Dear David,
I am doing 3D-RISM with the following parameters:
----buffer 15.0
--grdspc 0.5,0.5,0.5
--closure KH
--centering -1
Before using 48 core, tried with fewer cores and every time getting the
error "FATAL: allocation failure in ivector()" until the reaching 48 cores.
>From the Amber mailing list, I came to know this error come due to memory
issue.
I also tried with a system of 2775 atoms in different combination of cores
and time taken in every combination cores to run of five frames is as
follows:
No. of Cores Time (minutes)
6 10
8 8
10 8
12 5
24 5
I could not understand why my system taking longer time and 48 cores for
only one frame.
Do I need to change or add any parameter which can do the scaling up?
Best,
Priti
On Thu, Jul 5, 2018 at 7:18 AM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Jul 05, 2018, PRITI ROY wrote:
> >
> > Then another error was appeared which is as follows:
> > "rism3d.snglpnt.mpi: error while loading shared libraries:
> > libfftw3_mpi.so.3: cannot open shared object file: no such file or
> > directory"
> > and it is resolved by setting LD_LIBRARY_PATH as "export
> > LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/../amber16/lib""
>
> Note that this should be done in the $AMBERHOME/amber.sh script. You
> should
> expect to run this script everytime you log in -- most users put something
> like this in their startup script:
>
> export AMBERHOME=/path/to/amber18
> test -f $AMBERHOME/amber.sh && source $AMBERHOME/amber.sh.
>
> >
> > Now I am stuck in memory problem. My system has 5550 atoms, running one
> > frame of the trajectory with 48 cores and after 3hours its not yet
> > finished. I have 300ns long trajectory. Is it possible to speed up this
> > calculation with this system size?
>
> Indeed, rism3d can be extremely time consuming for large systems. But
> don't
> assume that more cores are always better: have you tried your system with
> fewer cores (say 4 or 8, or even 1)? If you use the --progress option, you
> can see what is happening: you may need to tweak convergence properties.
> It's hard to say more without knowing what closure, grid spacing, etc you
> are
> using. It's worth gaining experience on smaller systems that can complete
> in
> a few minutes, then scaling up.
>
> > Can I run this 3d-RISM calculation in GPU as I couldn't found any GPU
> based
> > executable of rism3d.snglpnt?
>
> We don't support 3D_RISM on GPU's (and as far as I know, no one else does
> either).
>
> ....good luck....dac
>
>
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Received on Thu Jul 05 2018 - 04:00:02 PDT
