GROMACS

Remove commrec from hardware detection

This is preparatory refactoring for aspects of #2395

The OpenCL logic was ineffective, because duty is not yet decided, and
anyway we might soon want the detection on PME-only ranks.

Replaced the thread-MPI single-rank assertion with a more direct
implementation.

Minimized contents of detecthardware.h

Refs #2395

Change-Id: I03af65805bd14515a0213d511ae8cdb627c2f05c

Document DOMAINDECOMP correctly

It is likely there are numerous cases where this is used mistakenly
when havePPDomainDecomposition expresses the real intent. If so,
runs with 1 PP and 1 PME rank may have buggy behaviour.

Refs #2395

Change-Id: I07be73a6c690887b3043140a2a78ae6fe6bb17f1

Require explicit MPI_COMM for gmx_bcast and gmx_barrier

This changes gmx_bcast and gmx_barrier to take the MPI communicator
explicitly instead of taking a pointer to t_commrec and using
mpi_comm_mygroup. This also allows to remove gmx_bcast_sim and leave
the responsibility of passing the right communicator to the caller.

This is a first step in breaking up t_commrec. These functions
are the subset of low-level networking functions which are used
before domain decomposition (and hence PP/PME ranks) is set up.

Refs #2395

Make init_dires independent of t_commrec

init_disres was requesting a full pointer to the commrec,
but only uses a single communicator and checks for master rank
and whether the run is parallel. This information is now passed
in explicitly, simplifying the planned splitting of t_commrec.

Note that passing a nullptr for commrec was (mis)used by
gmx_disre only - effectively signalling that init_disres was
called from an analysis tool and not from mdrun. This has
been made explicit.

Refs #2395

Make boxdeformation independent of t_commrec

boxdeformation requested a pointer to the full t_commrec,
but only used on communicator and information on whether
the current rank is master and whether the simulation
is run in parallel. This has been made explicit, simplifying
subsequent changes splitting up t_commrec.

Refs #2395

Divide default communicator from DD communicators

The communicators mpi_comm_mysim and mpi_comm_mygroup inside
t_commrec got initialized in init_commrec (to MPI_COMM_WORLD
if no multisim, to a subset otherwise). These communicators
were then used in subsequent setup work, before they got
reassigned during the construction of the DDBuilder object
and the construction of the actual domain decomposition object.
Effectively, this means that the same communicators (and, hence,
identical function calls) do very different things depending on
whether they get used before or after the setup of domain
decomposition. It also means that before DD set up, mpi_comm_mysim
and mpi_comm_mygroup are identical.

This change introduces an additional communicator within
t_commrec, mpiDefaulCommunicator, which helps to make these
implicit assumptions explicit. Consequently, this also redefines
PAR, MASTER, and SIMMASTER.

This change will allow to move the sim and group communicators,
which are now only created at DD time, into the DD object,
logically separating the DD object from t_commrec.

Refs #2395

Divide default communicator from DD communicators

The communicators mpi_comm_mysim and mpi_comm_mygroup inside
t_commrec got initialized in init_commrec (to MPI_COMM_WORLD
if no multisim, to a subset otherwise). These communicators
were then used in subsequent setup work, before they got
reassigned during the construction of the DDBuilder object
and the construction of the actual domain decomposition object.
Effectively, this means that the same communicators (and, hence,
identical function calls) do very different things depending on
whether they get used before or after the setup of domain
decomposition. It also means that before DD set up, mpi_comm_mysim
and mpi_comm_mygroup are identical.

This change introduces an additional communicator within
t_commrec, mpiDefaulCommunicator, which helps to make these
implicit assumptions explicit. Consequently, this also redefines
PAR, MASTER, and SIMMASTER.

This change will allow to move the sim and group communicators,
which are now only created at DD time, into the DD object,
logically separating the DD object from t_commrec.

Refs #2395