Re: [AMBER-Developers] AMBER Master Branch

From: Rai Nitin <>
Date: Fri, 20 May 2016 18:38:53 +0530

The new patch should mainly improve parallel performance.

For GB, one has to compile using MPI + OpenMP.

To build MPI + OpenMP
        If you have already built an MPI version you can take a backup of
pmemd.MPI executable since the
               MPI + OpenMP version is also named pmemd.MPI

        cd $AMBERHOME
        make clean
        ./configure ?intelmpi -openmp intel
        make install

Running GB simulations:
        export I_MPI_PIN_MODE=pm
        export I_MPI_PIN_DOMAIN=auto
                mpirun -np NSOCKETS \
        -env OMP_NUM_THREADS=NCORES*2 \
        -env KMP_AFFINITY="scatter,granularity=core" \
        -env KMP_STACKSIZE=10M \
        $AMBERHOME/bin/pmemdMPI ARGS

Running PME
        export I_MPI_PIN_MODE=pm
        export I_MPI_PIN_DOMAIN=auto
        mpirun -np NSOCKETS * NCORES \
        $AMBERHOME/bin/pmemd.hybrid.MPI ARGS

Substitute actual numbers for NSOCKETS and NCORES and arguments instead
        If you have a 2 socket server, each with 10 cores
        Then NSOCKETS = 2 and NCORES = 10
         FOR GB
                         MPI ranks=2, number of openmp threads = 20
        FOR PME
                MPI ranks=20

Please let us know if you face any problems.

From: David A Case <>
To: AMBER Developers Mailing List <>
Date: 20-05-2016 16:53
Subject: Re: [AMBER-Developers] AMBER Master Branch

On Mon, May 16, 2016, Charles Lin wrote:
> I was hoping if anyone had time they'd be able to help test out the
> current changes to pmemd in the master branch. We plan on pushing out
> this patch in around 2-2.5 weeks time. It has been sitting in the
> master branch since AMBER16 release. Its a fairly big update that
> increases performance around 1.2x-2x for CPU therefore it effects a lot
> of key files and routines in the code.

The new code compiles and passes all the tests on Intel 16.0.3 + MKL
under Linux.

Can you say where we should look for performance increases? My tests on
the jac benchmark for the serial code show no change in timings, compared
the amber16-with-patches branch. Haven't tried any other benchmarks yet.
(CPU is Intel(R) Xeon(R) CPU E5-2650 v3 . 2.30GHz.)


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