R help - Dec 2004 - core dump during make check when building 64-bit R on Solaris8/9

Hi,

After reading some of the posting in this list, I came across this
posting from:

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Fri 29 Oct 2004 - 08:02:40 EST
Replying to Re: [R] Errors during make check

He described a problem similar to mine, that build 64-bit R (I am
building R version 2.0.1) with sunperf library gives a core dump during
make check.  So I configured my build without the sunperf (BLAS and
lapack) library.  My configure statement looks like this:

./configure --prefix=/usr/local/R-2.0.1
--with-tcl-config=/usr/sfw/lib/tclCo
nfig.sh --with-tk-config=/usr/sfw/lib/tkConfig.sh --without-blas

The "make check" ran without a problem after this.

I hope that the sun compiler people can look into this and see if there
is a problem with the sunperf library.  Maybe Peter Dalgaard ha further
insights into this?  Thanks.

Regards,
Chee Seng


-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of CHAN Chee Seng
Sent: Monday, November 29, 2004 6:13 PM
To: r-help at stat.math.ethz.ch
Subject: [R] core dump during make check when building 64-bit R on
Solaris8/9

Hi,

I am building a 64-bit R 2.0.1 on Solaris 9.  The compiler is Sun Studio
8.  Make was successful but I have a core dump during a make check.  By
the way, this problem also happens on my Solaris 8 machine though I did
not get a core dump.  I do not have 64-bit versions of the readline,
tcl/tk, libncurses, etc libraries so these caused configure not to use
them with ELFCLASS32 errors.

I use the following flags in config.site:
CC="cc -xarch=v9"
CFLAGS="-xO5 -xlibmil -dalign"
F77="f95 -xarch=v9"
FFLAGS="-xO5 -xlibmil -dalign"
CXX="CC -xarch=v9"


I pasted the make check error messages below:
$ make check
collecting examples for package 'base' ...
 >>> Building/Updating help pages for package 'base'
     Formats: text html latex example 
running code in 'base-Ex.R' ...*** Error code 1
make: Fatal error: Command failed for target `base-Ex.Rout'
Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
*** Error code 1
make: Fatal error: Command failed for target `test-Examples-Base'
Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
*** Error code 1
make: Fatal error: Command failed for target `test-Examples'
Current working directory /export/home/cheeseng/R-2.0.1/tests
*** Error code 1
make: Fatal error: Command failed for target `test-all-basics'
Current working directory /export/home/cheeseng/R-2.0.1/tests
*** Error code 1
make: Fatal error: Command failed for target `check'


The last few lines in base-Ex.Rout.fail is:
> ### * kappa
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: kappa
> ### Title: Estimate the Condition Number
> ### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri
> ### Keywords: math
> 
> ### ** Examples
> 
> kappa(x1 <- cbind(1,1:10))# 15.71
[1] 15.70590


Doing a dbx on the core dump shows that the following:
program terminated by signal SEGV (no mapping at the fault address)
0xffffffff790fdf54: ___pl_dgesdd_64_+0x1654:    std      %f4, [%o1]

I hope some one have a more successful build and can show how you did
it.

Thanks,
Chee Seng
UNIX Administrator
Genome Institute of Singapore
60 Biopolis Street, Genome
#02-01 Singapore 138672
DID 64788065
------------------------------- 
This email is confidential and may be privileged.  If you are not the
intended recipient, please delete it and notify us immediately. Please
do not copy or use it for any purpose, or disclose its contents to any
other person. Thank you.

______________________________________________
R-help at stat.math.ethz.ch mailing list
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PLEASE do read the posting guide!
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We know of at least two builds which successfully used libsunperf, one 
(mine) with Studio ONE 7 and one with 9.  So this may well be a problem 
with your particular compiler suite.

On Wed, 1 Dec 2004, CHAN Chee Seng wrote:
> Hi,
>
> After reading some of the posting in this list, I came across this
> posting from:
>
> From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
> Date: Fri 29 Oct 2004 - 08:02:40 EST
> Replying to Re: [R] Errors during make check
>
> He described a problem similar to mine, that build 64-bit R (I am
> building R version 2.0.1) with sunperf library gives a core dump during
> make check.  So I configured my build without the sunperf (BLAS and
> lapack) library.  My configure statement looks like this:
>
> ./configure --prefix=/usr/local/R-2.0.1
> --with-tcl-config=/usr/sfw/lib/tclCo
> nfig.sh --with-tk-config=/usr/sfw/lib/tkConfig.sh --without-blas
>
> The "make check" ran without a problem after this.
>
> I hope that the sun compiler people can look into this and see if there
> is a problem with the sunperf library.  Maybe Peter Dalgaard ha further
> insights into this?  Thanks.
>
> Regards,
> Chee Seng
>
>
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of CHAN Chee Seng
> Sent: Monday, November 29, 2004 6:13 PM
> To: r-help at stat.math.ethz.ch
> Subject: [R] core dump during make check when building 64-bit R on
> Solaris8/9
>
> Hi,
>
> I am building a 64-bit R 2.0.1 on Solaris 9.  The compiler is Sun Studio
> 8.  Make was successful but I have a core dump during a make check.  By
> the way, this problem also happens on my Solaris 8 machine though I did
> not get a core dump.  I do not have 64-bit versions of the readline,
> tcl/tk, libncurses, etc libraries so these caused configure not to use
> them with ELFCLASS32 errors.
>
> I use the following flags in config.site:
> CC="cc -xarch=v9"
> CFLAGS="-xO5 -xlibmil -dalign"
> F77="f95 -xarch=v9"
> FFLAGS="-xO5 -xlibmil -dalign"
> CXX="CC -xarch=v9"
>
>
> I pasted the make check error messages below:
> $ make check
> collecting examples for package 'base' ...
> >>> Building/Updating help pages for package 'base'
>     Formats: text html latex example
> running code in 'base-Ex.R' ...*** Error code 1
> make: Fatal error: Command failed for target `base-Ex.Rout'
> Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
> *** Error code 1
> make: Fatal error: Command failed for target `test-Examples-Base'
> Current working directory /export/home/cheeseng/R-2.0.1/tests/Examples
> *** Error code 1
> make: Fatal error: Command failed for target `test-Examples'
> Current working directory /export/home/cheeseng/R-2.0.1/tests
> *** Error code 1
> make: Fatal error: Command failed for target `test-all-basics'
> Current working directory /export/home/cheeseng/R-2.0.1/tests
> *** Error code 1
> make: Fatal error: Command failed for target `check'
>
>
> The last few lines in base-Ex.Rout.fail is:
>> ### * kappa
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: kappa
>> ### Title: Estimate the Condition Number
>> ### Aliases: kappa kappa.default kappa.lm kappa.qr kappa.tri
>> ### Keywords: math
>>
>> ### ** Examples
>>
>> kappa(x1 <- cbind(1,1:10))# 15.71
> [1] 15.70590
>
>
> Doing a dbx on the core dump shows that the following:
> program terminated by signal SEGV (no mapping at the fault address)
> 0xffffffff790fdf54: ___pl_dgesdd_64_+0x1654:    std      %f4, [%o1]
>
> I hope some one have a more successful build and can show how you did
> it.
>
> Thanks,
> Chee Seng
> UNIX Administrator
> Genome Institute of Singapore
> 60 Biopolis Street, Genome
> #02-01 Singapore 138672
> DID 64788065
> -------------------------------
> This email is confidential and may be privileged.  If you are not the
> intended recipient, please delete it and notify us immediately. Please
> do not copy or use it for any purpose, or disclose its contents to any
> other person. Thank you.
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Hi All,

Thanks for all the replies.  As mentioned in first mail I am using Sun
Studio 8, which is giving me the problem.  I am glad that there are
people who got this to work.  However SS8 is all I have right now and
since there is a problem I would like to get this fixed somehow.

And Peter,

Yes, that's looks like the problem that I am facing (SEGV and the stack
trace).
My cc -V looks like this:

cc: Sun C 5.5 2003/03/12

I am using /opt/SUNWspro/lib/v9/libsunperf.so.4.  And I am not aware of
the difference between v9, v9a and v9b.

Can you write/send me the standalone program to show the problem so I
can send to some Sun people that I know?

BTW, how did you run R under dbx?  (Sorry but I am not familiar with
using dbx.)  I get this error:

Fatal error: R home directory is not defined

Thanks.

Regards,
Chee Seng

-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Wednesday, December 01, 2004 7:08 PM
To: Peter Dalgaard
Cc: CHAN Chee Seng; r-help at stat.math.ethz.ch
Subject: Re: [R] core dump during make check when building 64-bit R on
Solaris8/9

On Wed, 1 Dec 2004, Peter Dalgaard wrote:
> Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:
>
>> We know of at least two builds which successfully used libsunperf,
one
>> (mine) with Studio ONE 7 and one with 9.  So this may well be a
>> problem with your particular compiler suite.
>
> Or maybe libsunperf version issues. The one that caused me trouble was
libsunperf *is* part of the compiler suite, as your path below shows.
> this one
>
> /opt/FD8/SUNWspro/lib/v9b/libsunperf.so.4
>
> (on the DTU machines)
I am using

/opt/SunONE7/SUNWspro/lib/v9/libsunperf.so.4

The precise architecture selected comes into play, too (v9 vs v9b).

My point was that we do know of working examples.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Again, thanks for all the replies and suggestions.

At this point, I guess the only fix is NOT to use libsunperf from sun
studio 8.  If anyone really wants to use libsunperf, use sun one studio
7 or 9's instead.

I will also try and send a bug report to the sun folks (in case there
are people like me who are still stuck with Sun Studio 8 and would like
to update their buggy libsunperf), and post any findings back here.

Regards,
Chee Seng

-----Original Message-----
From: Peter Dalgaard [mailto:p.dalgaard at biostat.ku.dk] 
Sent: Friday, December 03, 2004 4:32 PM
To: CHAN Chee Seng
Cc: Prof Brian Ripley; Peter Dalgaard; r-help at stat.math.ethz.ch
Subject: Re: [R] core dump during make check when building 64-bit R on
Solaris8/9

"CHAN Chee Seng" <chancs at gis.a-star.edu.sg> writes:
> Can you write/send me the standalone program to show the problem so I
> can send to some Sun people that I know?
Not at this point, I was hoping you had the time.
 
> BTW, how did you run R under dbx?  (Sorry but I am not familiar with
> using dbx.)  I get this error:
R -d dbx

then "run", etc...


-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907