Does anybody successfully built latest R on AIX 5.3?

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Does anybody successfully built latest R on AIX 5.3?

Xiaobo.Gu

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Re: Does anybody successfully built latest R on AIX 5.3?

Xiaobo.Gu
I am trying to install
http://www.oss4aix.org/download/RPMS/gcc/gcc-4.2.4-2.aix5.3.ppc.rpm

but it dependents on package info, which I can't find a version for
AIX 5.3, can anyone who success fully built R on AIX 5.3 share which
version of gcc and the related packages to use, and where to download
them,thanks, following are the error messages:

# rpm -i ./libgcc-4.2.4-2.aix5.3.ppc.rpm
package libgcc-4.2.4-2 is already installed
# rpm -i ./gcc-4.2.4-2.aix5.3.ppc.rpm
error: failed dependencies:
        info is needed by gcc-4.2.4-2
# rpm -i ./info-4.13a-2.aix5.1.ppc.rpm
error: ./info-4.13a-2.aix5.1.ppc.rpm does not appear to be a RPM package



On Sat, Jun 4, 2011 at 1:16 PM, Xiaobo Gu <[hidden email]> wrote:
>
>

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Re: Does anybody successfully built latest R on AIX 5.3?

Stefan Theussl-3
In reply to this post by Xiaobo.Gu
We successfully built R on AIX 6.1 but the following instructions should
also work for 5.3.

We mainly used the software from OSS4AIX but also from the "AIX Toolbox
for Linux Applications" obtainable directly from IBM. Attached you'll
find our list of installed rpms. This and the instructions provided in
the "R Installation and Administration" manual should be all you need to
build R on AIX systems.

hth,
st

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Re: Does anybody successfully built latest R on AIX 5.3?

Xiaobo.Gu
Hi Stefan,
        Thanks for replying!

        I have just managed to installed gcc 4.2.4.2 on AIX this evening, and will try to install gfortran tomorrow, there are a few more questions

1. Are you running R 2.13.0
2. Can you share all the environment variables we have to set before running the configure script.
3. Can you share the full command line of configure script.
4. According to your experience, is there a huge performance lift compared to X86 CPUS, what's the clock speed of you Power CPU?


Regards,

Xiaobo Gu


> -----Original Message-----
> From: Stefan Theussl [mailto:[hidden email]]
> Sent: Wednesday, June 08, 2011 7:07 PM
> To: [hidden email]
> Cc: [hidden email]
> Subject: Re: [Rd] Does anybody successfully built latest R on AIX 5.3?
>
> We successfully built R on AIX 6.1 but the following instructions should also work for 5.3.
>
> We mainly used the software from OSS4AIX but also from the "AIX Toolbox for Linux
> Applications" obtainable directly from IBM. Attached you'll find our list of installed rpms.
> This and the instructions provided in the "R Installation and Administration" manual should
> be all you need to build R on AIX systems.
>
> hth,
> st

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Re: Does anybody successfully built latest R on AIX 5.3?

Stefan Theussl-3
On 06/08/2011 02:02 PM, XiaoboGu wrote:
> Hi Stefan,
> Thanks for replying!
>
> I have just managed to installed gcc 4.2.4.2 on AIX this evening, and will try to install gfortran tomorrow, there are a few more questions
>    
great.
> 1. Are you running R 2.13.0
>    
Currently we are running 2.12.0 (works with both GNU and IBM compilers).
I was not able to compile 2.13 with GNU compilers yet, IBM compilers
work though (are preferable anyway, since performance is higher):

R version 2.13.0 Patched (2011-06-08 r56086)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: powerpc-ibm-aix6.1.0.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > sessionInfo()
R version 2.13.0 Patched (2011-06-08 r56086)
Platform: powerpc-ibm-aix6.1.0.0 (64-bit)

locale:
[1] EN_US.UTF-8 EN_US.UTF-8 C C EN_US.UTF-8 EN_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
 >

However recommended package Matrix gives an error upon loading.
> 2. Can you share all the environment variables we have to set before running the configure script.
>    
See the manual and
https://r-forge.r-project.org/scm/viewvc.php/install_scripts/install_R_AIX.sh?view=markup&root=aix 

You may download this script (and patches), modify the paths
accordingly, run it (e.g., ./install_R_AIX.sh --ibm for 2.13) and R
should build fine.
There are a couple of notes and patches provided in the R/AIX repository
on R-Forge (e.g., how to get IBM BLAS linked etc., missing third-party
libs installed, etc.).

> 3. Can you share the full command line of configure script.
>    
see above.
> 4. According to your experience, is there a huge performance lift compared to X86 CPUS, what's the clock speed of you Power CPU?
>    
No there isn't. One can use the IBM BLAS library (ESSL), then one will
observe a significant speedup for linear algebra tasks. Note however,
ESSL does not incorporate the full BLAS specification (thus the patch).
In general, R  runs slower on the power architecture than on x86.
We have a Power 6 8core CPU @ 3.5 GHz. Actually, we use our system
mainly for memory-demanding applications (<=128GB RAM).

Best,
st

>
> Regards,
>
> Xiaobo Gu
>
>
>    
>> -----Original Message-----
>> From: Stefan Theussl [mailto:[hidden email]]
>> Sent: Wednesday, June 08, 2011 7:07 PM
>> To: [hidden email]
>> Cc: [hidden email]
>> Subject: Re: [Rd] Does anybody successfully built latest R on AIX 5.3?
>>
>> We successfully built R on AIX 6.1 but the following instructions should also work for 5.3.
>>
>> We mainly used the software from OSS4AIX but also from the "AIX Toolbox for Linux
>> Applications" obtainable directly from IBM. Attached you'll find our list of installed rpms.
>> This and the instructions provided in the "R Installation and Administration" manual should
>> be all you need to build R on AIX systems.
>>
>> hth,
>> st
>>      
>

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Re: Does anybody successfully built latest R on AIX 5.3?

Xiaobo.Gu


> -----Original Message-----
> From: Stefan Theussl [mailto:[hidden email]]
> Sent: Wednesday, June 08, 2011 8:40 PM
> To: XiaoboGu
> Cc: [hidden email]
> Subject: Re: [Rd] Does anybody successfully built latest R on AIX 5.3?
>
> On 06/08/2011 02:02 PM, XiaoboGu wrote:
> > Hi Stefan,
> > Thanks for replying!
> >
> > I have just managed to installed gcc 4.2.4.2 on AIX this evening, and will try to install
> gfortran tomorrow, there are a few more questions
> >
> great.
> > 1. Are you running R 2.13.0
> >
> Currently we are running 2.12.0 (works with both GNU and IBM compilers).
> I was not able to compile 2.13 with GNU compilers yet, IBM compilers
> work though (are preferable anyway, since performance is higher):
>
> R version 2.13.0 Patched (2011-06-08 r56086)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: powerpc-ibm-aix6.1.0.0 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>  > sessionInfo()
> R version 2.13.0 Patched (2011-06-08 r56086)
> Platform: powerpc-ibm-aix6.1.0.0 (64-bit)
>
> locale:
> [1] EN_US.UTF-8 EN_US.UTF-8 C C EN_US.UTF-8 EN_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>  >
>
> However recommended package Matrix gives an error upon loading.
> > 2. Can you share all the environment variables we have to set before running the configure
> script.
> >
> See the manual and
> https://r-forge.r-project.org/scm/viewvc.php/install_scripts/install_R_AIX.sh?view=markup
> &root=aix
>
> You may download this script (and patches), modify the paths
> accordingly, run it (e.g., ./install_R_AIX.sh --ibm for 2.13) and R
> should build fine.
> There are a couple of notes and patches provided in the R/AIX repository
> on R-Forge (e.g., how to get IBM BLAS linked etc., missing third-party
> libs installed, etc.).
>
> > 3. Can you share the full command line of configure script.
> >
> see above.
> > 4. According to your experience, is there a huge performance lift compared to X86 CPUS,
> what's the clock speed of you Power CPU?
> >
> No there isn't. One can use the IBM BLAS library (ESSL), then one will
> observe a significant speedup for linear algebra tasks. Note however,
> ESSL does not incorporate the full BLAS specification (thus the patch).
> In general, R  runs slower on the power architecture than on x86.

This is strange, we are hoping to improve R performance through high clock speed Power CPU(4.0 GHz above),
Now I think we should take more considerations, RAM is also cheaper for X86 than Power :)




> We have a Power 6 8core CPU @ 3.5 GHz. Actually, we use our system
> mainly for memory-demanding applications (<=128GB RAM).
>
> Best,
> st
> >
> > Regards,
> >
> > Xiaobo Gu
> >
> >
> >
> >> -----Original Message-----
> >> From: Stefan Theussl [mailto:[hidden email]]
> >> Sent: Wednesday, June 08, 2011 7:07 PM
> >> To: [hidden email]
> >> Cc: [hidden email]
> >> Subject: Re: [Rd] Does anybody successfully built latest R on AIX 5.3?
> >>
> >> We successfully built R on AIX 6.1 but the following instructions should also work for
> 5.3.
> >>
> >> We mainly used the software from OSS4AIX but also from the "AIX Toolbox for Linux
> >> Applications" obtainable directly from IBM. Attached you'll find our list of installed
> rpms.
> >> This and the instructions provided in the "R Installation and Administration" manual
> should
> >> be all you need to build R on AIX systems.
> >>
> >> hth,
> >> st
> >>
> >

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Re: Does anybody successfully built latest R on AIX 5.3?

Ei-ji Nakama
Hi,

> This is strange, we are hoping to improve R performance through high clock speed Power CPU(4.0 GHz above),
> Now I think we should take more considerations, RAM is also cheaper for X86 than Power :)

power is no good CPU.

$ lsdev -C | grep proc
proc0      Available 00-00    Processor
proc2      Available 00-02    Processor
$ lsattr -El proc0
frequency   4204000000     Processor Speed       False
smt_enabled true           Processor SMT enabled False
smt_threads 2              Processor SMT threads False
state       enable         Processor state       False
type        PowerPC_POWER6 Processor type        False
$ lsattr -El proc2
frequency   4204000000     Processor Speed       False
smt_enabled true           Processor SMT enabled False
smt_threads 2              Processor SMT threads False
state       enable         Processor state       False
type        PowerPC_POWER6 Processor type        False

As a result of DGEMM by GotoBLAS(http://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2).
$ GOTO_NUM_THREADS=1 ./bm 2000
   12.954 GFLOPS (N x N : N=2000 1.23517sec)
   12.719 GFLOPS (N x T : N=2000 1.25796sec)
   13.118 GFLOPS (T x N : N=2000 1.21965sec)
   12.726 GFLOPS (T x T : N=2000 1.25732sec)
$ GOTO_NUM_THREADS=2 ./bm 2000
   25.259 GFLOPS (N x N : N=2000 0.633444sec)
   24.050 GFLOPS (N x T : N=2000 0.665272sec)
   25.710 GFLOPS (T x N : N=2000 0.622316sec)
   24.075 GFLOPS (T x T : N=2000 0.664595sec)
$ GOTO_NUM_THREADS=4 ./bm 2000
   21.311 GFLOPS (N x N : N=2000 0.750802sec)
   25.778 GFLOPS (N x T : N=2000 0.620694sec)
   26.398 GFLOPS (T x N : N=2000 0.60611sec)
   25.826 GFLOPS (T x T : N=2000 0.619536sec)

It's fast with the structure (L2 shared cache) of the CPU to 2CPU.

Best Regards,
--
EI-JI Nakama  <nakama (a) ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb"  <nakama (a) ki.rim.or.jp>

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