Subject: Re: threaded applications randomly crash on -current
To: Frank van der Linden <>
From: Nicolas Joly <>
List: port-amd64
Date: 10/20/2004 20:06:34
On Wed, Oct 20, 2004 at 05:17:28PM +0200, Frank van der Linden wrote:
> 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,

Hi Frank,

> 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.

Looks very promising !

I'm running the patches for about 2 hours now, and no application
crash ... Previously, it took only a couple of min to hit this
problem.  I'll try all night, just to be sure.

Thanks a lot.

Nicolas Joly

Biological Software and Databanks.
Institut Pasteur, Paris.