Hi,
Could you send me off-list your topology, trajectory (relevant
portions only if it's really big), and cpptraj input so I can try to
reproduce? Thanks,
-Dan
On Thu, Jun 13, 2019 at 1:43 PM somdev pahari <somdevpahari1.gmail.com> wrote:
>
> Dear Daniel Sir,
>
> After several Hit-And-Trial I can conclude that this "core dumped" error is
> independent
> of threading, rather depends upon which portion of trajectory I am using. I
> am explaining.
> Total 1 to 420 number of *.nc files are there and each containing 1000
> frames.
> Say 414-420 gives me no core dumped message but 1-5 gives. More
> specifically *5.nc 1 19
> gives but *5.nc 1 18 don't. Anything wrong with my trajectories? It happens
> only with lipid
> and water but not with other co-solutes as I mentioned before.
>
>
> Regards
> Somdev
>
> On Fri, Jun 14, 2019 at 10:26 AM somdev pahari <somdevpahari1.gmail.com>
> wrote:
>
> > Dear Stefano, actually I have to calculate the bridging part for
> > comparison. For other co-solute case it works fine but only problem with
> > water.
> > Dear Daniel Sir, I never tried with single threaded. But before using OMP
> > version I used serial version of cpptraj but it took too much time so I
> > start using OMP version.
> > Ok, I will report quickly after using single threaded.
> >
> > Thank You
> >
> > On Thu 13 Jun, 2019, 9:25 PM Daniel Roe, <daniel.r.roe.gmail.com> wrote:
> >
> >> Hi,
> >>
> >> Do you get the segfault when running single threaded cpptraj?
> >>
> >> -Dan
> >>
> >> On Thu, Jun 13, 2019 at 10:41 AM somdev pahari <somdevpahari1.gmail.com>
> >> wrote:
> >> >
> >> > Dear AMBER community,
> >> >
> >> > I am using cpptraj.OMP for calculating hbond between lipid and water in
> >> my
> >> > Desktop.
> >> > Everything is running good but at the end I get something "Aborted (core
> >> > dumped)"
> >> > message. Though output files are created but do not cover my full
> >> > trajectory.
> >> > The cpptraj.OMP version is V4.14.0 (AmberTools V19.02) OpenMP.
> >> > Here below I attach a file containing the message. Please take a look
> >> and
> >> > give me your suggestions. Thanks in advance.
> >> >
> >> > Regards
> >> > Somdev Pahari
> >> > PhD Scholar
> >> > NIT Rourkela
> >> > Rourkela, Odisha
> >> > India
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> >>
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> >>
> >
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Received on Thu Jun 13 2019 - 11:00:03 PDT
