Various codeql updates #37

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Merged

brtnfld merged 48 commits into HDFGroup:develop from brtnfld:develop

Feb 12, 2025

.github/codeql-config.yml

-Original file line number
+Diff line change
@@ -0,0 +1,17 @@
+    # 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

.github/workflows/codeql.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -198,3 +198,26 @@ jobs: @@
             uses: github/codeql-action/analyze@v3
             with:
               category: "/language:c-cpp"
+              output: sarif-results
+              upload: failure-only
+          - name: filter-sarif
+            uses: advanced-security/filter-sarif@main
+            with:
+              patterns: |
+                -**/*
+                src/**/*
+              input: sarif-results/cpp.sarif
+              output: sarif-results/cpp.sarif
+          - name: Upload SARIF
+            uses: github/codeql-action/upload-sarif@v3
+            with:
+              sarif_file: sarif-results/cpp.sarif
+          - name: Upload loc as a Build Artifact
+            uses: actions/upload-artifact@v4
+            with:
+              name: sarif-results
+              path: sarif-results
+              retention-days: 1

.github/workflows/hdf5-latest.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -84,7 +84,7 @@ jobs: @@
             ctest --output-on-failure
         - name: Upload
-          uses: actions/upload-artifact@v3
+          uses: actions/upload-artifact@v4
           with:
             name: git.txt
             path: ${{ runner.workspace }}/vol-cache/hdf5/git.txt

.github/workflows/linux.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -16,7 +16,7 @@ on:
  
    jobs:

      vol-cache:

        runs-on: ubuntu-latest

        timeout-minutes: 60

        timeout-minutes: 20

        steps:

          - uses: actions/[email protected]

    @@ -60,7 +60,7 @@ jobs:
  
              # Compile HDF5

              mkdir -p hdf5/build

              cd hdf5/build

              cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HDF5_DIR -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DALLOW_UNSUPPORTED:BOOL=ON ..

              cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HDF5_DIR -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ALLOW_UNSUPPORTED:BOOL=ON ..

              make -j2 install

              cd -

              cd argobots

src/H5LS.c

-Original file line number
+Diff line change
@@ Expand Up / @@ -59,6 +59,9 @@ @@
     extern int RANK;
     extern int NPROC;
+    #define ERROR_MSG_SIZE 283
+    char error_msg[ERROR_MSG_SIZE];
     /*
        Get the corresponding mmap function struct based on the type of node local
        storage The user can modify this function to other storage
@@ Expand Down Expand Up / @@ -131,8 +134,9 @@ herr_t readLSConf(char *fname, cache_storage_t *LS) { @@
         MPI_Abort(MPI_COMM_WORLD, 100);
       }
       FILE *file = fopen(fname, "r");
-      LS->path = (char *)malloc(255);
-      strcpy(LS->path, "./");
+      LS->path = (char *)malloc(256);
+      strncpy(LS->path, "./", 255);
+      LS->path[255] = '\0';
       LS->mspace_total = 137438953472;
       strcpy(LS->type, "SSD");
       strcpy(LS->scope, "LOCAL");
@@ Expand All / @@ -144,16 +148,24 @@ herr_t readLSConf(char *fname, cache_storage_t *LS) { @@
         linenum++;
         if (line[0] == '#')
           continue;
-        if (sscanf(line, "%[^:]:%s", ip, mac) != 2) {
+        if (sscanf(line, "%255[^:]:%255s", ip, mac) != 2) {
           if (RANK == io_node())
             fprintf(stderr, "Syntax error, line %d\n", linenum);
           continue;
         }
+        ip[255] = '\0';
+        mac[255] = '\0';
+        if (strlen(ip) >= 256 || strlen(mac) >= 256) {
+          if (RANK == io_node())
+            fprintf(stderr, "Input too long, line %d\n", linenum);
+          continue;
+        }
         if (!strcmp(ip, "HDF5_CACHE_STORAGE_PATH"))
           if (strcmp(mac, "NULL") == 0)
             LS->path = NULL;
           else {
-            strcpy(LS->path, mac);
+            strncpy(LS->path, mac, 255);
+            LS->path[255] = '\0';
           }
         else if (!strcmp(ip, "HDF5_CACHE_FUSION_THRESHOLD")) {
@@ Expand All / @@ -166,9 +178,11 @@ herr_t readLSConf(char *fname, cache_storage_t *LS) { @@
         else if (!strcmp(ip, "HDF5_CACHE_WRITE_BUFFER_SIZE"))
           LS->write_buffer_size = (hsize_t)atof(mac);
         else if (!strcmp(ip, "HDF5_CACHE_STORAGE_TYPE")) {
-          strcpy(LS->type, mac);
+          strncpy(LS->type, mac, sizeof(LS->type) - 1);
+          LS->type[sizeof(LS->type) - 1] = '\0';
         } else if (!strcmp(ip, "HDF5_CACHE_STORAGE_SCOPE")) {
-          strcpy(LS->scope, mac);
+          strncpy(LS->scope, mac, sizeof(LS->scope) - 1);
+          LS->scope[sizeof(LS->scope) - 1] = '\0';
         } else if (!strcmp(ip, "HDF5_CACHE_REPLACEMENT_POLICY")) {
           if (get_replacement_policy_from_str(mac) > 0)
             LS->replacement_policy = get_replacement_policy_from_str(mac);
@@ Expand All / @@ -190,7 +204,12 @@ herr_t readLSConf(char *fname, cache_storage_t *LS) { @@
           (stat(LS->path, &sb) == 0 && S_ISDIR(sb.st_mode))) {
         return 0;
       } else {
-        LOG_ERROR(-1, "H5LSset: path %s does not exist\n", LS->path);
+        int ret = snprintf(error_msg, ERROR_MSG_SIZE,
+                           "H5LSset: path %s does not exist\n", LS->path);
+        if (ret < 0 || ret >= ERROR_MSG_SIZE) {
+          LOG_WARN(-1, "path error message truncated");
+        }
+        LOG_ERROR(-1, "%s", error_msg);
         MPI_Abort(MPI_COMM_WORLD, 112);
       }
     }
@@ Expand Down @@

src/H5LS_SSD.c

-Original file line number
+Diff line change
@@ Expand Up @@
       char *p = (char *)buf;
       int i;
       for (i = 0; i < nseq; i++) {
-        int err = pwrite(fd, &p[off[i]], len[i], offset + off_contig);
+        pwrite(fd, &p[off[i]], len[i], offset + off_contig);
         off_contig += len[i];
       }
     #ifdef __APPLE__
@@ Expand All @@
       strcpy(dname, mm->fname);
       mkdirRecursive(dirname(dname), 0755); // dirname will change dname in linux.
                                             // therefore, we make copy first.
-      struct stat info;
       mm->fd = open(mm->fname, O_RDWR | O_CREAT | O_TRUNC, 0644);
       return 0;
     }
@@ Expand Down Expand Up @@
     /* clean up read mmap buffer, files */
     static herr_t H5LS_SSD_remove_read_mmap(MMAP *mm, hsize_t size) {
-      herr_t ret;
       munmap(mm->buf, size);
       close(mm->fd);
       if (access(mm->fname, F_OK) == 0)
@@ Expand Down @@

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