Hi,
Don't use STDIN for cpptraj.MPI. I recommend putting your input into a
file and executing cpptraj in batch mode, e.g.
mpirun -n X cpptraj.MPI -i input.file
The reason is that only process 0 actually gets access to STDIN, so
all the other processes sit and wait for input that will never come. I
should probably improve that, and should at least trap that - I'll
create a GitHub issue to remind me. In the meantime executing via an
input script should work. Let me know if not.
-Dan
On Tue, Apr 23, 2019 at 9:01 AM Benard, Dany <Dany.Benard.evotec.com> wrote:
>
> Hi Pratul & Daniel,
>
> You are fast!
> In fact we tried to use the "hbond" option.
> We have the version 18 and the command line is:
> _____________________
> cpptraj.MPI complex_mr.top << EOF
>
> trajin prod1.nc 1 last 1
> trajin prod2.nc 1 last 1
>
> autoimage
>
> hbond :1-272 dist 3.4 angle 140.0 avgout avg_hb.dat printatomnum out vstime_hb nointramol \
> solvout solvent_avg.dat bridgeout bridge.dat \
> solventacceptor :WAT.O solventdonor :WAT \
> series uuseries uuhbonds.agr uvseries uvhbonds.agr \
>
> go
>
> EOF
> _____________________
>
> .Marta, please could you give more information?
>
> Thank you,
> Dany
>
> -----Message d'origine-----
> De : Pratul Agarwal <pratul.agarwal-lab.org>
> Envoyé : mardi 23 avril 2019 14:59
> À : AMBER Mailing List <amber.ambermd.org>
> Objet : Re: [AMBER] Issue with cpptraj.MPI
> [EXTERNE]
>
> My mistake. Please ignore "md.out" file comment. I assume you are not seeing output to any files, but what about initialization message?
>
> Could you share your script? Also do you have a large data set?
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
> -----Message d'origine-----
> De : Daniel Roe <.com daniel.r.roe.gmail >
> Envoyé : mardi 23 avril 2019 14:53
> À : AMBER Mailing List <amber.ambermd.org>
> Objet : Re: [AMBER] Issue with cpptraj.MPI
> [EXTERNE]
>
> Hi,
>
> What version of cpptraj are you running? What is the exact command line you are executing and what does your input file look like?
>
> -Dan
> -----Message d'origine-----
> De : Pratul Agarwal <pratul.agarwal-lab.org>
> Envoyé : mardi 23 avril 2019 14:52
> À : AMBER Mailing List <amber.ambermd.org>
> Objet : Re: [AMBER] Issue with cpptraj.MPI
>
> [EXTERNE]
>
> Could you please give additional information? Did you see any output at all in md.out file? How do you know the program is running? Are CPUs under load?
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 4/23/2019 8:44 AM, Benard, Dany wrote:
>
> Hi Amber Team,
>
> We have an issue with the cpptraj.MPI command line.
> We tried to run calculations on parallel CPU, the program seems running but nothing happens, no result no error message...
> Did you have already see this error before?
> Thank in advance for your help we are completly stuck.
>
> Best regards,
> [EvotecLogoMail.png]
> Dany BENARD
> Systems Engineer
> + 33.(0) 5.34.63.26.07
> Dany.benard.evotec.com<mailto:Dany.benard.evotec.com><mailto:Dany.benard.evotec.com><mailto:Dany.benard.evotec.com>
> www.evotec.com<http://www.evotec.com><http://www.evotec.com/><http://www.evotec.com/>
>
> Evotec (France) SE
> 195, route d'Espagne,
> 31036 Toulouse CEDEX (France)
>
>
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Received on Tue Apr 23 2019 - 07:00:02 PDT
