ncsa.jhdf5 MacOS ARM64 libs not loaded (until port Chombo/MB to io.jhdf)

virtualcell · Nov 4, 2024 · 3614ab5 · 3614ab5
1 parent f4fcbbb
commit 3614ab5
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Showing 6 changed files with 34 additions and 5 deletions.
diff --git a/vcell-core/src/main/java/cbit/vcell/export/server/ASCIIExporter.java b/vcell-core/src/main/java/cbit/vcell/export/server/ASCIIExporter.java
@@ -549,7 +549,12 @@ private List<ExportOutput> exportPDEData(OutputContext outputContext, long jobID
                                              GeometrySpecs geometrySpecs, ASCIISpecs asciiSpecs, String contextName, FileDataContainerManager fileDataContainerManager)
             throws DataAccessException, IOException{
 
-        NativeLib.HDF5.load();
+        // skip loading legacy native HDF5 library if the system is a macos arm64
+        // will get runtime errors for Chombo and MovingBoundary until HDF5 is updated
+        boolean MacosArm64 = System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X");
+        if (!MacosArm64) {
+            NativeLib.HDF5.load();
+        }
         ExportSpecs.SimNameSimDataID[] simNameSimDataIDs = asciiSpecs.getSimNameSimDataIDs();
         Vector<ExportOutput[]> exportOutputV = new Vector<ExportOutput[]>();
         double progressCounter = 0;

diff --git a/vcell-core/src/main/java/cbit/vcell/simdata/VtkMeshGenerator.java b/vcell-core/src/main/java/cbit/vcell/simdata/VtkMeshGenerator.java
@@ -38,7 +38,12 @@ public VtkMeshGenerator(User owner, KeyValue simKey, int jobIndex) {
 	@Override
 	public int execute() {
 		try {
-			NativeLib.HDF5.load();
+			// skip loading legacy native HDF5 library if the system is a macos arm64
+			// will get runtime errors for Chombo and MovingBoundary until HDF5 is updated
+			boolean MacosArm64 = System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X");
+			if (!MacosArm64) {
+				NativeLib.HDF5.load();
+			}
 			KeyValue u = new KeyValue(userkey);
 			User owner = new User(username,u);
 			KeyValue simKey = new KeyValue(simkey);

diff --git a/vcell-core/src/test/java/cbit/vcell/resource/NativeLibTest.java b/vcell-core/src/test/java/cbit/vcell/resource/NativeLibTest.java
@@ -15,6 +15,10 @@ public void init( ) {
 	@Test
 	public void loadEm( ) {
 		for (NativeLib nl : NativeLib.values()) {
+			// skip if nl is HDF5 and system is a macos arm64
+			if (nl == NativeLib.HDF5 && System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X")) {
+				continue;
+			}
 			nl.load();
 		}
 	}

diff --git a/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryH5FileStructureTest.java b/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryH5FileStructureTest.java
@@ -58,7 +58,12 @@ public class MovingBoundaryH5FileStructureTest {
     @BeforeAll
     public static void setup() {
         PropertyLoader.setProperty(PropertyLoader.installationRoot, new File("..").getAbsolutePath());
-        NativeLib.HDF5.load();
+        // skip loading legacy native HDF5 library if the system is a macos arm64
+        // will get runtime errors for Chombo and MovingBoundary until HDF5 is updated
+        boolean MacosArm64 = System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X");
+        if (!MacosArm64) {
+            NativeLib.HDF5.load();
+        }
     }
 
     //public static void main(String args[]) throws Exception {

diff --git a/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryResultTest.java b/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryResultTest.java
@@ -23,7 +23,12 @@ public class MovingBoundaryResultTest {
 	@BeforeAll
 	public static void setup() {
 		PropertyLoader.setProperty(PropertyLoader.installationRoot, new File("..").getAbsolutePath());
-		NativeLib.HDF5.load();
+		// skip loading legacy native HDF5 library if the system is a macos arm64
+		// will get runtime errors for Chombo and MovingBoundary until HDF5 is updated
+		boolean MacosArm64 = System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X");
+		if (!MacosArm64) {
+			NativeLib.HDF5.load();
+		}
 	}
     public MovingBoundaryResultTest() {
 		Logger lg = LogManager.getLogger("ncsa");

diff --git a/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryVH5PathTest.java b/vcell-core/src/test/java/cbit/vcell/solvers/mb/MovingBoundaryVH5PathTest.java
@@ -36,7 +36,12 @@ public class MovingBoundaryVH5PathTest {
     @BeforeEach
     public void setup( ) throws Exception {
 		PropertyLoader.setProperty(PropertyLoader.installationRoot, new File("..").getAbsolutePath());
-		NativeLib.HDF5.load();
+		// skip loading legacy native HDF5 library if the system is a macos arm64
+		// will get runtime errors for Chombo and MovingBoundary until HDF5 is updated
+		boolean MacosArm64 = System.getProperty("os.arch").equals("aarch64") && System.getProperty("os.name").equals("Mac OS X");
+		if (!MacosArm64) {
+			NativeLib.HDF5.load();
+		}
 
 
 		// retrieve an instance of H5File