VMD-L Mailing List

From: brad noyes (brad_at_wpi.edu)
Date: Tue Sep 09 2003 - 21:05:44 CDT

John,
Yes this is a little strange, and i'm kind of confused by it. Here's what i
know so far.

On FreeBSD there's a package called pth, this is not shipped with freebsd, it
is a 3rd party implementation (it's the GNU implementation according to the
package comment). The package contains libpth, and libpthread. I think when
the linker uses '-lpthread' it tries to use the libpthread library from the
pth package, which seems to not work. However if the linker tag '-lpthread'
is omitted, then it will compile, link and execute fine.

I did some testing and it seems that there is no need to explicitly link to a
threading library. I compiled VMD without '-lpthread' and without '-lpth'. It
worked successfully and executed fine. (You can see the ldd output in the
attached nolpthread.txt, the file lpthread.txt is the ldd output of VMD
linked against libpthread) I also compiled with '-lpthread' to make sure it
was still crashing for me, which it was. Upon execution i got a segmentation
fault (somewhere in pthread_mutex_setkind_np, i think).

Apparently FreeBSD is doing a major upgrade to the libpthread implementation
so it is in flux on the current releases. Information about the upgrade can
be found here http://www.freebsd.org/kse/index.html. In the web page it looks
like on FreeBSD 4.x system the linker tag '-pthread' would do the trick. But
i can't test this since i don't have a 4.x system.

FreeBSD 5.1
  -lpthread: seg fault
  -lpth: executes fine
  -pthread: same as no linker tag
  no linker tag: executes fine

FreeBSD 4.8
  -lpthread: seg fault (according Tsu-Fan Cheng form the list)
  -lpth: ???
  -pthread: ???
  no linker tag: ???

So i hope this makes some sense. Perhaps if Tsu-Fan Cheng gets back to us we
could ask him to try various linker options to see what works.

--brad

On Tuesday 09 September 2003 20:43, you wrote:
> Brad,
> libpthread is shipped broken by default on FreeBSD??!?!?!?
> Do you know what the actual problem with their libpthread
> implementation is? I would be very interested to know why
> the crash occurs, and what libpth does differently to cure
> the problem. Seems hokey to me for the default libpthread
> to have serious problems. As far as changing the configure
> script, do you know if this alternate "libpth" is shipped
> by default with all FreeBSD machines?
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Sep 09, 2003 at 05:43:10PM -0400, brad noyes wrote:
> > Hi,
> > i think i have found the problem for the crashes on freebsd. At least
> > this fix seems to work for my desktop. Apparently there is a problem with
> > libpthread on freebsd, and therefor it has been deprecated. Instead VMD
> > should link to libpth. So in the src/ directory you can edit the Makefile
> > and change all occurrences of "-lpthread" to "-lpth", then run make.
> >
> > Sorry this took me 2 months to figure out, but i was stumped until i read
> > about libpthread on an unrelated list.
> >
> > John, Could you make the necessary change in the configure script?
> >
> > --brad