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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 05 2018 - 08:30:03 PDT
