From steven.varga at gmail.com  Fri Jan 31 20:21:00 2014
From: steven.varga at gmail.com (Steven Varga)
Date: Fri, 31 Jan 2014 14:21:00 -0500
Subject: [Rd] INTEL MKL 11.1.0.080 R 3.0.2
In-Reply-To: <52EB8317.3060003@stats.ox.ac.uk>
References: <CAFkVQ9OqjiR8Ai7vmwJ0UQyMo6_3+7R-Drscvgzb7sndwtY7eg@mail.gmail.com>
	<52EB8317.3060003@stats.ox.ac.uk>
Message-ID: <CAFkVQ9NFfhaKef8fGU35-inmLE-tknm=Ex5jXL12+JRR3GL7qw@mail.gmail.com>

Thank you for your response,

and apologies for violating the posting guide.

I am having trouble compiling R 3.0.2 with gcc 4.8.1 and Intel MKL
11.1.0.080 [free downloaded version] on Ubuntu 13.10 running on
Intel(R) Core(TM) i7 CPU L 620 4G ram

MKL source:
https://registrationcenter.intel.com/RegCenter/NComForm.aspx?ProductID=1461&pass=yes

tried the following methods:
http://cran.r-project.org/doc/manuals/R-admin.html#MKL
http://software.intel.com/en-us/articles/using-intel-mkl-with-r
http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
http://software.intel.com/en-us/forums/topic/326016
with: intel MKL 11.1, LINUX, XeonPhi: none, GNUC/C++, Intel(R)64, Dynamic,
ILP64, Multi-threaded, both libgomp/libiomp5

Examining config.log with various settings indicated that MKL was not
used, which was confirmed with  ldd /usr/local/lib/R/bin/exec/R and nm
(static link version)

list of config.log, ldd dump, with various settings are attached.

any help is appreciated,
Steven Varga

On Fri, Jan 31, 2014 at 6:03 AM, Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
> On 31/01/2014 06:43, Steven Varga wrote:
>>
>> I am having trouble of compiling R 3.0.2 with MKL 11.1.0.080; tried the
>> following resources:
>>
>> http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
>> http://cran.r-project.org/doc/manuals/R-admin.html#MKL
>> http://software.intel.com/en-us/comment/reply/328415
>>
>> and getting the following:
>> *checking for dgemm_ in -Wl,--start-group -lmkl_gf_lp64 -lmkl_gnu_thread
>> -lmkl_core -Wl,--end-group -lgomp -lpthread... no*
>> *checking for dgemm_... no*
>>
>>
>>      libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f8daec19000)
>>      libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8dae915000)
>>      libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
>> (0x00007f8dade94000)
>>      libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>> (0x00007f8dadc77000)
>>      libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
>> (0x00007f8dad596000)
>>      libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
>> (0x00007f8dacf1a000)
>>
>>
>> Tried sourcing mkl from bash and used both local and online intel mkl link
>> util without success.
>>
>> can someone point what I am doing wrong?
>
>
> File config.log does, and we do not have access to it.
>
>
>> did anyone succeed with the above configuration?
>
>
> How could anyone know that?  (You have not even told us your OS nor
> compiler.)
>
>> thanks
>>
>>         [[alternative HTML version deleted]]
>
>
> See the posting guide ... HTML is not welcome here.
>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
>
> --
> 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
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0000000000520d60 t SubassignTypeFix.isra.0
00000000004ebad0 t SubAtom
000000000063a400 r substitutes
0000000000894450 b s_virtual.11368
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000000000088a440 b svsr.11680
0000000000456560 t switch_or_tee_stdout
00000000004601b0 t switch_stdout
000000000088a348 b s_xData.11439
00000000004ebca0 t SymbolFaceAtom
00000000006145a0 r SymbolTable
00000000004b9010 t SymbolValue
                 U symlink@@GLIBC_2.2.5
00000000004d2bf0 T SYMVALUE
00000000005816f0 t syncsearch
                 U sysconf@@GLIBC_2.2.5
                 U system@@GLIBC_2.2.5
00000000008916f0 b Sys_TempDir
0000000000631d60 r t.4228
0000000000630240 r t.4248
0000000000618de0 r table_wcwidth
00000000004d2350 T TAG
00000000004b84e0 t TagArg.isra.7
0000000000894500 b tagbuf
                 U tan@@GLIBC_2.2.5
                 U tanh@@GLIBC_2.2.5
0000000000600300 r tbl
000000000042d7b0 t tccrossprod
000000000087ab20 d test_result.10419
00000000004525a0 t text_close
00000000004527f0 t text_destroy
                 U textdomain@@GLIBC_2.2.5
00000000004525b0 t text_fgetc
00000000004b6dc0 t text_getc
0000000000452590 t text_open
0000000000455590 t text_seek
0000000000454f60 t text_vfprintf
00000000008837a0 d then_trap_opcode
00000000004eb760 t ThinSpace
000000000088a4b8 b ti
                 U tilde_expand
                 U time@@GLIBC_2.2.5
                 U timespec_get@@GLIBC_2.16
00000000004696c0 t TimeToSeed
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000000000049cdc0 t tmp_cleanup
                 U tmpfile@@GLIBC_2.2.5
000000000096bfd0 b tn.4238
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                 U towctrans@@GLIBC_2.2.5
                 U towlower@@GLIBC_2.2.5
                 U towupper@@GLIBC_2.2.5
000000000088a408 b tp.11708
000000000088a4c0 b tr
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00000000005d52f0 t tre_add_tag_right.isra.2
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00000000005debf0 T tre_ast_new_iter
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00000000005d4ed0 t tre_copy_ast
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00000000005d4550 T tre_regaexec
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00000000005d42b0 T tre_regexec
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00000000005deab0 T tre_stack_destroy
00000000005dea40 T tre_stack_new
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00000000005deb20 T tre_stack_pop_voidptr
00000000005de980 t tre_stack_push
00000000005deae0 T tre_stack_push_int
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00000000005db310 T tre_tnfa_run_parallel
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                 U trunc@@GLIBC_2.2.5
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                 U tzset@@GLIBC_2.2.5
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                 U umask@@GLIBC_2.2.5
                 U uname@@GLIBC_2.2.5
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                 U ungetc@@GLIBC_2.2.5
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                 U unlink@@GLIBC_2.2.5
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                 U unsetenv@@GLIBC_2.2.5
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                 U utimes@@GLIBC_2.2.5
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                 U __vasprintf_chk@@GLIBC_2.8
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0000000000533e20 t vequal
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000000000063a580 r verbs
0000000000498e20 t verrorcall_dflt
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0000000000486ff0 t VFontFamilyCode
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                 U __vfprintf_chk@@GLIBC_2.3.4
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000000000054fb40 T vmmin
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000000000087b8b0 d vsfac
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                 U __vsnprintf_chk@@GLIBC_2.3.4
                 U __vsprintf_chk@@GLIBC_2.3.4
000000000049ac60 t vwarningcall_dflt
000000000096c1a8 b w
000000000096c1c0 b w
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000000000088e480 b warned.12891
000000000049b9a0 t warningcall_dflt.constprop.5
00000000005fcba0 r WarningDB
                 U __wcrtomb_chk@@GLIBC_2.4
                 U __wcscpy_chk@@GLIBC_2.4
                 U wcsftime@@GLIBC_2.2.5
                 U wcslen@@GLIBC_2.2.5
                 U wcsncmp@@GLIBC_2.2.5
                 U __wcsncpy_chk@@GLIBC_2.4
                 U wcsncpy@@GLIBC_2.2.5
                 U wcstod@@GLIBC_2.2.5
                 U wcstombs@@GLIBC_2.2.5
                 U wctrans@@GLIBC_2.2.5
                 U wctype@@GLIBC_2.2.5
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0000000000579390 t w_init_maybe
                 U wmemcmp@@GLIBC_2.2.5
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                 U write@@GLIBC_2.2.5
                 U write_history
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                 U xdr_double@@GLIBC_2.2.5
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0000000000506d40 t XdrInReal
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                 U xdr_int@@GLIBC_2.2.5
                 U xdrmem_create@@GLIBC_2.2.5
                 U xdrstdio_create@@GLIBC_2.2.5
                 U xdr_string@@GLIBC_2.2.5
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000000000096beb0 b xlr.4889
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                 U __xstat@@GLIBC_2.2.5
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                 U zgemm_
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-------------- next part --------------
	linux-vdso.so.1 =>  (0x00007fffd6bfe000)
	libblas.so.3 => /usr/lib/libblas.so.3 (0x00007f5864649000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5864345000)
	libreadline.so.6 => /lib/x86_64-linux-gnu/libreadline.so.6 (0x00007f5864102000)
	liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f5863ee0000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f5863cd8000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5863ad3000)
	libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f58638c4000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f58636a7000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f58632de000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f5864c36000)
	libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f5862fc6000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f5862db0000)
	libtinfo.so.5 => /lib/x86_64-linux-gnu/libtinfo.so.5 (0x00007f5862b86000)
	libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f586294a000)
-------------- next part --------------

## confifential information removed

MKLROOT=/opt/intel/composer_xe_2013_sp1.0.080/mkl
XDG_VTNR=7
MANPATH=/opt/intel/composer_xe_2013_sp1.0.080/man/en_US:/opt/intel/composer_xe_2013_sp1.0.080/man/en_US:/usr/local/man:/usr/local/share/man:/usr/share/man:
INTEL_LICENSE_FILE=/opt/intel/composer_xe_2013_sp1.0.080/licenses:/opt/intel/licenses:/home/steven/intel/licenses
SHELL=/bin/bash
LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64
MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.0.080/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/mic
GTK_MODULES=overlay-scrollbar
LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:
CPATH=/opt/intel/composer_xe_2013_sp1.0.080/mkl/include
NLSPATH=/opt/intel/composer_xe_2013_sp1.0.080/compiler/lib/intel64/locale/%l_%t/%N:/opt/intel/composer_xe_2013_sp1.0.080/mkl/lib/intel64/locale/%l_%t/%N
PATH=/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64:/opt/intel/composer_xe_2013_sp1.0.080/mpirt/bin/intel64:/home/steven/bin/ec2/bin:/home/steven/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
MKL=-Wl,--start-group -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -Wl,--end-group -lgomp -lpthread
INCLUDE=/opt/intel/composer_xe_2013_sp1.0.080/mkl/include


[Rd] INTEL MKL 11.1.0.080 R 3.0.2
Steven Varga