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POSIGILL after fork in Sage/Python
 

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  1. POSIGILL after fork in Sage/Python
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    <p>I'm doing some calculations with <a href="http://sagemath.org" rel="nofollow">Sage</a>. I am playing around with <code>fork</code>. I have a very simple test case which is basically like this:</p> <pre><code>def fork_test(): import os pid = os.fork() if pid != 0: print "parent, child: %i" % pid os.waitpid(pid, 0) else: print "child" try: # some dummy matrix calculation finally: os._exit(0) </code></pre> <p>(Look below for <code>_fork_test_func()</code> for some matrix calculations.)</p> <p>And I'm getting:</p> <pre><code>------------------------------------------------------------------------ Unhandled SIGILL: An illegal instruction occurred in Sage. This probably occurred because a *compiled* component of Sage has a bug in it and is not properly wrapped with sig_on(), sig_off(). You might want to run Sage under gdb with 'sage -gdb' to debug this. Sage will now terminate. ------------------------------------------------------------------------ </code></pre> <p>With this (incomplete) backtrace:</p> <pre><code>Crashed Thread: 0 Dispatch queue: com.apple.root.default-priority Exception Type: EXC_BAD_INSTRUCTION (SIGILL) Exception Codes: 0x0000000000000001, 0x0000000000000000 Application Specific Information: BUG IN LIBDISPATCH: flawed group/semaphore logic Thread 0 Crashed:: Dispatch queue: com.apple.root.default-priority 0 libsystem_kernel.dylib 0x00007fff8c6d1d46 __kill + 10 1 libcsage.dylib 0x0000000101717f33 sigdie + 124 2 libcsage.dylib 0x0000000101717719 sage_signal_handler + 364 3 libsystem_c.dylib 0x00007fff86b1094a _sigtramp + 26 4 libdispatch.dylib 0x00007fff89a66c74 _dispatch_thread_semaphore_signal + 27 5 libdispatch.dylib 0x00007fff89a66f3e _dispatch_apply2 + 143 6 libdispatch.dylib 0x00007fff89a66e30 dispatch_apply_f + 440 7 libBLAS.dylib 0x00007fff906ca435 APL_dtrsm + 1963 8 libBLAS.dylib 0x00007fff906702b6 cblas_dtrsm + 882 9 matrix_modn_dense_double.so 0x0000000108612615 void FFLAS::Protected::ftrsmRightLowerNoTransUnit&lt;double&gt;::delayed&lt;FFPACK::Modular&lt;double&gt; &gt;(FFPACK::Modular&lt;double&gt; const&amp;, unsigned long, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long, unsigned long, unsigned long) + 2853 10 matrix_modn_dense_double.so 0x0000000108611daa void FFLAS::Protected::ftrsmRightLowerNoTransUnit&lt;double&gt;::delayed&lt;FFPACK::Modular&lt;double&gt; &gt;(FFPACK::Modular&lt;double&gt; const&amp;, unsigned long, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long, unsigned long, unsigned long) + 698 11 matrix_modn_dense_double.so 0x0000000108612ccf void FFLAS::Protected::ftrsmRightLowerNoTransUnit&lt;double&gt;::operator()&lt;FFPACK::Modular&lt;double&gt; &gt;(FFPACK::Modular&lt;double&gt; const&amp;, unsigned long, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long, FFPACK::Modular&lt;double&gt;::Element*, unsigned long) + 831 12 ??? 0x00007f99e481a028 0 + 140298940424232 Thread 1: 0 libsystem_kernel.dylib 0x00007fff8c6d26d6 __workq_kernreturn + 10 1 libsystem_c.dylib 0x00007fff86b24f4c _pthread_workq_return + 25 2 libsystem_c.dylib 0x00007fff86b24d13 _pthread_wqthread + 412 3 libsystem_c.dylib 0x00007fff86b0f1d1 start_wqthread + 13 Thread 2: 0 libsystem_kernel.dylib 0x00007fff8c6d26d6 __workq_kernreturn + 10 1 libsystem_c.dylib 0x00007fff86b24f4c _pthread_workq_return + 25 2 libsystem_c.dylib 0x00007fff86b24d13 _pthread_wqthread + 412 3 libsystem_c.dylib 0x00007fff86b0f1d1 start_wqthread + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x00007fff5ec8e418 rcx: 0x00007fff5ec8df28 rdx: 0x0000000000000000 rdi: 0x000000000000b8f7 rsi: 0x0000000000000004 rbp: 0x00007fff5ec8df40 rsp: 0x00007fff5ec8df28 r8: 0x00007fff5ec8e418 r9: 0x0000000000000000 r10: 0x000000000000000a r11: 0x0000000000000202 r12: 0x00007f99ea500de0 r13: 0x0000000000000003 r14: 0x00007fff5ec8e860 r15: 0x00007fff906ca447 rip: 0x00007fff8c6d1d46 rfl: 0x0000000000000202 cr2: 0x00007fff74a29848 Logical CPU: 0 </code></pre> <p>Is there something special I need to do after a <code>fork</code>? I looked up the <code>fork</code> decorator of Sage and it looks like it basically does the same.</p> <p>The crash also happens with the <code>fork</code> decorator of Sage itself. Another test case:</p> <pre><code>def fork_test2(): def test(): # do some stuff from sage.parallel.decorate import fork test_ = fork(test, verbose=True) test_() </code></pre> <hr> <p>Even simpler test case:</p> <pre><code>def _fork_test_func(): while True: m = matrix(QQ, 100, [randrange(-100,100) for i in range(100*100)]) m.right_kernel() def fork_test(): import os pid = os.fork() if pid != 0: print "parent, child: %i" % pid os.waitpid(pid, 0) else: print "child" try: _fork_test_func() finally: os._exit(0) </code></pre> <p>Results in a slightly different crash:</p> <pre><code>python(48672) malloc: *** error for object 0x11185f000: pointer being freed already on death-row *** set a breakpoint in malloc_error_break to debug </code></pre> <p>With backtrace:</p> <pre><code>Crashed Thread: 1 Dispatch queue: com.apple.root.default-priority Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Application Specific Information: *** error for object 0x11185f000: pointer being freed already on death-row Thread 0:: Dispatch queue: com.apple.main-thread 0 matrix2.so 0x0000000107fa403f __pyx_pw_4sage_6matrix_7matrix2_6Matrix_71right_kernel_matrix + 27551 1 ??? 0x000000000000000d 0 + 13 Thread 1 Crashed:: Dispatch queue: com.apple.root.default-priority 0 libsystem_kernel.dylib 0x00007fff8c6d239a __semwait_signal_nocancel + 10 1 libsystem_c.dylib 0x00007fff86b17e1b nanosleep$NOCANCEL + 138 2 libsystem_c.dylib 0x00007fff86b7b9a8 usleep$NOCANCEL + 54 3 libsystem_c.dylib 0x00007fff86b67eca __abort + 203 4 libsystem_c.dylib 0x00007fff86b67dff abort + 192 5 libsystem_c.dylib 0x00007fff86b43905 szone_error + 580 6 libsystem_c.dylib 0x00007fff86b43f7d free_large + 229 7 libsystem_c.dylib 0x00007fff86b3b8f8 free + 199 8 libBLAS.dylib 0x00007fff906b0431 __APL_dgemm_block_invoke_0 + 132 9 libdispatch.dylib 0x00007fff89a65f01 _dispatch_call_block_and_release + 15 10 libdispatch.dylib 0x00007fff89a620b6 _dispatch_client_callout + 8 11 libdispatch.dylib 0x00007fff89a631fa _dispatch_worker_thread2 + 304 12 libsystem_c.dylib 0x00007fff86b24d0b _pthread_wqthread + 404 13 libsystem_c.dylib 0x00007fff86b0f1d1 start_wqthread + 13 </code></pre> <p>The same happens also for this:</p> <pre><code>def fork_test2(): from sage.parallel.decorate import fork test_ = fork(_fork_test_func, verbose=True) test_() </code></pre> <p>-- but only if you used some other matrix calculations before.</p> <hr> <p>This test case also works on a fresh Sage session:</p> <pre><code>def _fork_test_func(iterator=None): if not iterator: import itertools iterator = itertools.count() for i in iterator: m = matrix(QQ, 100, [randrange(-100,100) for i in range(100*100)]) m.right_kernel() def fork_test(): _fork_test_func(range(10)) import os pid = os.fork() if pid != 0: print "parent, child: %i" % pid os.waitpid(pid, 0) else: print "child" try: _fork_test_func() finally: os._exit(0) </code></pre> <hr> <p>I have downloaded the binaries for MacOSX 64bit of Sage 5.8.</p> <p>(Note that I also asked on ask.sagemath.org <a href="http://ask.sagemath.org/question/2627/sigill-in-forked-process" rel="nofollow">here</a>.)</p>
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