This requires configuring |Gromacs| to build with an external MPI
library. By default, this :ref:`mdrun <gmx mdrun>` executable is run with
-:ref:`mdrun_mpi`. All of the considerations for running single-node
+``gmx_mpi mdrun``. All of the considerations for running single-node
:ref:`mdrun <gmx mdrun>` still apply, except that ``-ntmpi`` and ``-nt`` cause a fatal
error, and instead the number of ranks is controlled by the
MPI environment.
mpirun -np 16 gmx_mpi mdrun
-Starts :ref:`mdrun_mpi` with 16 ranks, which are mapped to
+Starts :ref:`gmx mdrun` with 16 ranks, which are mapped to
the hardware by the MPI library, e.g. as specified
in an MPI hostfile. The available cores will be
automatically split among ranks using OpenMP threads,
mpirun -np 16 gmx_mpi mdrun -npme 5
-Starts :ref:`mdrun_mpi` with 16 ranks, as above, and
+Starts :ref:`gmx mdrun` with 16 ranks, as above, and
require that 5 of them are dedicated to the PME
component.
mpirun -np 11 gmx_mpi mdrun -ntomp 2 -npme 6 -ntomp_pme 1
-Starts :ref:`mdrun_mpi` with 11 ranks, as above, and
+Starts :ref:`gmx mdrun` with 11 ranks, as above, and
require that six of them are dedicated to the PME
component with one OpenMP thread each. The remaining
five do the PP component, with two OpenMP threads
mpirun -np 4 gmx_mpi mdrun -ntomp 6 -nb gpu -gputasks 00
-Starts :ref:`mdrun_mpi` on a machine with two nodes, using
+Starts :ref:`gmx mdrun` on a machine with two nodes, using
four total ranks, each rank with six OpenMP threads,
and both ranks on a node sharing GPU with ID 0.
mpirun -np 8 gmx_mpi mdrun -ntomp 3 -gputasks 0000
Using a same/similar hardware as above,
-starts :ref:`mdrun_mpi` on a machine with two nodes, using
+starts :ref:`gmx mdrun` on a machine with two nodes, using
eight total ranks, each rank with three OpenMP threads,
and all four ranks on a node sharing GPU with ID 0.
This may or may not be faster than the previous setup
mpirun -np 20 gmx_mpi mdrun -ntomp 4 -gputasks 00
-Starts :ref:`mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+Starts :ref:`gmx mdrun` with 20 ranks, and assigns the CPU cores evenly
across ranks each to one OpenMP thread. This setup is likely to be
suitable when there are ten nodes, each with one GPU, and each node
has two sockets each of four cores.
mpirun -np 10 gmx_mpi mdrun -gpu_id 1
-Starts :ref:`mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+Starts :ref:`gmx mdrun` with 20 ranks, and assigns the CPU cores evenly
across ranks each to one OpenMP thread. This setup is likely to be
suitable when there are ten nodes, each with two GPUs, but another
job on each node is using GPU 0. The job scheduler should set the
mpirun -np 20 gmx_mpi mdrun -gpu_id 01
-Starts :ref:`mdrun_mpi` with 20 ranks. This setup is likely
+Starts :ref:`gmx mdrun` with 20 ranks. This setup is likely
to be suitable when there are ten nodes, each with two
GPUs, but there is no need to specify ``-gpu_id`` for the
normal case where all the GPUs on the node are available
* Don't use double precision unless you're absolute sure you need it.
* Compile the FFTW library (yourself) with the correct flags on x86 (in most
cases, the correct flags are automatically configured).
-* On x86, use gcc or icc as the compiler (not pgi or the Cray compiler).
+* On x86, use gcc as the compiler (not icc, pgi or the Cray compiler).
* On POWER, use gcc instead of IBM's xlc.
* Use a new compiler version, especially for gcc (e.g. from version 5 to 6
the performance of the compiled code improved a lot).
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff