Hi,
The bug is fixed in the GitHub version of cpptraj. Thanks for the report!
-Dan
On Thu, Jun 13, 2019 at 2:21 PM somdev pahari <somdevpahari1.gmail.com> wrote:
>
> Sir,
> of course, I am sending. Thanks,
>
>
> Somdev
>
> On Thu, Jun 13, 2019 at 11:28 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > 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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Received on Thu Jun 13 2019 - 16:30:02 PDT
