wiki:Public/User_Guide/TAMPI_NAM

Accessing Network Attached Memory (NAM) from Tasks using TAMPI

Table of contents:

Quick Overview

This page explains how to access Network Attached Memory (NAM) from tasks in hybrid task-based MPI+OmpSs-2 applications. The NAM memory regions can be accessed through MPI RMA windows thanks to the extensions on the MPI RMA interface that is implemented by ParaStation MPI. The user applications can allocate MPI windows that represent NAM memory regions and perform RMA operations on those NAM windows, such as MPI_Put and MPI_Get. Following the standard MPI RMA fence synchronization mode, applications can open access epochs on those windows by calling MPI_Win_fence, then perform the desired RMA operations on the NAM data, and finally, close the epoch with another call to MPI_Win_fence. This NAM support has been integrated into the OmpSs-2 tasking model, allowing accessing NAM regions from OmpSs-2 tasks efficiently and safely through the Task-Aware MPI (TAMPI) library.

In the following sections, we describe the TAMPI library and how hybrid task-based applications can access NAM memory regions. Finally, we show the Heat equation benchmark as an example of using this support to save snapshots of the computed matrix in a NAM allocation.

Task-Aware MPI (TAMPI)

The most common practice in hybrid applications is combining MPI and OpenMP in a fork-join approach, where computation phases are parallelized using OpenMP and communication phases are serialized. This is a simple approach but it usually does not scale as well as the MPI-only parallelizations. A more advanced technique is the taskification of both computation and communication phases using the task data dependencies to connect both task types and guarantee a correct execution order. This strategy allows applications to parallelize their workloads following the data-flow paradigm principles, where communications are integrated into the execution flow of tasks. However, MPI and OpenMP were not designed to be combined efficiently nor safely; MPI only defines threading levels to safely call MPI functions from multiple threads. For instance, calling blocking MPI operations from different tasks concurrently could end up in a communication deadlock.

The Task-Aware MPI library was recently proposed to overcome these limitations. TAMPI allows the safe and efficient taskification of MPI communications, including all blocking, non-blocking, point-to-point, and collective operations. The TAMPI library allows calling MPI communication operations from within tasks freely. On the one hand, blocking MPI operations (e.g. MPI_Recv) pause the calling task until the operation completes, but in the meantime, the tasking runtime system may use the CPU to execute other ready tasks.

On the other hand, non-blocking operations (e.g. MPI_Irecv) can be bound to a task through two API functions named TAMPI_Iwait and TAMPI_Iwaitall, which have the same parameters as the standard MPI_Wait and MPI_Waitall, respectively. These two TAMPI functions are non-blocking and asynchronous and can be used to bind the completion of the calling task to the finalization of the MPI requests passed as parameters. The calling task will continue its execution immediately without blocking, transferring the management of the MPI requests to the TAMPI library, and will be able to finish its execution freely. However, the calling task will not fully complete until (1) it finishes its execution and (2) all its bound MPI operations complete. Upon the task completion, its data dependencies will be released and its successor tasks will be ready to execute. Usually its successor tasks will be the ones that consume the received data or reuse a sending buffer. Notice that this approach requires tasks to define data dependencies on the communication buffers in order to guarantee a correct execution order between communication tasks and consumer/reuser tasks. We must highlight that a task can call those TAMPI functions several times, binding multiple MPI requests during its execution.

More information about the TAMPI library, some examples and its code are available at https://github.com/bsc-pm/tampi.

Accessing NAM through ParaStation MPI and TAMPI

Our main objective is to allow tasks to access data stored in NAM regions efficiently and potentially in parallel, e.g. using several tasks to put/get data to/from the NAM. The mechanism to access NAM regions is provided by the ParaStation MPI and is based on the MPI RMA model. ParaStation MPI allows allocating NAM regions as MPI RMA windows, so that they can be accessed remotely by the ranks that participate in those windows using the standard MPI_Put and MPI_Get RMA operations. This support is based on the fence synchronization mode of the MPI RMA model. This mode works as follows: (1) all ranks participating in a given window have to open an access epoch on that window calling MPI_Win_fence, (2) perform the desired RMA operations on the NAM window reading or writing NAM's data, and (3) close the epoch with another call to MPI_Win_fence. This mode of operation can be easily integrated into a hybrid task-based application by instantiating a task that opens the epoch on the NAM window with an MPI fence, followed by multiple concurrent tasks that write or read data to/from the NAM window, and finally, another task that closes the access epoch with a fence. Notice that tasks should define the corresponding dependencies on the window to ensure this strict order of execution.

However, since the MPI fence operations are blocking and synchronous, calling them from tasks is not safe. Having multiple windows and opening/closing epochs on them concurrently from different tasks could end up producing a communication deadlock. Thus, the taskification of the window fences and RMA operations should be managed by the TAMPI library so that we can execute them efficiently and safely, and potentially in parallel among different windows. To that end, we have extended the ParaStation MPI to provide a new non-blocking function called MPI_Win_ifence that starts a fence operation on a specific window and generates an MPI request to check its completion later on. This MPI request can be then naturally handled by the TAMPI library using the TAMPI_Iwait function, as shown below.

// Open RMA access epoch to write the NAM window
#pragma oss task inout(namWindow)
{
    MPI_Request request;
    MPI_Win_ifence(0, namWindow, &request);
    TAMPI_Iwait(&request, MPI_STATUS_IGNORE);
}

// Write to NAM region concurrently
for (...) {
    #pragma oss task concurrent(namWindow)
    MPI_Put(..., namWindow);
}

// Close RMA access epoch to write the NAM window
#pragma oss task inout(namWindow)
{
    MPI_Request request;
    MPI_Win_ifence(0, namWindow, &request);
    TAMPI_Iwait(&request, MPI_STATUS_IGNORE);
}

In this example, the first task opens an access epoch on the NAM window using the new MPI_Win_ifence. This function starts a fence operation, generates an MPI request and returns immediately. This request is then handled by the TAMPI library through the TAMPI_Iwait, which binds the completion of the calling task to the finalization of the fence operation. The task can continue executing immediately without blocking and finalize its execution. Once the fence operation finalizes, the task will complete automatically and its successor task will become ready. The successors are the tasks that perform MPI_Put operations on the NAM window concurrently. Notice that the dependencies of these tasks allow them to execute all MPI_Put in parallel, but always after the window epoch has been fully opened. After all MPI_Put tasks have executed, the last task can run and close the access epoch on the NAM window.

The extended version of ParaStation MPI supporting the new MPI_Win_ifence can be found in the ifence-nam branch at the https://gitlab.version.fz-juelich.de/DEEP-EST/psmpi repository. The Task-Aware MPI library did not need any extension to support the aforementioned mode of operation; the lastest stable release should be compatible.

Heat Benchmark

In this section, we exemplify the use of TAMPI and NAM windows through the Heat benchmark. We use an iterative Gauss-Seidel method to solve the Heat equation, which is a parabolic partial differential equation that describes the distribution of heat in a given region over time. This benchmark simulates the heat diffusion on a 2D matrix of floating-point elements during multiple timesteps. The 2D matrix is logically divided into 2D blocks and may have multiple rows and columns of blocks. The computation of an element at position M[r][c] in the timestep t depends on the value of the top and left elements (M[r-1][c] and M[r][c-1]) computed in the same timestep t, and the right and bottom elements (M[r][c+1] and M[r+1][c]) computed in the previous timestep t-1. We can extrapolate this logic to the context of blocks so that a block has a dependency on the computation of its adjacent blocks. Notice that the computation of the blocks in a diagonal is fully concurrent because there are no dependencies between them.

There are three different MPI versions, and all of them distribute the 2D matrix across the MPI ranks assigning consecutive rows of blocks to each rank. Note that the matrix is distributed by blocks vertically but not horizontally. Therefore, an MPI rank has two neighboring ranks: one above and another below. The exceptions are the first and last ranks since they have a single neighbor. This distribution requires the neighboring ranks to exchange the external rows (halos) from their boundary blocks in order to compute their local blocks in each timestep.

This benchmark is publicly available in the heat subfolder at the https://gitlab.version.fz-juelich.de/DEEP-EST/ompss-2-benchmarks repository. The first version is based on an MPI-only parallelization, while the other two are hybrid MPI+OmpSs-2 leveraging tasks and the TAMPI library. We briefly describe each one below:

  • 01.heat_mpi.bin: A straightforward MPI-only implementation using blocking MPI primitives (MPI_Send and MPI_Recv) to send and receive the halo rows. The computation of blocks and exchange of halos inside each rank is completely sequential.
  • 02.heat_itampi_ompss2_tasks.bin: A hybrid MPI+OmpSs-2 version leveraging TAMPI that performs both computation and communication using tasks and data dependencies. It instantiates a task to compute each of the blocks inside each rank and for each of the timesteps. It also creates sending and receiving tasks to exchange the block halo rows for each of the boundary blocks. The execution of tasks follows a data-flow model because tasks declare the dependencies on the data they read/modify. Moreover, communication tasks call non-blocking MPI primitives and leverage the non-blocking mechanism of TAMPI (TAMPI_Iwait), so communications are fully non-blocking and asynchronous from the user point of view. Communication tasks issue non-blocking operations that are transparently managed and periodically checked by TAMPI. These tasks do not explicitly wait for their communication, but they delay their completion (asynchronously) until their MPI communications finish.
  • 03.heat_tampirma_ompss2_tasks.bin: An implementation similar to 02.heat_itampi_ompss2_tasks.bin but using MPI RMA operations (MPI_Put) to exchange the block halo rows. This program leverages the MPI active target RMA communication using the MPI window fences to open/close RMA access epochs. It uses the TAMPI library and the new integration for the MPI_Win_ifence synchronization function. We use TAMPI_Iwait to bind the completion of a communication task to the finalization of a MPI_Win_ifence. Therefore, the opening/closing of RMA access epochs is completely non-blocking and asynchronous from the user point of view. As an optimization, we register multiple MPI RMA windows for each rank to allow concurrent communications through the different RMA windows. Each RMA window holds a part of the halo row, which may belong to multiple logical blocks. There is a communication task exchanging each part of the halo row through a different window.

Using NAM in Heat benchmark

In this benchmark, we use the NAM memory to save the computed matrix periodically. The idea is to save different states (snapshots) of the matrix during the execution in a persistent NAM memory region. Then, another program could retrieve all the matrix snapshots, process them and produce a GIF animation showing the heat's evolution throughout the execution. Notice that we cannot use regular RAM for that purpose because the matrix could be huge, and we may want to store tens of matrix snapshots. We also want to keep it persistently so that other programs could process the stored data later on. Moreover, the memory should be easily accessible by the multiple MPI ranks, or their tasks in parallel. The NAM memory satisfies all these requirements, and as previously stated, ParaStation MPI allows accessing NAM allocations through standard MPI RMA operations. We implement the NAM snapshots in the TAMPI variants: 02.heat_itampi_ompss2_tasks.bin and 03.heat_tampirma_ompss2_tasks.bin.

To that end, the Heat benchmark allocates a single MPI window that holds the whole NAM region, which is used by all ranks (via the MPI_COMM_WORLD communicator) and throughout the execution. Every few timesteps (specified by the user), it saves the whole matrix into a specific NAM subregion. Each timestep that saves a matrix snapshot employs a distinct NAM subregion. These subregions are placed one after the other, consecutively, without overlapping. Thus, the entire NAM region's size is the full matrix size multiplied by the number of times the matrix will be saved (i.e. number of snapshots). We allocate the NAM memory region using the Managed Contiguous layout (psnam_structure_managed_contiguous). This means that the MPI rank 0 allocates the whole region, but each rank acquires a consecutive memory subset, where it will store its blocks' data for every snapshot. For instance, the NAM allocation will first have the space for storing all snapshots of the blocks from rank 0, followed by the space for all snapshots of blocks from rank 1, and so on. By using that layout, NAM subregions are rank-addressed using the rank it belongs to, simplifying the saving and retrieving of snapshots.

When a timestep has to save a snapshot, the application instantiates multiple tasks that save the matrix data into the corresponding NAM subregion. Each MPI rank creates a task for writing (copying) the data of each of its matrix blocks into the NAM subregion. These communication tasks do not have any data dependency between them, so they can write data to the NAM using regular MPI_Put in parallel. Ranks only write to their own subregions, never in other ranks' subregions. Nevertheless, we must call all MPI_Puts inside an MPI RMA access epoch, so there must be a window fence call before all the MPI_Puts, and another one after them to close the epoch, for each of the snapshot timesteps. Here is where we leverage the new function MPI_Win_ifence along with the TAMPI non-blocking support. In this way, we can fully taskify both synchronization and writing of the NAM window, keeping the data-flow model and without closing the parallelism for doing the snapshots (e.g., with a taskwait). Thanks to the task data dependencies and TAMPI, we cleanly include the snapshots in the application's data-flow execution as any other regular communication task.

The following pseudo-code shows how the saving of snapshots works in 02.heat_itampi_ompss2_tasks.bin:

void solve() {
    int namSnapshotFreq = ...;
    int namSnapshotId = 0;

    for (t = 1; t <= timesteps; ++t) {
        // Computation and communication tasks declaring
        // dependencies on the blocks they process
        gaussSeidelSolver(..all blocks in current rank..);

        if (t % namSnapshotFreq == 0) {
            namSaveMatrix(namSnapshotId, namWindow, ...);
            ++namSnapshotId;
        }
    }
    #pragma oss taskwait
}

The function above is the main procedure that executes the Heat's timesteps applying the Gauss-Seidel method. All MPI ranks run this function concurrently, each one working with their corresponding blocks from the matrix. In each timestep, the gaussSeidelSolver function instantiates all the computation and communication tasks that process the rank's blocks and exchanges the halo rows with the neighboring ranks. These tasks declare the proper input/output dependencies on the blocks they are reading/writing. Every some timesteps, the algorithm calls namSaveMatrix that issues tasks that will perform a snapshot of the matrix after computing that timestep. Notice that namSaveMatrix will have to instantiate tasks with input dependencies on the matrix blocks in order to perform the snapshot at the right moment of the execution, i.e. after the gaussSeidelSolver tasks from that timestep. Notice also that we identify each snapshot with the namSnapshotId, which we use to know where we should store the snapshot data inside the NAM window. The taskwait at the end of the algorithm is the only one in the whole execution; we do not close the parallelism anywhere else.

void namSaveMatrix(int namSnapshotId, MPI_Win namWindow, ...) {
    // Compute snapshot offset inside NAM region
    int snapshotOffset = namSnapshotId*sizeof(..all blocks in current rank..);

    // Open RMA access epoch to write the NAM window for this timestep
    #pragma oss task in(..all blocks in current rank..) inout(namWindow)
    {
        MPI_Request request;
        MPI_Win_ifence(0, namWindow, &request);
        TAMPI_Iwait(&request, MPI_STATUS_IGNORE);
    }

    // Write all blocks from the current rank to NAM subregions concurrently
    for (B : all blocks in current rank) {
        #pragma oss task in(..block B..) concurrent(namWindow)
        {
            MPI_Put(/* source data */   ..block B..,
                    /* target rank */   currentRank,
                    /* target offset */ snapshotOffset + B,
                    /* target window */ namWindow);
        }
    }

    // Close RMA access epoch to write the NAM window for this timestep
    #pragma oss task in(..all blocks in current rank..) inout(namWindow)
    {
        MPI_Request request;
        MPI_Win_ifence(0, namWindow, &request);
        TAMPI_Iwait(&request, MPI_STATUS_IGNORE);
    }
}

The function above is the one called periodically from the primary procedure. It instantiates the tasks that will perform the snapshot of the current rank's blocks into their corresponding NAM memory subregion. The first step is to compute the offset of the current snapshot inside the NAM region using the snapshot identifier. Before writing to the NAM window, the application must ensure that an MPI RMA access epoch has been opened on that window. That is what the first task is doing. After all the blocks have been computed in that timestep and are ready to be read (notice its task dependencies), the first task will run and execute an MPI_Win_ifence to start the window epoch's opening. This MPI function generates an MPI request and serves as parameter of the subsequent call to TAMPI_Iwait, which binds the current task's completion to the finalization of the MPI request. These calls are non-blocking and asynchronous, so the fence operation may not be completed after returning. The task can finish its execution, but it will not complete until the fence operation finishes. Once it finishes, TAMPI will automatically complete the task and make its successor tasks ready. The successors of the fence task are the ones that perform the actual writing (copying) of data into the NAM memory by calling MPI_Put. All blocks can be saved in the NAM memory in parallel by different tasks. The source of the MPI_Put is the block itself (in regular RAM), while the destination is the place where the block should be written inside the NAM region. After all writer tasks finish, it is the turn for the task that closes the MPI RMA access epoch on the NAM window. This one should behave similarly to the one that opened the epoch.

Notice that all tasks declare the proper dependencies on both the matrix blocks and the NAM window to guarantee their correct execution order. Thanks to these data dependencies and the TAMPI non-blocking feature, we can cleanly add the execution of the snapshots into the task graph, being executed asynchronously, and being naturally interleaved with the other computation and communication tasks. Finally, it is worth noting that the blocks are written into the NAM memory in parallel, utilizing the machine's CPU and network resources efficiently.

Requirements

The requirements of this application are shown in the following lists. The main requirements are:

  • The GNU or Intel® Compiler Collection.
  • The ParaStation MPI installation supporting multi-threading, featuring the libNAM integration that allows access to NAM memory regions through MPI RMA windows, and supporting the new request-based MPI_Win_ifence function. The branch ifence-nam in the https://gitlab.version.fz-juelich.de/DEEP-EST/psmpi repository contains a ParaStation MPI supporting these features.
  • The Task-Aware MPI (TAMPI) library which defines a clean interoperability mechanism for MPI and OpenMP/OmpSs-2 tasks. It supports both blocking and non-blocking MPI operations by providing two different interoperability mechanisms. Downloads and more information at https://github.com/bsc-pm/tampi.
  • The OmpSs-2 model which is the second generation of the OmpSs programming model. It is a task-based programming model originated from the ideas of the OpenMP and StarSs programming models. The specification and user-guide are available at https://pm.bsc.es/ompss-2-docs/spec/ and https://pm.bsc.es/ompss-2-docs/user-guide/, respectively. OmpSs-2 requires both Mercurium and Nanos6 tools. Mercurium is a source-to-source compiler which provides the necessary support for transforming the high-level directives into a parallelized version of the application. The Nanos6 runtime system provides the services to manage all the parallelism in the application (e.g., task creation, synchronization, scheduling, etc.). Downloads at https://github.com/bsc-pm.
  • The NAM software allowing access to NAM memory.

Building & Executing on DEEP

The instructions to build and execute the Heat benchmark with NAM snapshots will appear here soon.

References

Last modified 20 months ago Last modified on Apr 26, 2021, 4:45:36 PM