Re: [AMBER] string methods in AMBER16

From: Chunli Yan <utchunliyan.gmail.com>
Date: Tue, 1 Aug 2017 16:07:35 -0400

Dear Pan,

I am running the sequential jobs not. Attached were my input files (plus
colvar file).

The job was running on comet (San Diego Supercomputer Center
<http://www.sdsc.edu/support/user_guides/comet.html>):

#!/bin/bash

#SBATCH --job-name="gpu_test"

#SBATCH --output="gpu_test"

#SBATCH --partition=gpu-shared

#SBATCH --nodes=1

#SBATCH --gres=gpu:p100:1

#SBATCH --ntasks-per-node=7

#SBATCH --export=ALL

#SBATCH -t 48:00:00


module load cuda/8.0

module load intel/2013_sp1.2.144

module load mvapich2_ib/2.1


cd /oasis/scratch/comet/cyan/temp_project/string/dna1

export AMBERHOME=/home/cyan/program/amber16/



ibrun -n 1 $AMBERHOME/bin/pmemd.cuda -O -i md01.in -o remd.mdout.001 -c
0.rst -r remd.rst.001 -x remd.mdcrd.001 -inf remd.mdinfo.001 -p dna.prmtop


Thanks,


Best,


*Chunli*



On Tue, Aug 1, 2017 at 3:59 PM, Feng Pan <fpan3.ncsu.edu> wrote:

> Hi, Chunli
>
> You should only use the pmemd.cuda.MPI to do string method since string
> method requires
> many images on the path.
>
> In the error, it seems some integer is divided by zero, could you send me
> the mdin file to
> check if any error in inputs?
>
> Best
> Feng
>
> On Tue, Aug 1, 2017 at 3:00 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
>
> > Hello,
> >
> > I want to test string methods using pmemd.cuda.
> >
> > Below is the steps how I compile amber16 with AmberTools16,
> >
> > 1. export AMBERHOME=`pwd`
> > 2. ./update_amber --update (I can not pass update.4 and update.9 that
> > relate to string methods)
> > 3. ./update_amber --apply patch=../../nfe_advance.patch/
> nfe_advance.patch
> > 4. ./configure -cuda intel
> > 5. make install
> >
> >
> > But I always have problems to pass update.4 and update.9, it complains
> > below:
> >
> >
> > Applying AmberTools 16/update.9.gz
> >
> > /home/cyan/program/amber16/updateutils/patch.py:334: PatchingWarning:
> > Permissions not found for every file in
> > .patches/AmberTools16_Unapplied_Patches/update.9.
> > All new files will be read-only!
> >
> > 'files will be read-only!') % self.name, PatchingWarning)
> >
> > Applying Amber 16/update.4.gz
> >
> > /home/cyan/program/amber16/updateutils/patch.py:334: PatchingWarning:
> > Permissions not found for every file in
> > .patches/Amber16_Unapplied_Patches/update.4.
> > All new files will be read-only!
> >
> > 'files will be read-only!') % self.name, PatchingWarning)
> >
> >
> > Once I finish the installing and ran string methods with pmemd.duda. I
> got
> > the following error:
> >
> >
> > forrtl: severe (71): integer divide by zero
> >
> > Image PC Routine Line
> Source
> >
> > libintlc.so.5 00002B862BA802C9 Unknown Unknown
> Unknown
> >
> > libintlc.so.5 00002B862BA7EB9E Unknown Unknown
> Unknown
> >
> > libifcore.so.5 00002B862A72908F Unknown Unknown
> Unknown
> >
> > libifcore.so.5 00002B862A690D7F Unknown Unknown
> Unknown
> >
> > libifcore.so.5 00002B862A6A2309 Unknown Unknown
> Unknown
> >
> > libpthread.so.0 000000397460F7E0 Unknown Unknown
> Unknown
> >
> > pmemd.cuda 000000000071B524 Unknown Unknown
> Unknown
> >
> > pmemd.cuda 00000000006C4EF6 Unknown Unknown
> Unknown
> >
> > pmemd.cuda 00000000004E5CD6 Unknown Unknown
> Unknown
> >
> > pmemd.cuda 0000000000409F66 Unknown Unknown
> Unknown
> >
> > libc.so.6 0000003973E1ED1D Unknown Unknown
> Unknown
> >
> > pmemd.cuda 0000000000409DE1 Unknown Unknown
> Unknown
> >
> > [comet-34-06.sdsc.edu:mpispawn_0][child_handler] MPI process (rank: 0,
> > pid:
> > 186206) exited with status 71
> >
> >
> > Does anyone know what is wrong in it?
> >
> >
> > Thanks,
> >
> >
> > Best,
> >
> >
> > *Chunli*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Tue Aug 01 2017 - 13:30:03 PDT
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