R devel - Aug 2003 - make check fails 1.7.1 with R-release patch in regression tests (PR#3868)

Full_Name: Kevin B. Hendricks
Version: 1.7.1 patched with R-release.diff
OS: Linux x86-64
Submission from: (NULL) (65.93.132.185)


Hi,

Built from R-1.7.1 source with R-release.diff patch attached on a 
RedHat 9 system for Linux x86-64 (dual Opteron system) runing in 64 bit mode.

Build completes fine.  But "make check" fails (R is killed because
Out-Of-Memory)
during reg-tests-1.R.   I have verified that the R-Release.diff patch has been
applied 
and the changes to the stopping critieria in that file have been made. 

My x86_64 machine has over 2 gig of main memory. 

Is the stopping cirtieria a function of the size of the machine registers in
use? 

All other tests seem to pass with no problems.  I have reproduced this error
condition
with and without optimized "atlas" libs in the build and even with -O0
(to
remove possiblility of compiler optimization error).

I am stumped on how to proceed.  Obviously the stopping criteria for some method
is never being
reached resulting in the out of memory condition.

Any hints on how to track this down further appreciated.  All altas tests run
and pass with flying colors (if that helps).

Thanks,

Kevin

On Thu, Aug 21, 2003 at 03:22:17PM +0200, khendricks@ivey.uwo.ca
wrote:
> Full_Name: Kevin B. Hendricks
> Version: 1.7.1 patched with R-release.diff
> OS: Linux x86-64
> Submission from: (NULL) (65.93.132.185)
> 
> 
> Hi,
> 
> Built from R-1.7.1 source with R-release.diff patch attached on a 
> RedHat 9 system for Linux x86-64 (dual Opteron system) runing in 64 bit
mode.
> 
> Build completes fine.  But "make check" fails (R is killed
because
> Out-Of-Memory)
> during reg-tests-1.R.   I have verified that the R-Release.diff patch has
been
> applied 
> and the changes to the stopping critieria in that file have been made. 
> 
> My x86_64 machine has over 2 gig of main memory. 
What I your compiler?  The GNU GSL people recetnly had to alter one of their
regression tests as gcc 3.3.1 (if I recall correctly) would all of a sudden
consume all available memory.

Just a quick shot in the dark, this may of course an entirely different
issue... But if you can try an older compiler, that may be worth the few
minutes it takes.

Dirk

-- 
Those are my principles, and if you don't like them... well, I have others.
                                                -- Groucho Marx

khendricks@ivey.uwo.ca writes:
> Built from R-1.7.1 source with R-release.diff patch attached on a 
> RedHat 9 system for Linux x86-64 (dual Opteron system) runing in 64 bit
mode.
> 
> Build completes fine.  But "make check" fails (R is killed
because
> Out-Of-Memory)
> during reg-tests-1.R.   I have verified that the R-Release.diff patch has
been
> applied 
> and the changes to the stopping critieria in that file have been made. 
> 
> My x86_64 machine has over 2 gig of main memory. 
> 
> Is the stopping cirtieria a function of the size of the machine registers
in
> use? 
> 
> All other tests seem to pass with no problems.  I have reproduced this
error
> condition
> with and without optimized "atlas" libs in the build and even
with -O0 (to
> remove possiblility of compiler optimization error).
> 
> I am stumped on how to proceed.  Obviously the stopping criteria for some
method
> is never being
> reached resulting in the out of memory condition.
> 
> Any hints on how to track this down further appreciated.  All altas tests
run
> and pass with flying colors (if that helps).
Hmm. 

(1) Does it happen *without* the patches?

(2) The canonical way to investigate is to
 
        (a) figure out which file is being processed and rerun R with
        output to the terminal. I.e.

        export SRCDIR=../R/tests # must be set, value depends on build setup 
        bin/R --vanilla < $SRCDIR/reg-tests-1.R

        This avoids buffering and so the last few lines should tell
        you approximately where things go wrong.

        You might want to cut the file down a bit, but in this case it
        is probably not necessary.

        (b) Run R under the debugger 
        bin/R -d gdb
        run --vanilla  < $SRCDIR/reg-tests-1.R

        when it hangs, try hitting control-C and do a "bt" (backtrace)
        command in gdb. You can then poke around in the stack and see
        if you can spot the problem. Or get back to us with some new
        clues. 
-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907

Hi Peter,

Thanks for your response.

I tracked it down to (info <-file.info(".")) hanging and then
started checking
the obvious as to what permissions that "tests" had and soon found out
that
everything was quite messed up (I had forgot to chown the files after 
unpacking them).

Once I cleaned that up and changed owership to a valid user id the hangs went 
away.

So please close this as user stupidiity on my part.  I simply forgot that tar 
keeps old user ids when unpacking and that I need to fix that myself before 
patching and building.

Thanks gain for your fast responses!

Kevin

On Thursday 21 August 2003 10:30, Peter Dalgaard BSA
wrote:
> khendricks@ivey.uwo.ca writes:
> > Built from R-1.7.1 source with R-release.diff patch attached on a
> > RedHat 9 system for Linux x86-64 (dual Opteron system) runing in 64
bit
> > mode.
> >
> > Build completes fine.  But "make check" fails (R is killed
because
> > Out-Of-Memory)
> > during reg-tests-1.R.   I have verified that the R-Release.diff patch
has
> > been applied
> > and the changes to the stopping critieria in that file have been made.
> >
> > My x86_64 machine has over 2 gig of main memory.
> >
> > Is the stopping cirtieria a function of the size of the machine
registers
> > in use?
> >
> > All other tests seem to pass with no problems.  I have reproduced this
> > error condition
> > with and without optimized "atlas" libs in the build and
even with -O0
> > (to remove possiblility of compiler optimization error).
> >
> > I am stumped on how to proceed.  Obviously the stopping criteria for
some
> > method is never being
> > reached resulting in the out of memory condition.
> >
> > Any hints on how to track this down further appreciated.  All altas
tests
> > run and pass with flying colors (if that helps).
>
> Hmm.
>
> (1) Does it happen *without* the patches?
>
> (2) The canonical way to investigate is to
>
>         (a) figure out which file is being processed and rerun R with
>         output to the terminal. I.e.
>
>         export SRCDIR=../R/tests # must be set, value depends on build
> setup bin/R --vanilla < $SRCDIR/reg-tests-1.R
>
>         This avoids buffering and so the last few lines should tell
>         you approximately where things go wrong.
>
>         You might want to cut the file down a bit, but in this case it
>         is probably not necessary.
>
>         (b) Run R under the debugger
>         bin/R -d gdb
>         run --vanilla  < $SRCDIR/reg-tests-1.R
>
>         when it hangs, try hitting control-C and do a "bt"
(backtrace)
>         command in gdb. You can then poke around in the stack and see
>         if you can spot the problem. Or get back to us with some new
>         clues.