Make libnuma into a soft dependency

.github/workflows/activate_miniconda.sh

@@ -4,4 +4,4 @@ if [ '!' -d $HOME/miniconda/bin ]; then
   bash "$HOME/.cache/miniconda/mambaforge.sh" -f -b -p $HOME/miniconda
 fi
 export PATH=$HOME/miniconda/bin:$PATH
-source activate
+. activate

.github/workflows/python.yaml

@@ -110,6 +110,28 @@ jobs:
         name: conda-pkgs-${{matrix.os}}
         path: /Users/runner/build
 
+  test_conda_package_install:
+    needs: build_and_test_conda_package
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        image:
+          - ubuntu:16.04
+          - ubuntu:latest
+          - centos:7
+          - centos:latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          submodules: 'recursive'
+      - name: Download conda packages
+        uses: actions/download-artifact@v2
+        with:
+          name: conda-pkgs-ubuntu-18.04
+          path: pkgs
+      - name: Install in docker container
+        run: python3 tests/install_conda_packages_test.py pkgs ${{matrix.image}}
 
   lint:
     runs-on: ${{matrix.os}}

conda_recipe/meta.yaml

@@ -104,7 +104,6 @@ outputs:
     test:
       requires:
         - {{ compiler('cxx') }}
-        - {{ cdt('numactl') }}
         - cmake>=3.17
         - make
       files:

libgalois/CMakeLists.txt

@@ -101,7 +101,9 @@ endif()
 
 if(NUMA_FOUND)
   target_compile_definitions(katana_galois PRIVATE KATANA_USE_NUMA)
-  target_link_libraries(katana_galois PRIVATE ${NUMA_LIBRARY})
+  file(REAL_PATH ${NUMA_LIBRARY} NUMA_LIBRARY_RESOLVED)
+  cmake_path(GET NUMA_LIBRARY_RESOLVED FILENAME KATANA_LIBNUMA_SO_NAME)
+  target_compile_definitions(katana_galois PRIVATE "KATANA_LIBNUMA_SO_NAME=\"${KATANA_LIBNUMA_SO_NAME}\"")
 else()
   message(WARNING "No NUMA Support.  Likely poor performance for multi-socket systems.")
 endif()

libgalois/src/HWTopoLinux.cpp

@@ -17,6 +17,8 @@
  * Documentation, or loss or inaccuracy of data of any kind.
  */
 
+#include <dlfcn.h>
+
 #include <algorithm>
 #include <array>
 #include <cassert>
@@ -34,7 +36,6 @@
 
 #ifdef KATANA_USE_NUMA
 #include <numa.h>
-#include <numaif.h>
 #endif
 
 #ifdef KATANA_USE_SCHED_SETAFFINITY
@@ -57,44 +58,68 @@ struct cpuinfo {
 
 bool
 operator<(const cpuinfo& lhs, const cpuinfo& rhs) {
-  if (lhs.smt != rhs.smt)
+  if (lhs.smt != rhs.smt) {
     return lhs.smt < rhs.smt;
-  if (lhs.physid != rhs.physid)
+  }
+  if (lhs.physid != rhs.physid) {
     return lhs.physid < rhs.physid;
-  if (lhs.coreid != rhs.coreid)
+  }
+  if (lhs.coreid != rhs.coreid) {
     return lhs.coreid < rhs.coreid;
+  }
   return lhs.proc < rhs.proc;
 }
 
+#ifdef KATANA_USE_NUMA
+int (*dynamic_numa_available)() = nullptr;
+int (*dynamic_numa_num_configured_nodes)() = nullptr;
+int (*dynamic_numa_node_of_cpu)(int cpu) = nullptr;
+
+void
+LoadLibNuma() {
+  // KATANA_LIBNUMA_SO_NAME is defined in libgalois/CMakeLists.txt
+  auto* lib = dlopen(KATANA_LIBNUMA_SO_NAME, RTLD_LAZY);
+  if (!lib) {
+    return;
+  }
+#define LOAD_SYM(name)                                                         \
+  dynamic_##name = reinterpret_cast<decltype(&name)>(dlsym(lib, #name))
+  LOAD_SYM(numa_available);
+  LOAD_SYM(numa_num_configured_nodes);
+  LOAD_SYM(numa_node_of_cpu);
+#undef LOAD_SYM
+}
+#endif
+
 unsigned
-getNumaNode(cpuinfo& c) {
-  static bool warnOnce = false;
+getNumaNode(const cpuinfo& c) {
 #ifdef KATANA_USE_NUMA
-  static bool numaAvail = false;
-
-  if (!warnOnce) {
-    warnOnce = true;
-    numaAvail = numa_available() >= 0;
-    numaAvail = numaAvail && numa_num_configured_nodes() > 0;
-    if (!numaAvail)
-      katana::gWarn(
+  static std::once_flag load_numa_once;
+  static bool numa_avail = false;
+
+  std::call_once(load_numa_once, [&]() {
+    LoadLibNuma();
+    numa_avail = dynamic_numa_available && dynamic_numa_available() >= 0;
+    numa_avail = numa_avail && dynamic_numa_num_configured_nodes() > 0;
+    if (!numa_avail) {
+      KATANA_LOG_WARN(
           "Numa support configured but not present at runtime.  "
           "Assuming numa topology matches socket topology.");
-  }
+    }
+  });
 
-  if (!numaAvail)
+  if (!numa_avail) {
     return c.physid;
-  int i = numa_node_of_cpu(c.proc);
-  if (i < 0)
-    KATANA_SYS_DIE("failed finding numa node for ", c.proc);
+  }
+  int i = dynamic_numa_node_of_cpu(c.proc);
+  if (i < 0) {
+    KATANA_LOG_FATAL("failed finding numa node for {}", c.proc);
+  }
   return i;
 #else
-  if (!warnOnce) {
-    warnOnce = true;
-    katana::gWarn(
-        "Numa Support Not configured (install libnuma-dev).  "
-        "Assuming numa topology matches socket topology.");
-  }
+  KATANA_WARN_ONCE(
+      "Numa Support Not configured (install libnuma-dev).  "
+      "Assuming numa topology matches socket topology.");
   return c.physid;
 #endif
 }
@@ -141,35 +166,40 @@ parseCPUInfo() {
 unsigned
 countSockets(const std::vector<cpuinfo>& info) {
   std::set<unsigned> pkgs;
-  for (auto& c : info)
+  for (auto& c : info) {
     pkgs.insert(c.physid);
+  }
   return pkgs.size();
 }
 
 unsigned
 countCores(const std::vector<cpuinfo>& info) {
   std::set<std::pair<int, int>> cores;
-  for (auto& c : info)
+  for (auto& c : info) {
     cores.insert(std::make_pair(c.physid, c.coreid));
+  }
   return cores.size();
 }
 
 unsigned
 countNumaNodes(const std::vector<cpuinfo>& info) {
   std::set<unsigned> nodes;
-  for (auto& c : info)
+  for (auto& c : info) {
     nodes.insert(c.numaNode);
+  }
   return nodes.size();
 }
 
 void
 markSMT(std::vector<cpuinfo>& info) {
-  for (unsigned int i = 1; i < info.size(); ++i)
+  for (unsigned int i = 1; i < info.size(); ++i) {
     if (info[i - 1].physid == info[i].physid &&
-        info[i - 1].coreid == info[i].coreid)
+        info[i - 1].coreid == info[i].coreid) {
       info[i].smt = true;
-    else
+    } else {
       info[i].smt = false;
+    }
+  }
 }
 
 std::vector<int>
@@ -210,12 +240,14 @@ void
 markValid(std::vector<cpuinfo>& info) {
   auto v = parseCPUSet();
   if (v.empty()) {
-    for (auto& c : info)
+    for (auto& c : info) {
       c.valid = true;
+    }
   } else {
     std::sort(v.begin(), v.end());
-    for (auto& c : info)
+    for (auto& c : info) {
       c.valid = std::binary_search(v.begin(), v.end(), c.proc);
+    }
   }
 }
 

scripts/katana_version/version.py

@@ -194,8 +194,8 @@ def get_config_version(k_commit, repo: Repo, version_file, no_dev=False) -> vers
                 version_str = version_file.read()
     elif version_file:
         # We have no git information. Wing it.
-        with open(Path(__file__).parent.parent.parent / CONFIG_VERSION_PATH, "rt") as version_file:
-            version_str = version_file.read()
+        with open(version_file, "rt") as version_fi:
+            version_str = version_fi.read()
     else:
         # We have no information. Something is really broken. Still don't crash to allow builds.
         version_str = "0.0.0"

tests/install_conda_packages_test.Dockerfile

@@ -0,0 +1,59 @@
+ARG BASE_IMAGE
+FROM ${BASE_IMAGE} AS base_with_conda
+
+COPY download_miniconda.sh /
+COPY activate_miniconda.sh /
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=America/Chicago
+ENV APT_GET="apt-get --yes --quiet"
+ENV YUM="yum -y"
+
+RUN set -eux; \
+    if command -v yum > /dev/null; then \
+        ${YUM} update; \
+        ${YUM} install curl; \
+        ${YUM} clean all; \
+    else \
+        ${APT_GET} update; \
+        ${APT_GET} dist-upgrade; \
+        ${APT_GET} install curl; \
+        ${APT_GET} clean; \
+    fi
+
+RUN set -eu; \
+    bash /download_miniconda.sh ubuntu-xxx; \
+    . /activate_miniconda.sh;
+
+ARG CONDA_CLEAN="conda clean --quiet --yes --all"
+
+RUN set -eu; \
+    . /activate_miniconda.sh; \
+    mamba update --quiet --yes --all; \
+    ${CONDA_CLEAN}
+
+FROM base_with_conda AS pre_install
+
+COPY packages /packages
+
+FROM pre_install AS test_python
+ARG CONDA_CLEAN="conda clean --quiet --yes --all"
+ARG MAMBA_INSTALL="mamba install --quiet --yes --channel /packages"
+
+RUN set -eu ; . /activate_miniconda.sh; set -x ; \
+    ${MAMBA_INSTALL} katana-python; \
+    ${CONDA_CLEAN}
+
+RUN set -eu ; . /activate_miniconda.sh; set -x ; \
+    python -c "import katana.analytics; katana.analytics.bfs; print(katana.__version__)"
+
+FROM pre_install AS test_tools
+ARG CONDA_CLEAN="conda clean --quiet --yes --all"
+ARG MAMBA_INSTALL="mamba install --quiet --yes --channel /packages"
+
+RUN set -eu ; . /activate_miniconda.sh; set -x ; \
+    ${MAMBA_INSTALL} katana-tools; \
+    ${CONDA_CLEAN}
+
+RUN set -eu ; . /activate_miniconda.sh; set -x ; \
+    graph-convert --version

tests/install_conda_packages_test.py

@@ -0,0 +1,37 @@
+#! /bin/python
+
+import argparse
+from pathlib import Path
+from subprocess import Popen, PIPE
+from sys import stderr
+import tarfile
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Install katana packages in a docker image and test them. " "Only runs a trivial test."
+    )
+    parser.add_argument("package_dir", type=Path, help="The directory containing the conda packages to install.")
+    parser.add_argument("docker_image", type=str, help="The docker image to use.")
+
+    args = parser.parse_args()
+
+    docker_proc = Popen(["docker", "build", "-", "--build-arg", f"BASE_IMAGE={args.docker_image}",], stdin=PIPE)
+    with docker_proc.stdin, tarfile.open(fileobj=docker_proc.stdin, mode="w:gz") as context_tar:
+        context_tar.add(Path(args.package_dir).absolute(), arcname="packages")
+        context_tar.add(Path(__file__).parent / "install_conda_packages_test.Dockerfile", arcname="Dockerfile")
+        context_tar.add(
+            Path(__file__).parent.parent / ".github" / "workflows" / "download_miniconda.sh",
+            arcname="download_miniconda.sh",
+        )
+        context_tar.add(
+            Path(__file__).parent.parent / ".github" / "workflows" / "activate_miniconda.sh",
+            arcname="activate_miniconda.sh",
+        )
+    err_code = docker_proc.wait()
+    if err_code != 0:
+        print(f"Failed to install and test Conda packages from {args.package_dir} in {args.docker_image}", file=stderr)
+
+
+if __name__ == "__main__":
+    main()