Re: [AMBER] Sudden termination of the heating simulation with sander.MPI

From: Nikolay N. Kuzmich <nnkuzmich.gmail.com>
Date: Thu, 22 Mar 2018 18:42:47 +0300

Dear Carlos and Malkeet,

thank you for your help.
After I changed the number of CPU threads from 8 (maximum available) to 6,
the heating went okay.

Kind regards,
Nick

Message: 11
Date: Wed, 21 Mar 2018 12:47:44 +0000
From: malkeet singh Bahia <msbahia17.gmail.com>
Subject: Re: [AMBER] Sudden termination of the heating simulation with
        sander.MPI
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAJvJZpNpb=uPMwohf3OB0DsrRSAH668WnEKAwsyFhTERuP5DvQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

hello Nick!
Could you send me your input files? I can try on my system and tell you
what's wrong.
Most probably, the problem is of heat.in (or whatever is your input *.in
file) file.

thanks!
msb


On Wed, 21 Mar 2018 at 14:25 Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:

> Dear AMBER users and developers,
>
> when I perform heating of my system on CPUs with sander.MPI,
> the simulation stops unexpectedly - it happened three times after various
> numbers of steps.
> The were no error messages in the output file, just
> Exit 65 mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i ... etc. in
> terminal.
> The Langevin thermostat with moderate speed of heating was used
> (gamma_ln=0.01 or 0.005), from 10 to 300K.
> I would be glad to find out any opinion why could it happen.
> Probably I shouldn't use all of the cores/threads available?
>
> Sincerely,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 
--
Thanks & Warm Regards
?
Malkeet S. Bahia, PhD
Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
PBC Indo-Israel Post-doc fellowship
Dept. of Chemistry, Building 211, Room no. 211
Bar Ilan University,  Ramat Gan, 5290002,  ISRAEL
Mobile: +91-9815988501 (India, watts app only)
+972-584553434 (Israel number)
------------------------------
Message: 12
Date: Wed, 21 Mar 2018 12:52:51 +0000
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] Sudden termination of the heating simulation with
        sander.MPI
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAGk3s-Q6c2eBrZxkx7C7VRijK0V4DokRCBURti0QHsUp6MKXig.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Try running without mpi and you'll have a better chance of getting the
error message written to mdout.
On Wed, Mar 21, 2018, 7:25 AM Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear AMBER users and developers,
>
> when I perform heating of my system on CPUs with sander.MPI,
> the simulation stops unexpectedly - it happened three times after various
> numbers of steps.
> The were no error messages in the output file, just
> Exit 65     mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i ... etc. in
> terminal.
> The Langevin thermostat with moderate speed of heating was used
> (gamma_ln=0.01 or 0.005), from 10 to 300K.
> I would be glad to find out any opinion why could it happen.
> Probably I shouldn't use all of the cores/threads available?
>
> Sincerely,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 22 2018 - 09:00:02 PDT
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