Re: [AMBER] How to run the test in HPC cluster and GPU

From: Charles Lin <Charles.lin.silicontx.com>
Date: Fri, 5 Oct 2018 15:14:49 +0000

Assuming a bash environment:

cd $AMBERHOME/test
export DO_PARALLEL="mpirun -np 2" #you can replace 2 with however many mpi tasks you want to run with
make test

The DO_PARALLEL environment variable just sets the test run scripts to replace $DO_PARALLEL with that command. You'll have to make sure that you have mpi installed or are using some sort of mpi package which you can check with "which mpirun" (generally people use mpich, mvapich, openmpi, or intel mpi), if you don't have an mpi package installed or loaded (might be a module since you're on a cluster environment) then you'll just get a bunch of failures looking for mpi. You'll also need to make sure you installed the mpi version of amber because the MPI tests run with the MPI binary (cpptraj.MPI, pmemd.MPI etc).

Cd $AMBERHOME
./configure -mpi gnu
make

-Charlie

´╗┐On 10/4/18, 7:16 AM, "Saikat Pal" <saikatpaliitg.yahoo.com> wrote:

    Dear all,
    Recently we have bought amber18 package. I want to know how to run the test. In our HPC slurm is using.
>From page no 25 of manual 18:# Note the value below may depend on your MPI implementation
    export DO_PARALLEL="mpirun -np 2"
    make test
    # Note, some tests, like the replica exchange tests, require more
    # than 2 threads, so we suggest that you test with either 4 or 8
    # threads as well
    export DO_PARALLEL="mpirun -np 8"
    make test


    I want to perform make test.

    Thanks and Regards,
    Saikat Pal



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Received on Fri Oct 05 2018 - 08:30:03 PDT
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