Task #4716: Added libnuma support to add memory binding

CMake/FindLibNuma.cmake

+# - Try to find libnuma.
+# Variables used by this module:
+#  LIBNUMA_ROOT_DIR     - LIBNUMA root directory
+# Variables defined by this module:
+#  LIBNUMA_FOUND        - system has LIBNUMA
+#  LIBNUMA_INCLUDE_DIR  - the LIBNUMA include directory (cached)
+#  LIBNUMA_INCLUDE_DIRS - the LIBNUMA include directories
+#                       (identical to LIBNUMA_INCLUDE_DIR)
+#  LIBNUMA_LIBRARY      - the LIBNUMA library (cached)
+#  LIBNUMA_LIBRARIES    - the LIBNUMA libraries
+#                       (identical to LIBNUMA_LIBRARY)
+
+# Copyright (C) 2009
+# ASTRON (Netherlands Institute for Radio Astronomy)
+# P.O.Box 2, 7990 AA Dwingeloo, The Netherlands
+#
+# This file is part of the LOFAR software suite.
+# The LOFAR software suite is free software: you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# The LOFAR software suite is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with the LOFAR software suite. If not, see <http://www.gnu.org/licenses/>.
+#
+# $Id$
+
+if(NOT LIBNUMA_FOUND)
+
+  find_path(LIBNUMA_INCLUDE_DIR numa.h
+    HINTS ${LIBNUMA_ROOT_DIR} PATH_SUFFIXES include)
+  find_library(LIBNUMA_LIBRARY numa
+    HINTS ${LIBNUMA_ROOT_DIR} PATH_SUFFIXES lib lib64)
+  mark_as_advanced(LIBNUMA_INCLUDE_DIR LIBNUMA_LIBRARY)
+
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(LIBNUMA DEFAULT_MSG 
+    LIBNUMA_LIBRARY LIBNUMA_INCLUDE_DIR)
+
+  set(LIBNUMA_INCLUDE_DIRS ${LIBNUMA_INCLUDE_DIR})
+  set(LIBNUMA_LIBRARIES ${LIBNUMA_LIBRARY})
+
+endif(NOT LIBNUMA_FOUND)

RTCP/Cobalt/GPUProc/CMakeLists.txt

@@ -50,6 +50,7 @@ lofar_package(GPUProc 1.0 DEPENDS ${_gpuproc_deps})
 lofar_find_package(OpenMP REQUIRED)
 lofar_find_package(Boost REQUIRED)
 lofar_find_package(MPI)
+lofar_find_package(LibNuma)
 lofar_find_package(FFTW3 COMPONENTS single double threads REQUIRED)  # 'double threads' for FFT unit test refs
 lofar_find_package(UnitTest++)
 
@@ -81,4 +82,4 @@ endif()
 add_subdirectory(src)
 add_subdirectory(test)
 add_subdirectory(share/gpu/kernels)
-add_subdirectory(etc)
\ No newline at end of file
+add_subdirectory(etc)

RTCP/Cobalt/GPUProc/src/rtcp.cc

@@ -34,6 +34,11 @@
 #include <sys/resource.h>
 #include <sys/mman.h>
 
+#ifdef HAVE_LIBNUMA
+#include <numa.h>
+#include <numaif.h>
+#endif
+
 #ifdef HAVE_MPI
 #include <mpi.h>
 #endif
@@ -175,18 +180,6 @@ int main(int argc, char **argv)
   if (setrlimit(RLIMIT_MEMLOCK, &unlimited) < 0)
     THROW_SYSCALL("setrlimit(RLIMIT_MEMLOCK, unlimited)");
 
-  /*
-   * Initialise OpenMP
-   */
-
-  LOG_INFO_STR("----- Initialising OpenMP");
-
-  // Allow usage of nested omp calls
-  omp_set_nested(true);
-
-  // Allow OpenMP thread registration
-  OMPThread::init();
-
   /*
    * INIT stage
    */
@@ -207,11 +200,9 @@ int main(int argc, char **argv)
 
   LOG_INFO_STR("----- Initialising NUMA bindings");
 
-  // TODO: How to migrate the memory that's currently in use
-  // (and mlocked!) to the selected CPU?
-
   // The set of GPUs we're allowed to use
   vector<gpu::Device> devices;
+
   // If we are testing we do not want dependency on hardware specific cpu configuration
   // Just use all gpu's
   if(rank >= 0 && (size_t)rank < ps.settings.nodes.size()) {
@@ -219,11 +210,49 @@ int main(int argc, char **argv)
     int cpuId = ps.settings.nodes[rank].cpu;
     setProcessorAffinity(cpuId);
 
+#ifdef HAVE_LIBNUMA
+    // force node + memory binding for future allocations
+    struct bitmask *numa_node = numa_allocate_nodemask();
+    numa_bitmask_clearall(numa_node);
+    numa_bitmask_setbit(numa_node, cpuId);
+    numa_bind(numa_node);
+    numa_bitmask_free(numa_node);
+
+    // only allow allocation on this node in case
+    // the numa_alloc_* functions are used
+    numa_set_strict(1);
+
+    // retrieve and report memory binding
+    numa_node = numa_get_membind();
+    vector<string> nodestrs;
+    for (size_t i = 0; i < numa_node->size; i++)
+      if (numa_bitmask_isbitset(numa_node, i))
+        nodestrs.push_back(str(format("%s") % i));
+
+    // migrate currently used memory to our node
+    numa_migrate_pages(0, numa_all_nodes_ptr, numa_node);
+
+    numa_bitmask_free(numa_node);
+
+    LOG_DEBUG_STR("Bound to memory on nodes " << nodestrs);
+#else
+    LOG_WARN_STR("Cannot bind memory (no libnuma support)");
+#endif
+
+    // Bindings are done -- Lock everything in memory
+    if (mlockall(MCL_CURRENT | MCL_FUTURE) < 0)
+      THROW_SYSCALL("mlockall");
+
     // derive the set of gpus we're allowed to use
     const vector<unsigned> &gpuIds = ps.settings.nodes[rank].gpus;
-    LOG_DEBUG_STR("Binding to GPUs " << gpuIds);
-    for (size_t i = 0; i < gpuIds.size(); ++i)
-      devices.push_back(allDevices[i]);
+    vector<string> gpuPciIds;
+    for (size_t i = 0; i < gpuIds.size(); ++i) {
+      gpu::Device &d = allDevices[gpuIds[i]];
+
+      devices.push_back(d);
+      gpuPciIds.push_back(d.pciId());
+    }
+    LOG_DEBUG_STR("Binding to GPUs " << gpuIds << " = " << gpuPciIds);
 
     // Select on the local NUMA InfiniBand interface (OpenMPI only, for now)
     const string nic = ps.settings.nodes[rank].nic;
@@ -239,11 +268,17 @@ int main(int argc, char **argv)
     devices = allDevices;
   }
 
-  // Bindings are done -- Lock everything in memory
-  if (mlockall(MCL_CURRENT | MCL_FUTURE) < 0)
-    THROW_SYSCALL("mlockall");
+  /*
+   * Initialise OpenMP
+   */
+
+  LOG_INFO_STR("----- Initialising OpenMP");
 
-  LOG_DEBUG_STR("All memory is now pinned.");
+  // Allow usage of nested omp calls
+  omp_set_nested(true);
+
+  // Allow OpenMP thread registration
+  OMPThread::init();
 
   // Only ONE host should start the Storage processes
   SmartPtr<StorageProcesses> storageProcesses;

lofar_config.h.cmake

@@ -126,6 +126,9 @@
 /* Define if LAM is installed */
 #cmakedefine HAVE_LAM 1
 
+/* Define if libnuma is installed */
+#cmakedefine HAVE_LIBNUMA 1
+
 /* Define if libssh2 is installed */
 #cmakedefine HAVE_LIBSSH2 1