Thanks, I'm downloading it now. I was able to run the given input with
cpptraj on the shorter trajectory you provided with no issues;
valgrind showed no memory errors. This is starting to feel like an
out-of-memory type issue, but I will keep digging.
I'm already seeing some areas where quality of life improvements can
be made to cpptraj (e.g. every frame does not need to be printed to
stdout for 'onlyframes' etc).
I'll report when/if I find anything. Thanks for the files.
-Dan
On Thu, Dec 8, 2022 at 8:51 AM Andrzej Dorobisz via AMBER
<amber.ambermd.org> wrote:
>
> Hi,
> I just uploaded the input data (22 GB) so you can download and test
> cpptraj on it.
>
> - file E81A.nc
> https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/E81A.nc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134155Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=d01eba1bf5f637ccd55f1f28cdd0623ded099ad95a226a66108f8bc8cc1eeca9
> <https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/E81A.nc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134155Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=d01eba1bf5f637ccd55f1f28cdd0623ded099ad95a226a66108f8bc8cc1eeca9>
>
> - all other files (E81A.top + input-cpptraj.txt)
> https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/cpptraj-SIGSEGV-files.zip?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=ca2814b488dbe69ed12261ad8b64b057870d155779cba7b147ce9d05af2f7f70
> <https://s3.cloud.cyfronet.pl/share/amber-cpptraj-issue/cpptraj-SIGSEGV-files.zip?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=71M2J3OGZ6O5J6K1WAFP%2F20221208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221208T134129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Signature=ca2814b488dbe69ed12261ad8b64b057870d155779cba7b147ce9d05af2f7f70>
>
> The error occurs after about 1 hour and 30 minutes.
>
>
> Regards,
> Andrzej
>
>
> On 6.12.2022 16:43, Daniel Roe via AMBER wrote:
> > Hi,
> >
> > On Tue, Dec 6, 2022 at 10:21 AM Andrzej Dorobisz
> > <andrzej.dorobisz.cyfronet.krakow.pl> wrote:
> >> Thank you for the quick reply. I can send the topology file but I don't
> >> know how to extract frames from the trajectory file (../input/E81A.nc).
> > The input would be something like:
> >
> > parm E81A.top
> > trajin E81A.nc 1 10
> > trajout E81A.1-10.nc
> >
> > -Dan
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Dec 08 2022 - 07:30:02 PST
