[SciPy-user] scipy 0.7.0.dev4373 + atlas FAILED (failures=2, errors=12)

Johann Cohen-Tanugi cohen@slac.stanford....
Sun May 18 03:58:32 CDT 2008


well, I am not sure the doc marathon will deal with building scipy, at 
least as a priority.... This is going to remain a very tough issue 
because scipy depends on packages that are complex and hard to build. 
Note that if you dont need smart lin. algebra you still have plenty of 
good stuff in scipy despite this lapack failure. Maybe what would be 
nice is for the scipy build process to clearly disable some specific 
libs if something goes wrong and report it at the end of the build. Then 
when testing likewise it would disable the corresponding test 
functions.... yes this is complete vaporware I know....

Now on the specific problem you have, I don't completely recall now but 
when I was struggling with compiling lapack one of the woes I was facing 
was a mismatch of fortran compilers, so can you make sure in the python 
setup.py config that you are using gfortran all the way through, and not 
g77 in any step of the builds of either lapack/blas/scipy?
well my 2 cents,
HTH,
Johann


Xavier Gnata wrote:
> David Cournapeau wrote:
>   
>> Xavier Gnata wrote:
>>   
>>     
>>>> Not sure about this one. Probably a real bug.
>>>>       
>>>>         
>> This error is often seen when mixing g77/gfortran. hardy still uses g77 
>> as the default fortran compiler, so it is easy to make a mistake there.
>>
>>   
>>     
>>> Thanks for our support :)
>>> I used to use the atlas unbutu package but I would like to understand 
>>> how to compile ATLAS and to see if there is a real performance 
>>> improvement or not. As you said,it should note be that large...
>>>     
>>>       
>> It is large if you are using a recent core 2 duo: the atlas package 
>> (sse2) are built for pentium4 which has a deficient L1 cache, whereas 
>> core 2 duo has much better behaviour. For large matrices, this can be 
>> significant.
>>
>> How did you build lapack ? From lapack 3.1.1, you only need to use this 
>> as the make.inc:
>>
>> ####################################################################
>> #  LAPACK make include file.                                       #
>> #  LAPACK, Version 3.1.1                                           #
>> #  February 2007                                                   #
>> ####################################################################
>> #
>> SHELL = /bin/sh
>> #
>> #  The machine (platform) identifier to append to the library names
>> #
>> PLAT = _LINUX
>> #
>> #  Modify the FORTRAN and OPTS definitions to refer to the
>> #  compiler and desired compiler options for your machine.  NOOPT
>> #  refers to the compiler options desired when NO OPTIMIZATION is
>> #  selected.  Define LOADER and LOADOPTS to refer to the loader and
>> #  desired load options for your machine.
>> #
>> FORTRAN  = gfortran
>> OPTS     = -O2 -fPIC
>> DRVOPTS  = $(OPTS)
>> NOOPT    = -O0 -fPIC
>> LOADER   = gfortran
>> LOADOPTS =
>> #
>> # Timer for the SECOND and DSECND routines
>> #
>> # Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME
>> #TIMER    = EXT_ETIME
>> # For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION 
>> ETIME_
>> # TIMER    = EXT_ETIME_
>> # For gfortran compiler: SECOND and DSECND will use a call to the 
>> INTERNAL FUNCTION ETIME
>> TIMER    = INT_ETIME
>> # If your Fortran compiler does not provide etime (like Nag Fortran 
>> Compiler, etc...)
>> # SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME
>> # TIMER    = INT_CPU_TIME
>> # If neither of this works...you can use the NONE value... In that case, 
>> SECOND and DSECND will always return 0
>> # TIMER     = NONE
>> #
>> #  The archiver and the flag(s) to use when building archive (library)
>> #  If you system has no ranlib, set RANLIB = echo.
>> #
>> ARCH     = ar
>> ARCHFLAGS= cr
>> RANLIB   = ranlib
>>
>> LAPACKLIB = liblapack_pic.
>>
>> And then, to build atlas:
>>
>> ./configure -C if gfortran -Fa alg -fPIC 
>> --with-netlib-lapack=PATH_TO_LAPACK/liblapack_pic.a
>>
>> But really, you have to think about the pain to build and make sure it 
>> works with the time you gain by having a faster atlas. I bet that for 
>> the time you need to make it work, you could have inverted millions of 
>> big matrices :)
>>
>> cheers,
>>
>> David
>> _______________________________________________
>>   
>>     
>
> Ok I give up and I use the ubuntu packages.
> I hope that the documentation project will provide us with a nice "how 
> to install scipy without errors".
> btw, this odcumentation project is the best news of the day ;)
>
> Xavier
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>   


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