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On Wed, Oct 20, 2004 at 04:54:08PM +0200, Nicolas Joly wrote:
> While trying some bioinfo applications on our amd64 machines running
> 2.99.10 and 2.0H kernels (we currently run them on Tru64/alpha), i
> noticed that the threaded ones randomly crash (at least NCBI blast and
> WashU hmmer).
> 
> In the meantime, they run flawlessly on other systems i tested, under
> the same conditions: NetBSD/i386 2.99.10, NetBSD/alpha 2.99.10,
> Linux/amd64 CentOS-3.3RC1 and Tru64/alpha v5.1.

Hi Nicolas,

I have some pthread fixes sitting in my mailbox.. have not had a chance
to give them a final lookover, but I suspect that you may be seeing
this issue.

Wolfgang Solfrank came up with this patch, I'll attach it so that you
can test it.

- Frank

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Index: sys/arch/amd64/include/mcontext.h
===================================================================
RCS file: /cvsroot/src/sys/arch/amd64/include/mcontext.h,v
retrieving revision 1.4
diff -u -r1.4 mcontext.h
--- sys/arch/amd64/include/mcontext.h	13 Oct 2003 18:38:34 -0000	1.4
+++ sys/arch/amd64/include/mcontext.h	4 Oct 2004 08:34:31 -0000
@@ -95,7 +95,7 @@
 
 #define _UC_UCONTEXT_ALIGN	(~0xf)
 
-#define _UC_MACHINE_SP(uc)	((uc)->uc_mcontext.__gregs[_REG_URSP])
+#define _UC_MACHINE_SP(uc)	((uc)->uc_mcontext.__gregs[_REG_URSP] - 128)
 #define _UC_MACHINE_PC(uc)	((uc)->uc_mcontext.__gregs[_REG_RIP])
 #define _UC_MACHINE_INTRV(uc)	((uc)->uc_mcontext.__gregs[_REG_RAX])
 
Index: lib/libpthread/arch/x86_64/_context_u.S
===================================================================
RCS file: /cvsroot/src/lib/libpthread/arch/x86_64/_context_u.S,v
retrieving revision 1.3
diff -u -r1.3 _context_u.S
--- lib/libpthread/arch/x86_64/_context_u.S	8 Nov 2003 21:45:59 -0000	1.3
+++ lib/libpthread/arch/x86_64/_context_u.S	4 Oct 2004 08:34:31 -0000
@@ -53,6 +53,11 @@
 	fxsave	UC_FPREGS(%rdi)					; \
 	movl	$(_UC_USER | _UC_CPU | _UC_FPU),UC_FLAGS(%rdi)
 
+#define	lretqm(x) \
+	.byte	0x48						; \
+	.byte	0xca						; \
+	.word	x
+
 #define SETC \
 	movl	UC_FLAGS(%rdi), %eax				; \
 	btl	$_UC_USER_BIT, %eax				; \
@@ -91,28 +96,28 @@
 	movq	(UC_REGS + _REG_RDX * 8)(%rdi), %rdx		; \
 	movq	(UC_REGS + _REG_RSI * 8)(%rdi), %rsi		; \
 	movw	(UC_REGS + _REG_CS * 8)(%rdi), %ax		; \
-	movq	%rax, -8(%r11)					; \
+	movq	%rax, -128-8(%r11)				; \
 	movw	(UC_REGS + _REG_DS * 8)(%rdi), %ax		; \
-	movq	%rax, -32(%r11)					; \
+	movq	%rax, -128-32(%r11)				; \
 	movq	(UC_REGS + _REG_RIP * 8)(%rdi), %rax		; \
-	movq	%rax, -16(%r11)					; \
+	movq	%rax, -128-16(%r11)				; \
 	movq	(UC_REGS + _REG_RAX * 8)(%rdi), %rax		; \
-	movq	%rax, -24(%r11)					; \
+	movq	%rax, -128-24(%r11)				; \
 	movq	(UC_REGS + _REG_R11 * 8)(%rdi), %rax		; \
-	movq	%rax, -40(%r11)					; \
+	movq	%rax, -128-40(%r11)				; \
 	movq	(UC_REGS + _REG_RFL * 8)(%rdi), %rax		; \
-	movq	%rax, -48(%r11)					; \
+	movq	%rax, -128-48(%r11)				; \
 								; \
 	movw	(UC_REGS + _REG_SS * 8)(%rdi), %ss		; \
 	movq	(UC_REGS + _REG_RDI)(%rdi), %rdi		; \
-	leaq	-48(%r11), %rsp					; \
+	leaq	-128-48(%r11), %rsp				; \
 								; \
 	popfq							; \
 	popq	%r11						; \
 	popq	%rax						; \
 	movl	%eax,%ds					; \
 	popq	%rax						; \
-	lretq
+	lretqm(128)
 
 ENTRY(_getcontext_u)
 	GETC

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