[Bioperl-l] can people with HP/Irix/Alpha confirm these reported problems with bioperl-1.0 ?

[Jason Stajich]

Thanks for the report Mark!

I still want the Makefile generation to get fixed to avoid this problem as
it is really a silly one, but glad you are up and running.

-j

On Wed, 24 Apr 2002, Mark Dalphin wrote:

> I can report a fix for Irix (IRIX64 6.5).
>
> I consulted with one of our SysAdmins, Richard Stokotelny, and he found
> a kernel tuning parameter which alters the ARG_MAX limit.
>
> This change has permitted me to install BioPerl 1.0 without any
> problems. (If a number bigger than 64k is entered, Irix has a kernel
> panic during the re-boot. I used 50000.)
>
> Richard says to do the following:
> =====================================================
> as root on your SGI,
> # systune -i
> systune-> ncargs <a number LESS than 65535>
> <it asks if you are sure>
> systune-> quit
>
> autoconfig -v
> /etc/reboot
>
> =======================================================
>
> > > This is a troubling bug report. Can others confirm? I've had zero
> > > trouble with OpenBSD and Linux but don't have easy access to Irix, HPUX
> > > or Alpha systems. We may have gotten bitten by the huge size of our
> > > distribution.
> >
> > Serge seems to know what he is talking about. In the past I've had the same
> > problem in IRIX but I never bothered to find out what exactly was wrong.
> > Thanks Serge!
> >
> > Confirmed on IRIX:
> >
> > cetus /tmp/bioperl-1.0> make
> > make: execvp: /bin/sh: Arg list too long
> > make: *** [pm_to_blib] Error 127
> > cetus /tmp/bioperl-1.0>
> >
> > I got curious and ran Serges program on various platforms:
> >
> > IRIX64:  ARG_MAX =   20480
> > SUNOS:   ARG_MAX = 1048320
> > OSF1:    ARG_MAX =   38912
> > LINUX:   ARG_MAX =  131072
> >
> > I've no access to HPUX.
> >
> >
> > Looks like we have to come up with a 1.01 quite soon.
> >
> >         -Heikki
> >
> >
> > > Actually, HP just donated a Itanium box to us so I'll have HPUX to work
> > > on in a few days.
> > >
> > > -Chris
> > >
> > >   ----------------------------------------------------------------------------
> > >
> > > Subject: [Bioperl-guts-l] Notification: incoming/1133
> > > Date: Fri, 22 Mar 2002 13:31:25 -0500
> > > From: bioperl-bugs@bioperl.org
> > > To: bioperl-guts-l@bioperl.org
> > >
> > > JitterBug notification
> > >
> > > new message incoming/1133
> > >
> > > Message summary for PR#1133
> > >         From: batalov@gnf.org
> > >         Subject: bioperl-1.0 doesn't build
> > >         Date: Fri, 22 Mar 2002 13:31:24 -0500
> > >         0 replies       0 followups
> > >
> > > ====> ORIGINAL MESSAGE FOLLOWS <====
> > >
> > > >From batalov@gnf.org Fri Mar 22 13:31:24 2002
> > > Received: from localhost (localhost [127.0.0.1])
> > >         by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g2MIVOkO005811
> > >         for <bioperl-bugs@pw600a.bioperl.org>; Fri, 22 Mar 2002 13:31:24 -0500
> > > Date: Fri, 22 Mar 2002 13:31:24 -0500
> > > Message-Id: <200203221831.g2MIVOkO005811@pw600a.bioperl.org>
> > > From: batalov@gnf.org
> > > To: bioperl-bugs@bioperl.org
> > > Subject: bioperl-1.0 doesn't build
> > >
> > > Full_Name: Serge Batalov
> > > Module: bioperl
> > > Version: 1.0
> > > PerlVer: 5.6.1
> > > OS: IRIX,HP,DEC/Compaq-Alpha
> > > Submission from: pat.gnf.org (63.196.132.64)
> > >
> > > #> perl -MCPAN -e shell
> > > #>     ...install Bundle::...
> > > #> install B/BI/BIRNEY/bioperl-1.0.tar.gz
> > > fails in 'make' with 'Arg list too long' message
> > >
> > > What happens is that a list of things to MakeMake is too long for the
> > > command line (in "# --- MakeMaker pm_to_blib section")
> > >
> > > For the reference, command-line length limit is not
> > > a shell limit; it is built in kernel/libc.
> > > It has to do with the execvp()
> > > limit ARG_MAX, which is 4096 characters in POSIX,
> > > but most systems have it inflated, to different extents.
> > >
> > > Test it with
> > > --------arg_max.c--------
> > > #include <unistd.h>
> > > main() {
> > >   printf("ARG_MAX = %ld\n  This is the maximum length of the arguments to the
> > > exec() family of functions\n",
> > >          sysconf(_SC_ARG_MAX));
> > >   exit(0);
> > > }
> > > --------
> > >
> > > Linux is the second most generous (most systems tested show 64K).
> > > It is topped only by SUN (tried 5.8), where it is 128K.
> > > IRIX and DEC/Alpha have 20K limit.
> > > HP -- just 8K.
> > >
> > > It would be prudent to stick to the POSIX limit, and
> > > split the pm_to_blib into pieces.
>
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu