An example of JNI call and GC/Safepoint interaction. Shows that native call doesn't block GC/Safepoint. JNI postpones a GC if it's in a critical section.

command_prompt

$ java -version
java version "1.6.0_29"
Java(TM) SE Runtime Environment (build 1.6.0_29-b11)
Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02, mixed mode)
$ vi TestSafepoint.java
$ javac TestSafepoint.java
$ javah TestSafepoint
$ vi test.c
$ gcc -fPIC -shared -I$JAVA_HOME/include -I$JAVA_HOME/include/linux -o libtestsp.so test.c 
$ export LD_LIBRARY_PATH=.
$ export JAVA_OPTS='-XX:+PrintGCDetails -XX:+PrintSafepointStatistics -XX:PrintSafepointStatisticsCount=1'
$ java -cp . $JAVA_OPTS TestSafepoint > log.txt

log.txt

[GC [PSYoungGen: 14016K->192K(16320K)] 14016K->192K(53696K), 0.0013830 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.133: ParallelGCFailedAllocation       [       8          1              0    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 14208K->160K(16320K)] 14208K->160K(53696K), 0.0012110 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.146: ParallelGCFailedAllocation       [       8          0              1    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 14176K->160K(16320K)] 14176K->160K(53696K), 0.0008710 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.159: ParallelGCFailedAllocation       [       8          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 14176K->160K(30336K)] 14176K->160K(67712K), 0.0010290 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.172: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 28192K->160K(30336K)] 28192K->160K(67712K), 0.0010830 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.213: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 28192K->160K(56256K)] 28192K->160K(93632K), 0.0010080 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.237: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 56224K->0K(56256K)] 56224K->124K(93632K), 0.0011680 secs] [Times: user=0.00 sys=0.00, real=0.01 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.319: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     1    ]  0   
[GC [PSYoungGen: 56064K->0K(112384K)] 56188K->124K(149760K), 0.0005150 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.365: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 112128K->0K(112384K)] 112252K->124K(149760K), 0.0007000 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.526: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 112128K->0K(179712K)] 112252K->124K(217088K), 0.0005000 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.617: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 179456K->0K(179712K)] 179580K->124K(217088K), 0.0007790 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.844: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 179456K->0K(287360K)] 179580K->124K(324736K), 0.0005330 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
0.989: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 287168K->0K(273600K)] 287292K->124K(310976K), 0.0005120 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
1.350: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 273536K->0K(260608K)] 273660K->124K(297984K), 0.0005070 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
1.570: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 260544K->0K(248448K)] 260668K->124K(285824K), 0.0006080 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
1.780: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 248192K->0K(236544K)] 248316K->124K(273920K), 0.0006320 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
1.987: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 236480K->0K(225600K)] 236604K->124K(262976K), 0.0004820 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
2.183: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 225344K->0K(214848K)] 225468K->124K(252224K), 0.0005960 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
2.364: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 214784K->0K(204992K)] 214908K->124K(242368K), 0.0004840 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
2.537: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 204736K->0K(195264K)] 204860K->124K(232640K), 0.0005910 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
2.702: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 195200K->0K(186368K)] 195324K->124K(223744K), 0.0005000 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
2.859: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 186112K->0K(177536K)] 186236K->124K(214912K), 0.0006090 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.010: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 177472K->0K(169472K)] 177596K->124K(206848K), 0.0005080 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.153: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 169280K->0K(161536K)] 169404K->124K(198912K), 0.0005660 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.289: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 161472K->0K(154240K)] 161596K->124K(191616K), 0.0005080 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.420: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
[GC [PSYoungGen: 154048K->0K(147072K)] 154172K->124K(184448K), 0.0005690 secs] [Times: user=0.00 sys=0.00, real=0.00 secs] 
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.544: ParallelGCFailedAllocation       [       7          0              0    ]      [     0     0     0     0     0    ]  0   
Heap
 PSYoungGen      total 147072K, used 115438K [0x00000000edc00000, 0x00000000ff3b0000, 0x0000000100000000)
  eden space 147008K, 78% used [0x00000000edc00000,0x00000000f4cbb878,0x00000000f6b90000)
  from space 64K, 0% used [0x00000000ff3a0000,0x00000000ff3a0000,0x00000000ff3b0000)
  to   space 192K, 0% used [0x00000000ff350000,0x00000000ff350000,0x00000000ff380000)
 PSOldGen        total 37376K, used 124K [0x00000000c9400000, 0x00000000cb880000, 0x00000000edc00000)
  object space 37376K, 0% used [0x00000000c9400000,0x00000000c941f060,0x00000000cb880000)
 PSPermGen       total 21248K, used 2571K [0x00000000c4200000, 0x00000000c56c0000, 0x00000000c9400000)
  object space 21248K, 12% used [0x00000000c4200000,0x00000000c4482f58,0x00000000c56c0000)
         vmop                    [threads: total initially_running wait_to_block]    [time: spin block sync cleanup vmop] page_trap_count
3.635: no vm operation                  [       6          1              1    ]      [     0     0     0     0     0    ]  0   

Polling page always armed
ParallelGCFailedAllocation        26
    0 VM operations coalesced during safepoint
Maximum sync time      0 ms
Maximum vm operation time (except for Exit VM operation)      1 ms

test.c

#include "jni.h"
#include "TestSafepoint.h"
#include <unistd.h>

void JNICALL Java_TestSafepoint_nativeSleep(JNIEnv* env, jclass cls, jlong millis) {
  usleep(millis);
}

TestSafepoint.h

/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class TestSafepoint */

#ifndef _Included_TestSafepoint
#define _Included_TestSafepoint
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     TestSafepoint
 * Method:    nativeSleep
 * Signature: (J)V
 */
JNIEXPORT void JNICALL Java_TestSafepoint_nativeSleep
  (JNIEnv *, jclass, jlong);

#ifdef __cplusplus
}
#endif
#endif

TestSafepoint.java

import java.util.*;

public class TestSafepoint {
  static {
    System.loadLibrary("testsp");
  }
  
  public static native void nativeSleep(long millis);
  
  public static void main(String[] args) {
    new Thread(new Runnable() {
      @Override
      public void run() {
        nativeSleep(10000);
      }
    }).start();
    for (int i = 0; i < 100000000; i++) {
      new LinkedHashMap<Object, Object>(); // trigger minor GCs
    }
  }
}

normal JNI calls are "safepoint region"s, which doesn't block GCs.