Re: [Rd] AIX testers needed

From: Jason Barnhart <jasoncbarnhart_at_msn.com>
Date: Mon, 21 May 2007 10:40:07 -0700

Thank you for responding.

I should have added -a on my ulimit command. Here are its results; which I believe are not the limiting factor.

%/ > ulimit -a

core file size        (blocks, -c) 1048575
data seg size         (kbytes, -d) unlimited
file size             (blocks, -f) unlimited
max memory size       (kbytes, -m) 32768
open files                    (-n) 2000
pipe size          (512 bytes, -p) 64
stack size            (kbytes, -s) hard
cpu time             (seconds, -t) unlimited
max user processes            (-u) 128
virtual memory        (kbytes, -v) unlimited

Here are my gcc-v results. They are very similiar.

%/ > gcc -v
Using built-in specs.
Target: powerpc-ibm-aix5.3.0.0
Configured with: ../gcc-4.1.2/configure

    --prefix=/opt/sas/msd/home/barnharj/usr/local
    --program-suffix=-4.1.2
    --enable-threads=aix
    --enable-languages=c,c++,fortran
    --disable-nls
    --with-mpfr=/opt/sas/msd/home/barnharj/usr/local
    --with-gmp=/opt/sas/msd/home/barnharj/usr/local
Thread model: aix
gcc version 4.1.2

My results for gcc -print-multi-lib are indentical to yours.

It should be noted that I did not attempt a 64 bit build. My system is not configured properly for that just yet.

Via private correspondence someone also suggested the following system("ulimit -d unlimited") during an R session. That failed as did issuing the command before launching R.

I'll keep investigating.

My call to configure is listed below.

/configure --prefix=$HOME/usr/local --program-suffix=rc --with-readline=no  --with-x=no --enable-memory-profiling

> Hi.
>
> system("ulimit") of AIX gives back file block size.
> A limit of memory is `ulimit -m'.
>
> I made gcc-4.1.2 and made R-2.5.0+patched, but the problem did not
> happen.
>
> $ gcc-4.1 -v
> Using built-in specs.
> Target: powerpc-ibm-aix5.2.0.0
> Configured with: ../configure --with-as=/usr/bin/as
> --with-ld=/usr/bin/ld --disable-nls --prefix=/usr/local1/gcc-4.1.2
> --enable-threads --host=powerpc-ibm-aix5.2.0.0 --program-suffix=-4.1
> --with-gmp=/usr/local1 --with-mpfr=/usr/local1
> --enable-languages=c,c++,f95
> Thread model: aix
> gcc version 4.1.2
>
> $ gcc-4.1 -print-multi-lib
> .;
> pthread;@pthread
> ppc64;@maix64
> pthread/ppc64;@pthread_at_maix64
>
> $ export OBJECT_MODE=64
> $ ./configure CC="gcc-4.1 -maix64" \
> F77="gfortran-4.1 -maix64" \
> CXX="g++-4.1 -maix64" \
> --enable-BLAS-shlib --without-iconv
>
>
> 2007/5/19, Jason Barnhart <jasoncbarnhart_at_msn.com>:
>> Per the request to test the latest tarball referenced below, I have
>> built R on AIX 5.3. There is a memory issue, please see 3) below.
>>
>> 1) Build with --enable-BLAS-shlib option. Builds and
>> passes "make check".
>>
>> 2) GNU libiconv was installed; R configured *without*
>> the --without-
>> iconv option. Builds and passes "make check."
>>
>> 3) Memory issue:
>> a) Although the server possesses 8GB of RAM and
>> system("ulimit") returns "unlimited" as its value, R does
>> not
>> "have enough memory."
>>
>> b) This code works on R-2.4.0 on WinXP with 2GB of RAM, but
>> fails on the AIX build. Example code:
>>
>> > xx <- matrix(rep(1e+10,1e7),nrow=1e4,ncol=1e3)
>> > tmp.df <- as.data.frame(cbind(xx,xx,xx))
>> Error: cannot allocate vector of size 228.9 Mb
>> > gc()
>> used (Mb) gc trigger (Mb) max used (Mb)
>> Ncells 233035 6.3 467875 12.5 350000 9.4
>> Vcells 10104141 77.1 31854441 243.1 30104289 229.7
>>
>> 4) Used gcc-4.1.2; I have not tried the native compiler.
>>
>> Questions:
>>
>> 1) Are there suggestions on how to diagnose and resolve the
>> memory
>> issue? I'm still building my tool chain and I am in the midst
>> of
>> installing gdb.
>>
>> 2) Regarding the build process itself, is there more
>> documentation
>> or results that I should forward?
>>
>> Thanks,
>> -jason
>>
>>
>> > version _
>> platform powerpc-ibm-aix5.3.0.0
>> arch powerpc
>> os aix5.3.0.0
>> system powerpc, aix5.3.0.0
>> status RC
>> major 2
>> minor 5.0
>> year 2007
>> month 04
>> day 22
>> svn rev 41276
>> language R
>> version.string R version 2.5.0 RC (2007-04-22 r41276)
>>
>>
>> ----- Original Message -----
>> From: "Prof Brian Ripley" <ripley_at_stats.ox.ac.uk>
>> To: <R-devel_at_r-project.org>
>> Cc: "Sheth, Jagat K" <jagat.k.sheth_at_citigroup.com>; "kamil
>> Marcinkowski" <kamil_at_ualberta.ca>; "Tiong Lim"
>> <t.lim_at_auckland.ac.nz>;
>> "Eric Harley" <ericctharley_at_gmail.com>; "Matthew Beason"
>> <mbeason_at_harrahs.com>; <watplatt_at_us.ibm.com>
>> Sent: Wednesday, March 28, 2007 11:27 PM
>> Subject: [Rd] AIX testers needed
>>
>>
>> > With much thanks to Ei-ji Nakama, R 2.5.0 alpha supports building
>> > on
>> > AIX
>> > (at least AIX 5.2 on one system).
>> >
>> > Would anyone able to test this please get the latest tarball from
>> >
>> > http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz
>> >
>> > and try installing (after reading the AIX notes in R-admin.html
>> > section
>> > C.9).
>> >
>> > In particular it would be very helpful to know if
>> >
>> > 1) --enable-BLAS-shlib works (it is the default everywhere except
>> > AIX and
>> > Darwin)
>> >
>> > 2) if people succeed in installing GNU libiconv and building
>> > without
>> > needing --without-iconv.
>> >
>> > I am Cc:ing all the people I tracked down who reported attempted
>> > AIX
>> > installations in 2006 in the hope that they may still be
>> > interested.
>> >
>> > Please report success and any hints or problems in the R-devel
>> > list.
>> >
>> > --
>> > 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
>> >
>> > ______________________________________________
>> > R-devel_at_r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >
>>
>> ______________________________________________
>> R-devel_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>>
>
>
> --
> EI-JI Nakama <nakama_at_ki.rim.or.jp>
> "\u4e2d\u9593\u6804\u6cbb" <nakama_at_ki.rim.or.jp>
>



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Mon 21 May 2007 - 17:54:36 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 22 May 2007 - 05:34:00 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.