Thread: How to call a C sort function to sort a Java Array.

My name is David, I'm interning this summer doing some High Performance Computing work. I'm significantly out of my comfort zone here; I am primarily a network/network security geek, not a programming guy. I took one Java based class called problem solving with programming where we wrote like 3 programs in Java and did everything else in pseudocode and using a program called Alice Alice.org to do things graphically. Learned basically no actual programming syntax. Also have done some self-taught perl, but only through one book and I didn't finish it, I only got about half way through it. So my expertise in programming are pretty much null.

That being said, I currently am tasked with having to figure out how to make JNI work... specifically at this time I am tasked with writing an array in Java, and designing a C program that can be called by means of JNI to sort the array. I have chosen to work with the Merge Sort algorithm. My method of coding is not one where I write the entire thing from scratch, I don't particularly have a need to master languages at this point, rather I just need to make them work. I am interested in learning, but time is of the essence for me right now. So thus far what I have done is take sample codes and tweak them to meet my purpose. However, I currently am unable to make things work. So I am asking for help.

I am going to paste 3 codes here, the first one will be my basic self-written instructions for JNI (Hello World Instructions), the second one will be my Java Array, and the third one will be my MergeSort function. I am not asking for you to DO my work for me by telling me how to manipulate my code, but rather I am asking for you to send me in the direction of resources that will be of some aid to me. Links, books (preferrably e-books so I don't have to go to a library), anything that you can send my direction that may help will be deeply appreciated. Thanks so much!

JNI Instructions:

/*The process for calling a C function in Java is as follows:
 
1)Write the Java Program name. Eg. HelloWorld.java
2)Compile it: javac HelloWorld.java
3)Create a header file: javah -jni HelloWorld
4)Create a C program eg. HelloWorld.java
5)Compile the C program creating a shared library eg. libhello.so (My specifc command is cc -m32 -I/usr/java/jdk1.7.0_05/include -I/usr/java/jdk1.7.0_05/include/linux -shared -o libhello.so -fPIC HelloWorld.c 
6) Copy the library to the java.library.path, or LD_LIBRARY_PATH (in my case I have set it to /usr/local/lib. 
7)Run ldconfig (/sbin/ldconfig)
8)Run the java program: java HelloWorld. */
 
/*__________________________________________________________________________*/
 
//Writing the code:
//For the HelloWorld program: 
 
//In java:
//You need to name a class:
class HelloWorld {
//You then need to declare a native method:
public native void displayHelloWorld();
//You now need a static initializer:
static {
//Load the library:
System.loadLibrary("hello");
}
/*Main function to call the native method (call the C code)*/
public static void main(String[] args) {
new HelloWorld().displayHelloWorld();
}
}
 
//In C:
#include <jni.h> //JNI header
#include "HelloWorld.h" //Header created by the javah -jni command parameter
#include <stdio.h> //Standard input/output header for C.
 
//Now we must use a portion of the code provided by the JNI header.
JNIEXPORT void JNICALL
Java_HelloWorld_displayHelloWorld(JNIENV *env, jobject obj) 
//Naming convention: Java_JavaProgramName_displayCProgramName
{
    printf("Hello World!\n");
    return;
}

Java Array:

 class JavaArray {
     private native int MergeSort(int[] arr);
     public static void main(String[] args) 
     {
         int arr[] = {7, 8, 6, 3, 1, 19, 20, 13, 27, 4};
     }
     static 
     {
         System.loadLibrary("MergeSort");
     }   
 }

Hacked and pieced together crappy C Merge Sort code:

#include <jni.h>
#include <stdio.h>
#include "JavaArray.h"
 
 JNIEXPORT jint JNICALL 
 Java_JavaArray_MergeSort(JNIEnv *env, jobject obj, jintArray arr[],jint low,jint mid,jint high)
 {
   jint i,j,k,l,b[10];
 l=low;
 i=low;
 j=mid+1;
 while((l<=mid)&&(j<=high))
   {
    if(arr[l]<=arr[j])
      {
       b[i]=arr[l];
       l++;
      }
    else
      {
       b[i]=arr[j];
       j++;
      }
    i++;
   }
 if(l>mid)
   {
    for(k=j;k<=high;k++)
       {
        b[i]=arr[k];
        i++;
       }
   }
 else
   {
    for(k=l;k<=mid;k++)
       {
        b[i]=arr[k];
        i++;
       }
   }
 for(k=low;k<=high;k++)
    {
     arr[k]=b[k];
    }
}
 
void partition(jint arr[],jint low,jint high)
{
 jint mid;
 if(low<high)
   {
    mid=(low+high)/2;
    partition(arr,low,mid);
    partition(arr,mid+1,high);
    sort(arr,low,mid,high);
   }
 
 }

This sort of looks like taking a medical student in his first week of medical school and asking him to read a manual on and then perform neurosurgery. Don't you need to know how to walk or even crawl before you try to fly?

Yeah I've read that, aussiemcgr, I actually found a link to that page in another thread on this forum. And it DID in fact help me significantly getting my Hello World stuff to work the other day. So thanks for throwing that out there, to you, and whomever else points people in that direction. It was very helpful, I just haven't found the solution to my issues in there currently. I'm getting the following error:

 cc -m32 -I/usr/java/jdk1.7.0_05/include -I/usr/java/jdk1.7.0_05/include/linux -shared -o libMergeSort.so -fPIC MergeSort.c
MergeSort.c:7: error: conflicting types for ‘Java_JavaArray_MergeSort’
JavaArray.h:16: error: previous declaration of ‘Java_JavaArray_MergeSort’ was here
MergeSort.c: In function ‘Java_JavaArray_MergeSort’:
MergeSort.c:16: warning: assignment makes integer from pointer without a cast
MergeSort.c:21: warning: assignment makes integer from pointer without a cast
MergeSort.c:30: warning: assignment makes integer from pointer without a cast
MergeSort.c:38: warning: assignment makes integer from pointer without a cast
MergeSort.c:44: warning: assignment makes pointer from integer without a cast

Your method parameters are not matching. You need to show your JavaArray.h file, methinks.

Originally Posted by Fubarable

Your method parameters are not matching. You need to show your JavaArray.h file, methinks.

Well, mentioning the JavaArray.h file made me take a look at some things so I changed my Java code a tiny bit. I appreciate your comments.

JavaArray.java now looks like:

 class JavaArray {
     private native int MergeSort(int[] arr, int low, int mid, int high);
     public static void main(String[] args) 
     {
         int arr[] = {7, 8, 6, 3, 1, 19, 20, 13, 27, 4};
     }
     static 
     {
         System.loadLibrary("MergeSort");
     }   
 }

And my JavaArray.h file looks like:

/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class JavaArray */
 
#ifndef _Included_JavaArray
#define _Included_JavaArray
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     JavaArray
 * Method:    MergeSort
 * Signature: ([IIII)I
 */
JNIEXPORT jint JNICALL Java_JavaArray_MergeSort
  (JNIEnv *, jobject, jintArray, jint, jint, jint);
 
#ifdef __cplusplus
}
#endif
#endif

That looks better, and looks to be in agreement with your c code. Does it work now?

Nope still got the same errors.

Now, the C code I had posted had "jint low, jint mid, jint high" in it, and the java code has the same. However when I compile the Java code, and do javah -jni JavaArray the JavaArray.h file jsut says "jint, jint, jint". Now I know it says not to edit the .h file, but should I edit it so that it resmbles my C code more appropriately? Or is there something I'm missing in the Java Code that will get me the right .h file?

No, don't edit the .h file. Your .c file's method signature must match that of the .h file, and then call the c library's method using the parameters that have been passed in to it by Java. You probably should repost your .h file and your .c bridge file.

Just to warn you, it's been several years since I've fiddled with JNI. I mainly use JNA (Java Native Access) instead since it is a *lot* easier to deal with. But it requires c code, or (I think) c++ code that is called with C calling conventions.

Sorry, my .c bridge file?

My current .h file is:

/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class JavaArray */
 
#ifndef _Included_JavaArray
#define _Included_JavaArray
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     JavaArray
 * Method:    MergeSort
 * Signature: ([IIII)I
 */
JNIEXPORT jint JNICALL Java_JavaArray_MergeSort
  (JNIEnv *, jobject, jintArray, jint, jint, jint);
 
#ifdef __cplusplus
}
#endif
#endif

And my MergeSort.c file is:

#include <jni.h>
#include <stdio.h>
#include "JavaArray.h"
 
 JNIEXPORT jint JNICALL Java_JavaArray_MergeSort
  (JNIEnv *, jobject, jintArray, jint low, jint mid, jint high)
 {
 jint i,j,k,l,b[10];
 l=low;
 i=low;
 j=mid+1;
 while((l<=mid)&&(j<=high))
   {
    if(arr[l]<=arr[j])
      {
       b[i]=arr[l];
       l++;
      }
    else
      {
       b[i]=arr[j];
       j++;
      }
    i++;
   }
 if(l>mid)
   {
    for(k=j;k<=high;k++)
       {
        b[i]=arr[k];
        i++;
       }
   }
 else
   {
    for(k=l;k<=mid;k++)
       {
        b[i]=arr[k];
        i++;
       }
   }
 for(k=low;k<=high;k++)
    {
     arr[k]=b[k];
    }
}
 
void partition(jint arr[],jint low,jint high)
{
 jint mid;
 if(low<high)
   {
    mid=(low+high)/2;
    partition(arr,low,mid);
    partition(arr,mid+1,high);
    sort(arr,low,mid,high);
   }
 
 }

Compiling in the manner that I do, the only other file created is my library file - libMergeSort.so (I'm using linux). And currently, that's not being created because my program will not compile under the current circumstances.

No, you've got to create the bridge C class. That's where all the work of JNI occurs. Again, read a detailed tutorial on this and you'll see.

Read the instruction file that I posted in my original post.

Specifically, these instructions. And for creating a HelloWorld program, and a couple of other simpler math programs (addition programs) this process worked properly. I created no additional bridge file.

My process:

/*The process for calling a C function in Java is as follows:
 
1)Write the Java Program name. Eg. HelloWorld.java
2)Compile it: javac HelloWorld.java
3)Create a header file: javah -jni HelloWorld
4)Create a C program eg. HelloWorld.java
5)Compile the C program creating a shared library eg. libhello.so (My specifc command is cc -m32 -I/usr/java/jdk1.7.0_05/include -I/usr/java/jdk1.7.0_05/include/linux -shared -o libhello.so -fPIC HelloWorld.c 
6) Copy the library to the java.library.path, or LD_LIBRARY_PATH (in my case I have set it to /usr/local/lib. 
7)Run ldconfig (/sbin/ldconfig)
8)Run the java program: java HelloWorld. */

It is step 4) create a C program eg. HelloWorld.java (it should be HelloWorld.c). You're not doing that.

That is MergeSort.c, and I've never had to create it with the same name as the java file. And my instructions was just a typo, I meant to write down .c not .java. Anyway, my MergeSort.C program is the "bridge" file.

To show what I mean, I'll post a WORKING example with code, program names, and commands used:

IntArray.java

 class IntArray {
     private native int sumArray(int[] arr);
     public static void main(String[] args) {
         IntArray p = new IntArray();
         int arr[] = new int[10];
         for (int i = 0; i < 10; i++) {
             arr[i] = i;
         }
         int sum = p.sumArray(arr);
         System.out.println("sum = " + sum);
     }
     static {
         System.loadLibrary("IntArray");
     }
 }

commands as follows:
javac IntArray.java
javah -jni IntArray

sumArray.c

 #include <jni.h>
 #include <stdio.h>
 #include "IntArray.h"
 
 JNIEXPORT jint JNICALL 
 Java_IntArray_sumArray(JNIEnv *env, jobject obj, jintArray arr)
 {
     jint buf[10];
     jint i, sum = 0;
     (*env)->GetIntArrayRegion(env, arr, 0, 10, buf);
     for (i = 0; i < 10; i++) {
         sum += buf[i];
     }
     return sum;
 }

commands as follows:
cc -m32 -I/usr/java/jdk1.7.0_05/include -I/usr/java/jdk1.7.0_05/include/linux -shared -0 libIntArray.so -fPIC sumArray.c
cp libIntArray /usr/local/lib
ldconfig
java IntArray
Output:

[root@pe11196 Desktop]# java IntArray
sum = 45
[root@pe11196 Desktop]#

Originally Posted by copeg

I know this comment doesn't directly address your immediate JNI needs, but here goes - sorting an array in java is easy - in fact, the algorithm is already written for you. I'd like to hope there is some benefit for using JNI that I've missed...

I know sorting an array in Java is easy. Because I'm unsure what level of clearance my actual project has, I can't fully explain anything to you. What I can say is this: There is an open source data management application that is used frequently for management of huge amounts of data in various fields. It is written entirely in Java. However, Java has limitations in networking, and in Memory access. In C, those limitations do not exist in the same way, so my mentor and his team have developed a back-end sort of application in C that they would like to communincate with the Java application. So, my mentor has got me researching JNI, and asked for me to find out how to sort a Java array with a C function.

Thanks for your interest.

Thanks helloworld,

So instead of what you quoted me saying, should it be:

JNIEXPORT jint JNICALL Java_JavaArray_MergeSort
  (JNIEnv *env, jobject obj, jintArray arr, jint low, jint mid, jint high)

And to properly transfer the array into the C array, is it this nifty little piece here? Or is there more to it:

    (*env)->GetIntArrayRegion(env, arr, 0, 10, buf);

Thanks for your help.

Originally Posted by helloworld922

That's the basic jist of it. You need to ensure your buffer is large enough and that you're transferring over the correct portion of the array. You'll also need to transfer the array back.

Instead of GetIntArrayRegion could I do GetIntArrayElements? and also ReleaseIntArrayElements? and if not, to release it then would I do ReleaseIntArrayRegion?

Originally Posted by Fubarable

Just to warn you, it's been several years since I've fiddled with JNI. I mainly use JNA (Java Native Access) instead since it is a *lot* easier to deal with. But it requires c code, or (I think) c++ code that is called with C calling conventions.

Think you could tell me a bit more about JNA? I just emailed my mentor about it, and researched it a bit on wikipedia. After my explanation about using a Java Front-end with a C back-end do you think JNA is a better option than JNI? Thanks so much for your help, and mentioning it. I appreciate your patience.