CHAN Chee Seng
2004-Dec-01 05:59 UTC
[R] 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Prof Brian Ripley
2004-Dec-01 07:42 UTC
[R] core dump during make check when building 64-bit R on Solaris8/9
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
CHAN Chee Seng
2004-Dec-03 03:38 UTC
[R] core dump during make check when building 64-bit R on Solaris8/9
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 waslibsunperf *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
CHAN Chee Seng
2004-Dec-06 05:19 UTC
[R] core dump during make check when building 64-bit R on Solaris8/9
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