the output in the first computer:
>
> <...>
>> PTRAJ: hbond distance 3.2 angle 135.0 print 0.02 solventdonor WAT O solventacceptor WAT O H1 solventacceptor WAT O H2 solventneighbor 12 hbfile u1e2h2_1_exdR_sol_prod01_watbrdg.dat avgfile u1e2h2_1_exdR_sol_prod01_hbavg.dat series hbt out u1e2h2_1_exdR_sol_prod01_hbt.dat
>> [No output trajectory specified (trajout)]
>> ../u1e2h2_1_exdR_sol_prod01_001.mdcrd: 100 frames.
>> ../u1e2h2_1_exdR_sol_prod01_002.mdcrd: 100 frames.
> <...>
>> PTRAJ: Successfully read the input file.
>> Coordinate processing will occur on 2500 frames.
>> Summary of I/O and actions follows:
>>
>> INPUT COORDINATE FILES
>> File (../u1e2h2_1_exdR_sol_prod01_001.mdcrd) is a NetCDF AMBER trajectory with box info with 100 sets
>> File (../u1e2h2_1_exdR_sol_prod01_002.mdcrd) is a NetCDF AMBER trajectory with box info with 100 sets
> <...>
>
> And this is the equivalent output from the second computer:
>
> <...>
>> PTRAJ: hbond distance 3.2 angle 135.0 print 0.02 solventdonor WAT O solventacceptor WAT O H1 solventacceptor WAT O H2 so
>> lventneighbor 12 hbfile u1e2h2_1_exdR_sol_prod_watbrdg.dat avgfile u1e2h2_1_exdR_sol_prod_hbavg.dat series hbt out u1e2h
>> 2_1_exdR_sol_prod_hbt.dat
>> [No output trajectory specified (trajout)]
>> ../u1e2h2_1_exdR_sol_prod01_001.mdcrd: 100 frames.
>> ../u1e2h2_1_exdR_sol_prod01_002.mdcrd: 100 frames.
> <...>
>> PTRAJ: Successfully read the input file.
>> Coordinate processing will occur on 25 frames.
>> Summary of I/O and actions follows:
>>
>> INPUT COORDINATE FILES
>> File (../u1e2h2_1_exdR_sol_prod01_001.mdcrd) is a NetCDF AMBER trajectory with box info with 1 sets
>> File (../u1e2h2_1_exdR_sol_prod01_002.mdcrd) is a NetCDF AMBER trajectory with box info with 1 sets
> <...>
>
> Same input and command files in both cases.
>
> The second computer sees 100 frames per file but analyses just one of
> them. In both cases I have results at the end, but of course they are
> different.
>
> The reason I want to use the second computer is that this is an SMP
> machine with a lot of memory where I could analyse three times this
> number of frames (from 3 replicate production runs) The first computers
> chokes on the resulting 7500 frames, giving a segmentation fault,
> probably owing to lack of memory.
>
> Has anyone observed this behaviour before. Any ideas to overcome it?
>
> Best regards,
>
Hi again,
It is still very weird, but I have solved the problem.
My input file had trajin lines like:
> trajin ../u1e2h2_1_exdR_sol_prod01_001.mdcrd 1 last 1
> trajin ../u1e2h2_1_exdR_sol_prod01_002.mdcrd 1 last 1
<...>
Now, in the OSX machine and in a third machine (Linux) this poses no
problem to ptraj, which simply sends out a:
> WARNING in getArgumentInteger(): Scanning integer argument failed
for each of these lines, but then carries out the calculations for all
the frames.
I found in the AMBER list archives that this arises from using
"lastframe" in ptraj, whereas this option is only supported by cpptraj.
Indeed, when I replaced 'last' by '100' (the number of frames per file)
ptraj recognized 100 frames per file in all three machines.
Why the 'last' option works with ptraj in two of these machines (an OSX
and a Linux) but not in the third one (Linux) remains a mistery, but one
I can now live with.
Post this in case it helps others some day.
Cheers,
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Fri Mar 15 2013 - 03:30:02 PDT
