Hi, Pan,
I submit the job as you said and hope it will work.
Thanks,
Best,
*Chunli*
On Tue, Aug 1, 2017 at 4:37 PM, Feng Pan <fpan3.ncsu.edu> wrote:
> Hi, Chunli
>
> For sequence job, the copies for each image will run in sequence but
> for different images you still need parallel threads.
> Here you define 8 images so you need 8 GPUs and run with pmemd.cuda.MPI
>
> Feng
>
> On Tue, Aug 1, 2017 at 4:07 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
>
> > 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
> > >
> >
> > _______________________________________________
> > 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 - 14:00:03 PDT
