243 lines
10 KiB
Markdown
243 lines
10 KiB
Markdown
# MPI model
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The [Message Passing Interface (MPI)][mpi] is a standard library interface
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specification for message-passing communication libraries targeting parallel
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computing architectures. The interface defines functions for point-to-point
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communication primitives, collectives, remote memory access (RMA), I/O and
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process management.
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The [Sonar][sonar] library instruments the most essential MPI functions that any
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user application or any external library may execute. Sonar tracks the calls to
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these MPI functions made at each point. Both users and developers can use this
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information to analyze the time spent inside MPI functions. The next section
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explains a view that is provided to achieve this goal.
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The Sonar library is compatible with the MPI standards 3.0, 3.1 and 4.0. See the
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[MPI documentation][mpi docs] for more information about the MPI standards and
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their functions.
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[mpi]: https://www.mpi-forum.org
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[mpi docs]: https://www.mpi-forum.org/docs
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[sonar]: https://github.com/bsc-pm/sonar
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[sonar docs]: https://github.com/bsc-pm/sonar#readme
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Sonar requires an installation of the ovni library and an MPI library. Use the
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option `--with-ovni=prefix` when building Sonar to specify the ovni prefix. The
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building procedure will compile and install the `libsonar-mpi.so`. See the
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[Sonar documentation][sonar docs] for more details about the building steps.
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An application can instrument the MPI function calls by linking with the Sonar
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library `libsonar-mpi.so`. At run-time, the Sonar library does not enable the
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instrumentation by default. Sonar instruments the MPI functions when the
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environment variable `SONAR_MPI_INSTRUMENT` is defined to `ovni`. Its default
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value is `none`.
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As an example, a user can generate a trace with MPI function events of an MPI
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program `app.c` in this way:
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```
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$ mpicc -c app.c -o app.o
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$ mpicc app.o -o app -L${SONAR_PREFIX}/lib -lsonar-mpi
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$ export SONAR_MPI_INSTRUMENT=ovni
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$ mpirun -n 2 ./app
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```
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This will generate an ovni trace in the `ovni` directory, which can be emulated
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using the `ovniemu` tool.
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!!! Note
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Notice that the order of libraries at the linking stage is important. The
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Sonar library should always have precedence on the MPI library. That's the
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usual behavior when using `mpicc` tools. The `mpicc` tool should link the
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application with the MPI libraries as the last libraries in the list of
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application's dependencies. If this order is not respected, the Sonar
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library would not be able to intercept the MPI function calls and instrument
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them.
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!!! Note
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Notice the Task-Aware MPI (TAMPI), as well as other external libraries,
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intercepts the MPI functions and may call MPI functions instead. Thus, the
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order in which such libraries and Sonar are linked to the application will
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also alter the resulting ovni trace. Give precedence to the Sonar library to
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instrument the MPI function calls made by the application. You can achieve
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by linking your application with the linking options `-lsonar-mpi -ltampi`.
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Otherwise, give precendence to the TAMPI library to track the real MPI
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functions that are being executed (i.e., the ones that the MPI library
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actually runs). In this case, use the linking options `-ltampi -lsonar-mpi`.
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## Function view
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The function view attempts to provide a general overview of which are the MPI
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functions being executed at any point in time. The function view shows the MPI
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functions called by each thread (and for each CPU, the MPI functions executed
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by the running thread in that CPU).
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The function states shown in this view are listed below. Each function state
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(in bold) includes a list of all the MPI functions that are instrumented as
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that particular state. Notice that only the most important functions are
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instrumented. Also, notice that not all functions have their own state. For
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instance, the large count MPI (with `_c` suffix) introduced in MPI 4.0, the
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extended functions (with `v` or `w` suffix), and Fortran functions (with lower
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case name and `_` suffix) are instrumented as their simple C function without
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suffix.
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- *Setup functions*: The running thread is executing MPI setup functions to
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initialize and finalize the MPI environment. The following function states
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are shown:
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- **MPI_Init**: `MPI_Init`, `mpi_init_`
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- **MPI_Init_thread**: `MPI_Init_thread`, `mpi_init_thread_`
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- **MPI_Finalize**: `MPI_Finalize`, `mpi_finalize_`
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- *Request functions*: The running thread is executing MPI functions that wait
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or test MPI requests after being generated by non-blocking MPI operations. The
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following functions are instrumented:
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- **MPI_Wait**: `MPI_Wait`, `mpi_wait_`
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- **MPI_Waitall**: `MPI_Waitall`, `mpi_waitall_`
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- **MPI_Waitany**: `MPI_Waitany`, `mpi_waitany_`
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- **MPI_Waitsome**: `MPI_Waitsome`, `mpi_waitsome_`
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- **MPI_Test**: `MPI_Test`, `mpi_test_`
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- **MPI_Testall**: `MPI_Testall`, `mpi_testall_`
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- **MPI_Testany**: `MPI_Testany`, `mpi_testany_`
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- **MPI_Testsome**: `MPI_Testsome`, `mpi_testsome_`
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- *Point-to-point functions*: The running thread is communicating through MPI
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by executing point-to-point primitives. The instrumented functions are:
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- **MPI_Recv**: `MPI_Recv`, `MPI_Recv_c`, `mpi_recv_`
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- **MPI_Send**: `MPI_Send`, `MPI_Send_c`, `mpi_send_`
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- **MPI_Bsend**: `MPI_Bsend`, `MPI_Bsend_c`, `mpi_bsend_`
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- **MPI_Rsend**: `MPI_Rsend`, `MPI_Rsend_c`, `mpi_rsend_`
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- **MPI_Ssend**: `MPI_Ssend`, `MPI_Ssend_c`, `mpi_ssend_`
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- **MPI_Sendrecv**: `MPI_Sendrecv`, `MPI_Sendrecv_c`, `mpi_sendrecv_`
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- **MPI_Sendrecv_replace**: `MPI_Sendrecv_replace`, `MPI_Sendrecv_replace_c`,
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`mpi_sendrecv_replace_`
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- **MPI_Irecv**: `MPI_Irecv`, `MPI_Irecv_c`, `mpi_irecv_`
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- **MPI_Isend**: `MPI_Isend`, `MPI_Isend_c`, `mpi_isend_`
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- **MPI_Ibsend**: `MPI_Ibsend`, `MPI_Ibsend_c`, `mpi_ibsend_`
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- **MPI_Irsend**: `MPI_Irsend`, `MPI_Irsend_c`, `mpi_irsend_`
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- **MPI_Issend**: `MPI_Issend`, `MPI_Issend_c`, `mpi_issend_`
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- **MPI_Isendrecv**: `MPI_Isendrecv`, `MPI_Isendrecv_c`, `mpi_isendrecv_`
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- **MPI_Isendrecv_replace**: `MPI_Isendrecv_replace`,
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`MPI_Isendrecv_replace_c`, `mpi_isendrecv_replace_`
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- *Collective functions*: The running thread is communicating through MPI by
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executing collective functions. The instrumented functions are:
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- **MPI_Gather**: `MPI_Gather`, `MPI_Gatherv`, `MPI_Gather_c`,
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`MPI_Gatherv_c`, `mpi_gather_`, `mpi_gatherv_`
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- **MPI_Allgather**: `MPI_Allgather`, `MPI_Allgatherv`, `MPI_Allgather_c`,
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`MPI_Allgatherv_c`, `mpi_allgather_`, `mpi_allgatherv_`
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- **MPI_Scatter**: `MPI_Scatter`, `MPI_Scatterv`, `MPI_Scatter_c`,
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`MPI_Scatterv_c`, `mpi_scatter_`, `mpi_scatterv_`
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- **MPI_Reduce**: `MPI_Reduce`, `MPI_Reduce_c`, `mpi_reduce_`
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- **MPI_Reduce_scatter**: `MPI_Reduce_scatter`, `MPI_Reduce_scatter_c`,
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`mpi_reduce_scatter_`
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- **MPI_Reduce_scatter_block**: `MPI_Reduce_scatter_block`,
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`MPI_Reduce_scatter_block_c`, `mpi_reduce_scatter_block_`
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- **MPI_Allreduce**: `MPI_Allreduce`, `MPI_Allreduce_c`, `mpi_allreduce_`
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- **MPI_Barrier**: `MPI_Barrier`, `MPI_Barrier_c`, `mpi_barrier_`
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- **MPI_Bcast**: `MPI_Bcast`, `MPI_Bcast_c`, `mpi_bcast`
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- **MPI_Alltoall**: `MPI_Alltoall`, `MPI_Alltoallv`, `MPI_Alltoallw`,
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`MPI_Alltoall_c`, `MPI_Alltoallv_c`, `MPI_Alltoallw_c`, `mpi_alltoall_`,
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`mpi_alltoallv_`, `mpi_alltoallw_`
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- **MPI_Scan**: `MPI_Scan`, `MPI_Scan_c`, `mpi_scan_`
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- **MPI_Exscan**: `MPI_Exscan`, `MPI_Exscan_c`, `mpi_exscan_`
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- **MPI_Igather**: `MPI_Igather`, `MPI_Igatherv`, `MPI_Igather_c`,
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`MPI_Igatherv_c`, `mpi_igather_`, `mpi_igatherv_`
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- **MPI_Iallgather**: `MPI_Iallgather`, `MPI_Iallgatherv`,
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`MPI_Iallgather_c`, `MPI_Iallgatherv_c`, `mpi_iallgather_`,
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`mpi_iallgatherv_`
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- **MPI_Iscatter**: `MPI_Iscatter`, `MPI_Iscatterv`, `MPI_Iscatter_c`,
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`MPI_Iscatterv_c`, `mpi_iscatter_`, `mpi_iscatterv_`
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- **MPI_Ireduce**: `MPI_Ireduce`, `MPI_Ireduce_c`, `mpi_ireduce_`
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- **MPI_Iallreduce**: `MPI_Iallreduce`, `MPI_Iallreduce_c`, `mpi_iallreduce_`
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- **MPI_Ireduce_scatter**: `MPI_Ireduce_scatter`, `MPI_Ireduce_scatter_c`,
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`mpi_ireduce_scatter_`
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- **MPI_Ireduce_scatter_block**: `MPI_Ireduce_scatter_block`,
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`MPI_Ireduce_scatter_block_c`, `mpi_ireduce_scatter_block_`
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- **MPI_Ibarrier**: `MPI_Ibarrier`, `MPI_Ibarrier_c`, `mpi_ibarrier_`
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- **MPI_Ibcast**: `MPI_Ibcast`, `MPI_Ibcast_c`, `mpi_ibcast_`
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- **MPI_Ialltoall**: `MPI_Ialltoall`, `MPI_Ialltoallv`, `MPI_Ialltoallw`,
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`MPI_Ialltoall_c`, `MPI_Ialltoallv_c`, `MPI_Ialltoallw_c`,
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`mpi_ialltoall_`, `mpi_ialltoallv_`, `mpi_ialltoallw_`
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- **MPI_Iscan**: `MPI_Iscan`, `MPI_Iscan_c`, `mpi_iscan_`
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- **MPI_Iexscan**: `MPI_Iexscan`, `MPI_Iexscan_c`, `mpi_iexscan_`
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!!! Note
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The Sonar library does not support large count MPI functions for the Fortran
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language yet, and thus, these functions are not instrumented.
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The figure below shows an example of the MPI function view. The program executes
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a distributed stencil algorithm with MPI and OmpSs-2. There are several MPI
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processes, each running OmpSs-2 tasks on an exclusive set of CPUs. Most of these
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are computation tasks, while the others are concurrent tasks performing
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communications using the blocking mode of the TAMPI library. These use `MPI_Send`
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and `MPI_Recv` functions to send and receive blocks of data. The program was
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linked with Sonar and preceding the TAMPI library. Thus, the trace shows the
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blocking MPI function calls made by the application.
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The light green areas correspond to the `MPI_Init_thread` calls, the grey ones
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are `MPI_Send` calls and the dark green areas are `MPI_Recv` calls. There are
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other secondary calls like `MPI_Bcast` (orange), `MPI_Barrier` (blue) and
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`MPI_Finalize` (red) calls.
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As mentioned above, the trace shows the blocking MPI functions called by the
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application because Sonar was placed before TAMPI in the linking order. However,
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these blocking calls may not be actually executed by the MPI library; TAMPI will
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transparently replace them with non-blocking calls (e.g., `MPI_Isend` and
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`MPI_Irecv`) and a polling mechanism for the generated MPI requests. If you want
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to explore the actual MPI functions being executed, you should link the Sonar
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library after TAMPI.
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