Draft: Fix most Severe/High CodeQL issues

.github/codeql-config.yml

@@ -0,0 +1,31 @@
+# Query filters to include or exclude specific queries
+query-filters:
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-short-global-name/
+      id: cpp/short-global-name
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-commented-out-code/ 
+      id: cpp/commented-out-code
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-poorly-documented-function/
+      id: cpp/poorly-documented-function
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-trivial-switch/
+      id: cpp/trivial-switch
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-irregular-enum-init/
+      id: cpp/irregular-enum-init
+  - exclude:
+      # See: https://codeql.github.com/codeql-query-help/cpp/cpp-guarded-free/
+      id: cpp/guarded-free
+
+# Directories to scan for vulnerabilities
+paths:
+  - src
+
+# Directories and files to ignore during the scan
+paths-ignore:
+  - scripts
+  - examples
+  - docs
+  - benchmark

.github/workflows/codeql.yml

@@ -0,0 +1,119 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL Advanced"
+
+env:
+  CMAKE_POLICY_VERSION_MINIMUM: 3.5
+
+on:
+  push:
+    branches: [ "pdc_codeql" ]
+  pull_request:
+    branches: [ "pdc_codeql" ]
+  schedule:
+    - cron: '33 23 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: actions
+          build-mode: none
+        - language: c-cpp
+          build-mode: manual
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install libopenmpi-dev libhdf5-dev uuid-dev cmake
+
+    - name: Build PDC Dependencies
+      run: |
+        # libfabric
+        wget https://github.com/ofiwg/libfabric/archive/refs/tags/v1.12.1.tar.gz
+        tar xf v1.12.1.tar.gz
+        cd libfabric-1.12.1
+        ./autogen.sh
+        ./configure --disable-usnic --disable-mrail --disable-rstream --disable-perf --disable-efa --disable-psm2 --disable-psm --disable-verbs --disable-shm --disable-static --disable-silent-rules
+        make -j2 && sudo make install
+        cd ..
+
+        # Mercury
+        git clone --recursive https://github.com/mercury-hpc/mercury.git
+        cd mercury
+        git checkout v2.2.0
+        mkdir build && cd build
+        cmake ../  -DCMAKE_C_COMPILER=gcc -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=ON -DNA_USE_OFI=ON -DNA_USE_SM=OFF -DMERCURY_USE_CHECKSUMS=OFF -DCMAKE_POLICY_VERSION_MINIMUM=3.5
+        make -j2 && sudo make install
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        config-file: ./.github/codeql-config.yml
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    - name: Build PDC
+      shell: bash
+      run: |
+        mkdir build && cd build
+        cmake ../ -DBUILD_MPI_TESTING=ON -DBUILD_SHARED_LIBS=ON -DPDC_SERVER_CACHE=ON -DBUILD_TESTING=ON -DPDC_ENABLE_MPI=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_POLICY_VERSION_MINIMUM=3.5
+        make -j2 && sudo make install
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

examples/bdcats.c

@@ -33,7 +33,8 @@
 #include <inttypes.h>
 #include "pdc.h"
 
-#define NPARTICLES 8388608
+#define NPARTICLES    8388608
+#define MAX_PARTICLES (NPARTICLES * 2)
 
 double
 uniform_random_number()
@@ -82,6 +83,11 @@ main(int argc, char **argv)
             LOG_INFO("Writing %" PRIu64 " number of particles with %d clients.\n", numparticles, size);
     }
 
+    if (numparticles > MAX_PARTICLES) {
+        LOG_ERRROR("numparticles exceeds max size\n");
+        goto done;
+    }
+
     x = (float *)malloc(numparticles * sizeof(float));
     y = (float *)malloc(numparticles * sizeof(float));
     z = (float *)malloc(numparticles * sizeof(float));
@@ -463,6 +469,7 @@ main(int argc, char **argv)
     free(offset_remote);
     free(mysize);
 
+done:
 #ifdef ENABLE_MPI
     MPI_Finalize();
 #endif

examples/bdcats_batch.c

@@ -33,8 +33,9 @@
 #include <inttypes.h>
 #include "pdc.h"
 
-#define NPARTICLES 8388608
-#define N_OBJS     8
+#define NPARTICLES    8388608
+#define MAX_PARTICLES (NPARTICLES * 2)
+#define N_OBJS        8
 
 double
 uniform_random_number()
@@ -115,6 +116,11 @@ main(int argc, char **argv)
                  sleep_time, timestep, numparticles, test_method);
     }
 
+    if (numparticles > MAX_PARTICLES) {
+        LOG_ERRROR("numparticles exceeds max size\n");
+        goto done;
+    }
+
     x = (float *)malloc(numparticles * sizeof(float));
     y = (float *)malloc(numparticles * sizeof(float));
     z = (float *)malloc(numparticles * sizeof(float));
@@ -710,6 +716,8 @@ main(int argc, char **argv)
     free(pz);
     free(id1);
     free(id2);
+
+done:
 #ifdef ENABLE_MPI
     MPI_Finalize();
 #endif

examples/bdcats_old.c

@@ -33,7 +33,8 @@
 #include <inttypes.h>
 #include "pdc.h"
 
-#define NPARTICLES 8388608
+#define NPARTICLES    8388608
+#define MAX_PARTICLES (NPARTICLES * 2)
 
 double
 uniform_random_number()
@@ -390,6 +391,7 @@ main(int argc, char **argv)
     free(offset_remote);
     free(mysize);
 
+done:
 #ifdef ENABLE_MPI
     MPI_Finalize();
 #endif