Add JNI-based BLAS, LAPACK, and ARPACK implementations (#1)

* v2-SNAPSHOT

* Add JNI-based wrapper for BLAS

* Print which implementation is currently running for benchmark

Since java or native can mean more things, let's just log it out.

* Add JDK17 profile, just in case.

* Try JNIBLAS before ForeignLinkerBLAS

The former is faster because it doesn't require to copy memory from the
heap to native memory

* Use Fortran symbols directly

Still without using any external library.

* Remove leftover debug comments

* Rename dev.ludovic.netlib.blas.VectorizedBLAS to dev.ludovic.netlib.blas.VectorBLAS

This aligns with dev.ludovic.netlib.blas.ForeignLinkerBLAS

* fixup! Rename dev.ludovic.netlib.blas.VectorizedBLAS to dev.ludovic.netlib.blas.VectorBLAS

* Remove com.github.fommil from BLAS fully and WIP for LAPACK

* Make sure critical JNI regions don't contain unecessary JNI calls

* Do better error handling + Load org.netlib.util.*W types

* Base implementation for LAPACK + Implement calls used by Spark

I still need to come up with proper testing.

* Add native implementation for benchmarking JDK 8 and 11

It's now supported with JNIBLAS, JNILAPACK, and (upcoming) JNIARPACK.

* Allow manual trigger of the workflow

* Relax the compiler warnings for now

* Fix installed dependencies

* Implement some more BLAS calls in JNIBLAS

* Fix bound condition check

It triggered the "Vector API breaks JNI". Turns out testing just got
better and uncovered a bug.

* Add code coverage information

* Add scaffolding for JNIARPACK

* Make sure license is consistent across all files

* There might be cases where we want to make a release on a SNAPSHOT tag

* Add scaffolding for all ARPACK, BLAS, and LAPACK routines

* Fix surefire:test

jacoco wouldn't setup the argLine variable. Just set it to ""

* Add missing libarpack2-dev dependency on CI

* Cache M2 repository to speed up CI

* Relax caching across JDK versions

* Implement all BLAS routines for JNIBLAS

* Add generator for JNI

* Compiler complains that __ret may be uninitialized

It's because it doesn't know Throw never returns

* Generate function for NotImplemented + Reduce whitespace noise

* Remove -Wno-unused-function and -Wno-unused-parameter warnings

* Generate the totality of jni.c for BLAS, ARPACK, and LAPACK

It makes it much much easier to manager

* Add null and index checks for double/float arrays

* Cache more often

* Use full name of library for dev.ludovic.netlib.{blas,lapack,arpack}.nativeLib

* Skip unimplemented tests

* Wrap calls to Objects.requireNonNull for consistency with checkIndex

* Add {BLAS,LAPACK,ARPACK}.getInstance helpers

* Rename _*_offset parameters to offset*

* Remove unused test resources and methods

Author: luhenry

.github/workflows/build-and-test.yml

@@ -20,10 +20,15 @@ jobs:
         jdk: [8, 11, 16]
     steps:
     - uses: actions/checkout@v2
+    - name: Cache M2 local repository
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2/repository
+        key: m2
     - name: Install dependencies
       run: |
         sudo apt-get -y update
-        sudo apt-get -y install libopenblas-dev gcc-aarch64-linux-gnu gcc-x86-64-linux-gnu
+        sudo apt-get -y install libopenblas-dev libarpack2-dev gcc-aarch64-linux-gnu gcc-x86-64-linux-gnu
     # Build with JDK 16
     - name: Set up JDK 16
       uses: actions/setup-java@v1

.github/workflows/release.yml

@@ -5,7 +5,6 @@ on:
   push:
     tags:
       - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
-      - '!v*-SNAPSHOT' # But not v*-SNAPSHOT, i.e. v2-SNAPSHOT
   workflow_dispatch:
 
 name: Release
@@ -21,10 +20,15 @@ jobs:
         jdk: [8, 11, 16]
     steps:
     - uses: actions/checkout@v2
+    - name: Cache M2 local repository
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2/repository
+        key: m2
     - name: Install dependencies
       run: |
         sudo apt-get -y update
-        sudo apt-get -y install libopenblas-dev gcc-aarch64-linux-gnu gcc-x86-64-linux-gnu
+        sudo apt-get -y install libopenblas-dev libarpack2-dev gcc-aarch64-linux-gnu gcc-x86-64-linux-gnu
     # Build with JDK 16
     - name: Set up JDK 16
       uses: actions/setup-java@v1
@@ -49,6 +53,15 @@ jobs:
       release_upload_url: ${{ steps.create_release.outputs.upload_url  }}
     steps:
     - uses: actions/checkout@v2
+    - name: Cache M2 local repository
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2/repository
+        key: m2
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y update
+        sudo apt-get -y install gcc-aarch64-linux-gnu gcc-x86-64-linux-gnu
     - name: Set up JDK 16
       uses: actions/setup-java@v1
       with: # running setup-java again overwrites the settings.xml
@@ -85,7 +98,7 @@ jobs:
     strategy:
       matrix:
         jdk: [8, 11, 16]
-        implementation: ["f2j", "java"]
+        implementation: ["f2j", "java", "native"]
         filter: ["dev.ludovic.netlib.benchmarks.blas.l1", "dev.ludovic.netlib.benchmarks.blas.l2", "dev.ludovic.netlib.benchmarks.blas.l3"]
         include:
         - jdk: 16
@@ -100,18 +113,6 @@ jobs:
           implementation: "java"
           filter: "dev.ludovic.netlib.benchmarks.blas.l3"
           jvmArgs: "--add-modules=jdk.incubator.vector"
-        - jdk: 16
-          implementation: "native"
-          filter: "dev.ludovic.netlib.benchmarks.blas.l1"
-          jvmArgs: "--add-modules=jdk.incubator.foreign -Dforeign.restricted=permit"
-        - jdk: 16
-          implementation: "native"
-          filter: "dev.ludovic.netlib.benchmarks.blas.l2"
-          jvmArgs: "--add-modules=jdk.incubator.foreign -Dforeign.restricted=permit"
-        - jdk: 16
-          implementation: "native"
-          filter: "dev.ludovic.netlib.benchmarks.blas.l3"
-          jvmArgs: "--add-modules=jdk.incubator.foreign -Dforeign.restricted=permit"
     steps:
     - name: Set up JDK ${{ matrix.jdk }}
       uses: actions/setup-java@v1

arpack/pom.xml

@@ -30,25 +30,24 @@ information or have any questions.
   <parent>
     <groupId>dev.ludovic.netlib</groupId>
     <artifactId>parent</artifactId>
-    <version>1.3.2</version>
+    <version>2-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
   <groupId>dev.ludovic.netlib</groupId>
   <artifactId>arpack</artifactId>
-  <version>1.3.2</version>
+  <version>2-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <properties>
     <junit.version>5.5.2</junit.version>
-    <netlib.java.version>1.1.2</netlib.java.version>
   </properties>
 
   <dependencies>
     <dependency>
-      <groupId>com.github.fommil.netlib</groupId>
-      <artifactId>core</artifactId>
-      <version>${netlib.java.version}</version>
+      <groupId>net.sourceforge.f2j</groupId>
+      <artifactId>arpack_combined_all</artifactId>
+      <version>0.1</version>
     </dependency>
 
     <dependency>
@@ -64,4 +63,12 @@ information or have any questions.
       <scope>test</scope>
     </dependency>
   </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-antrun-plugin</artifactId>
+      </plugin>
+    </plugins>
+  </build>
 </project>

arpack/src/main/java/dev/ludovic/netlib/ARPACK.java

@@ -25,8 +25,20 @@
 
 package dev.ludovic.netlib;
 
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 public interface ARPACK {
 
+  public static ARPACK getInstance() {
+    try {
+      return dev.ludovic.netlib.NativeARPACK.getInstance();
+    } catch (Throwable t) {
+      Logger.getLogger(ARPACK.class.getName()).warning("Failed to load implementation from:dev.ludovic.netlib.NativeARPACK");
+    }
+    return dev.ludovic.netlib.JavaARPACK.getInstance();
+  }
+
   public void dmout(int lout, int m, int n, double[] a, int lda, int idigit, String ifmt);
   public void dmout(int lout, int m, int n, double[] a, int offseta, int lda, int idigit, String ifmt);
   public void smout(int lout, int m, int n, float[] a, int lda, int idigit, String ifmt);

arpack/src/main/java/dev/ludovic/netlib/JavaARPACK.java

@@ -28,6 +28,6 @@
 public interface JavaARPACK extends ARPACK {
 
   public static JavaARPACK getInstance() {
-    return dev.ludovic.netlib.arpack.NetlibF2jARPACK.getInstance();
+    return dev.ludovic.netlib.arpack.F2jARPACK.getInstance();
   }
 }

arpack/src/main/java/dev/ludovic/netlib/NativeARPACK.java

@@ -32,9 +32,9 @@ public interface NativeARPACK extends ARPACK {
 
   public static NativeARPACK getInstance() {
     try {
-      return dev.ludovic.netlib.arpack.NetlibNativeARPACK.getInstance();
+      return dev.ludovic.netlib.arpack.JNIARPACK.getInstance();
     } catch (Throwable t) {
-      Logger.getLogger(NativeARPACK.class.getName()).warning("Failed to load implementation from:dev.ludovic.netlib.arpack.NetlibNativeARPACK");
+      Logger.getLogger(NativeARPACK.class.getName()).warning("Failed to load implementation from:dev.ludovic.netlib.arpack.JNIARPACK");
     }
     throw new RuntimeException("Unable to load native implementation");
   }