Sander does not work on gpus.
On Fri, Mar 1, 2024, 10:42 PM Montalvillo, Fernando via AMBER <
amber.ambermd.org> wrote:
> Yes, the error output was empty and the .out output looked fine and just
> told that the mpi was being run correctly.
>
> I actually figured it out myself but did not know how to answer myself in
> the amber list. I tried doing the pmemd version of the tutorial instead and
> the output file also stopped also at the 999th step. However, the mdout
> file had more information. It said there was a problem regarding mbar. It
> turns out some of the options of mbar that were in the input file were
> deprecated since amber16 or 18, I don't remember what it said in the manual.
>
> It would be helpful if the error or mdout file would print if there is
> deprecated options but I totally understand this might be difficult to
> implement in the amber suite with all the packages there are.
>
>
> The reason I wanted to learn sander TI is because now that
> sander.quick.cuda.MPI has been released, in theory, TI using QM/MM should
> be feasible and more easy to set up. The problem that I am facing right now
> is requesting multiple GPUs with sander.quick.cuda.MPI. I have only managed
> to request CPUs. Does anyone have any idea how to request GPUs for parallel
> simulations?
>
> Thank you for your answer,
> Fernando
> ________________________________
> From: David A Case <dacase1.gmail.com>
> Sent: Friday, March 1, 2024 7:29 PM
> To: Montalvillo, Fernando <Fernando.Montalvillo.UTDallas.edu>; AMBER
> Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Sander.mpi haults at 999 steps
>
> On Tue, Feb 27, 2024, Montalvillo, Fernando via AMBER wrote:
>
> >I installed Amber20 with AmberTools23 (i don't know if that is a
> >problem).
>
> I'm not sure if this is relevant to your problem,, but Amber20 should not
> be
> installed with AmberTools23. I suggest you upgrade to Amber22, which is
> compatible with AmberTools23.
>
> >
> >#!/bin/bash
> >#SBATCH --job-name=ti_ligands
> >#SBATCH --nodes=1
> >#SBATCH --ntasks=16
>
> Try a job with ntasks=2, just to see if anything changes
>
> >#SBATCH --partition=torabifard
> >#SBATCH --time=48:00:00
> >#SBATCH --output=ti_complex_%j.out
> >#SBATCH --error=ti_complex_%j.err
>
> Did you examine the .out and .err files?
>
> ....dac
>
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Received on Sat Mar 02 2024 - 04:00:02 PST
