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JNI Crash when calling MEDIAN function #418

tildedave opened this issue Apr 9, 2019 · 2 comments

JNI Crash when calling MEDIAN function #418

tildedave opened this issue Apr 9, 2019 · 2 comments


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@tildedave tildedave commented Apr 9, 2019

Hi, I've run into a strange issue in JNI using the sqlite-jdbc driver and I was hoping someone here might have some ideas on how to get further. When calling the MEDIAN function on a sufficiently large array of sufficiently large doubles in descending order, a SIGSEGV causes my application to crash. The values being sorted from largest to smallest seems to matter, in that I can't reproduce this without it.

I've reproduced this crash in a project here: and it crashes on both my Mac Powerbook and an x86_64 Virtualbox.

I wasn't able to reproduce this with a C program so my assumption is that this is some issue in how the JNI library is being built and packaged. Mostly I'm looking to understand this issue better so I can figure out what the right way to prevent it from happening is (we use these extension functions quite heavily).

Program Reproducing Error

List<Double> values = new ArrayList<>();

Random r = new Random();
for (int i = 0; i < 50_000; i++) {
    values.add((double) (r.nextInt(1_400_000)));
// Does not fail without reverse sorting
values.sort((o1, o2) -> -o1.compareTo(o2));

SQLiteConnection connection = (SQLiteConnection) DriverManager.getConnection("jdbc:sqlite::memory:");

try (Statement stmt = connection.createStatement()) {
    stmt.execute("CREATE TABLE table_0(\"num\" real NOT NULL)");

try (PreparedStatement stmt = connection.prepareStatement("INSERT INTO table_0 VALUES (?)")) {
    for(Double value: values) {
        stmt.setDouble(1, value);

try (Statement stmt = connection.createStatement()) {
    stmt.execute("SELECT MEDIAN(\"num\") FROM table_0");

Info From strace/GDB

On x86_64 Linux when run under strace the final failure is:

[pid 23956] --- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_ACCERR, si_addr=0x7fda523caff8} ---
[pid 23956] --- SIGSEGV {si_signo=SIGSEGV, si_code=SI_KERNEL, si_addr=0} ---

The dumped core ends up looking like:

(gdb) bt 10
#0  0x00007f79925db7a0 in ?? () from /tmp/
#1  0x00007f79925db7a5 in ?? () from /tmp/
#2  0x00007f79925db7a5 in ?? () from /tmp/
#3  0x00007f79925db7a5 in ?? () from /tmp/
#4  0x00007f79925db7a5 in ?? () from /tmp/
#5  0x00007f79925db7a5 in ?? () from /tmp/
#6  0x00007f79925db7a5 in ?? () from /tmp/
#7  0x00007f79925db7a5 in ?? () from /tmp/
#8  0x00007f79925db7a5 in ?? () from /tmp/
#9  0x00007f79925db7a5 in ?? () from /tmp/
(many similar frames follow)
#32255 0x00007f7993a6d4fc in ?? ()
#32256 0x00007f79aa44d6f0 in ?? ()
#32257 0x00007f7993a96ff0 in ?? ()
#32258 0x00007f7993b63db0 in ?? ()
#32259 0x00007f7993a6d5e8 in ?? ()
#32260 0x00007f79aa44d650 in ?? ()
#32261 0x00007f79aa44d6e0 in ?? ()
#32262 0x00007f79aa44d740 in ?? ()
#32263 0x00007f799437fa90 in ?? ()
#32264 0x0000000000000000 in ?? ()

I dug around online and the SEGV_ACCERR error I'm getting looks like an illegal memory access from a stack frame violation.

Other Things I Checked

  • Both and 3.25.2 versions of xerial/sqlite-jdbc fail, no difference.
  • In-memory and on disk versions of SQLite both fail
  • I was unable to reproduce this with a C program that linked sqlite3 3.27.1 and compiled extension-functions.c in (both the version in this repo and the last-updated-2010 version on The C program takes a while to perform the SELECT MEDIAN query (~10 seconds) but it does complete.

Thanks for any help that you can provide.

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@tildedave tildedave commented Sep 30, 2019

I traced the stack violation down to the code in extension-functions.c, in the xFinal flow (after each xStep has been run):

void node_iterate(node *n, map_iterator iter, void* p){
    if(n->l) {
      node_iterate(n->l, iter, p);
    iter(n->data, n->count, p);
    if(n->r) {
      node_iterate(n->r, iter, p);

I'm not too familiar with how the JNI stack gets set and how it relates to the C stack, but on my machine it crashed after 16k entries, not enough . This also explains why the error happens when everything is sorted from largest to smallest. I checked node_insert (which gets run during xStep) and this was written in a tail-recursive style so the compiler can optimize out the extra stack frames.

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@tildedave tildedave commented Oct 1, 2019

I was able to fix this by increasing the stack space to the JVM with the -Xss argument. I'll bring up the behavior of this function with the SQLite mailing list and see if it might make more sense for this to use a malloced stack for node traversal.

@tildedave tildedave closed this Oct 1, 2019
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