[petsc-dev] SuperLU link error on BGP FEN

Barry Smith bsmith at mcs.anl.gov
Thu Dec 2 18:49:20 CST 2010 

On Dec 2, 2010, at 4:29 PM, William (Bill) E. Allcock wrote:

> John,
> 
> My first suggestion would be to use the petsc already built for Intrepid if that is an option.
> 
> Either way, others have had luck using the local disks on the FEN to speed up their builds.  I think someone may have even put together a script that trys to do that automagically.  Not sure if that would work for you, but if you send mail to support, they should be able to provide details.

   Bill,

    This could be a great idea. From my perspective it would be good if it was the "preferred" (even default) approach for large builds on system; documented, promoted and supported by the support group. It has the added benefit of decreasing the load on the file server that surely has a negative affect on all users.

   Thanks

   Barry

> 
> Bill
> On Dec 2, 2010, at 2:37 PM, John R. Cary wrote:
> 
>> So after > 40 mins of configuring, it failed at
>> 
>> Unable to download package SuperLU from: http://ftp.mcs.anl.gov/pub/petsc/externalpackages/superlu_4.0-March_7_2010.tar.gz
>> * If your network is disconnected - please reconnect and rerun config/configure.py
>> * Alternatively, you can download the above URL manually, to /yourselectedlocation/superlu_4.0-March_7_2010.tar.gz
>> and use the configure option:
>> --download-SuperLU=/yourselectedlocation/superlu_4.0-March_7_2010.tar.gz
>> *******************************************************************************
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/configure", line 257, in petsc_configure
>>   framework.configure(out = sys.stdout)
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/framework.py", line 944, in configure
>>   child.configure()
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 456, in configure
>>   self.executeTest(self.configureLibrary)
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/base.py", line 97, in executeTest
>>   ret = apply(test, args,kargs)
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 395, in configureLibrary
>>   for location, directory, lib, incl in self.generateGuesses():
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 206, in generateGuesses
>>   d = self.checkDownload(1)
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 283, in checkDownload
>>   return self.getInstallDir()
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 164, in getInstallDir
>>   self.packageDir = self.getDir()
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 326, in getDir
>>   self.downLoad()
>> File "/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/petsc-3.1-p4/ser/config/BuildSystem/config/package.py", line 347, in downLoad
>>   raise RuntimeError(e)
>> 
>> 
>> I have seen this before, and I usually just start over with the configure.  So at least
>> another 40 minutes, I think.
>> 
>> John
>> 
>> On 12/2/2010 1:30 PM, Satish Balay wrote:
>>> On Thu, 2 Dec 2010, Barry Smith wrote:
>>> 
>>>> On Dec 2, 2010, at 1:59 PM, John R. Cary wrote:
>>>> 
>>>>> Anyway, given the pokeyness of the FENs on surveyor, it should be some
>>>>> time before midnight!
>>>>  This is completely unacceptable! PETSc takes less than 10 minutes to configure and compile on my $2000 laptop (and probably half as long on Satish's $1000 laptop). On a $100 million machine it takes one half a day?
>>>> 
>>>>  That is frankly disgusting and indicates extreme problems with the configuration of that machine. Why has this problem not been fixed years ago?
>>>> 
>>> Part of the issue could be: John builds PETSc as part of a collection
>>> of pacakges - so the whole build takes a while.
>>> 
>>> Just petsc part is not that long..
>>> 
>>> Still its probably slower than laptops - perhaps due to nfs [vs local
>>> FS] - and the slower PPC cpu?? [vs newer faster intel cpus...]. And
>>> also comercial compilers tend to take longer times than gcc..
>>> 
>>> Satish
>>> 
>>>>> John
>>>>> 
>>>>>> satish
>>>>>> 
>>>>>> On Thu, 2 Dec 2010, Matthew Knepley wrote:
>>>>>> 
>>>>>>> We always always always always need configure.log.
>>>>>>> 
>>>>>>>   Matt
>>>>>>> 
>>>>>>> On Thu, Dec 2, 2010 at 8:41 AM, John R. Cary<cary at txcorp.com>   wrote:
>>>>>>> 
>>>>>>>> I am trying to link facets on a FEN of surveyor.alcf.anl.gov.  It ends
>>>>>>>> with the error,
>>>>>>>> 
>>>>>>>> /gpfs/home/projects/facets/surveyor/contrib-xlc-9.0/petsc-3.1-p4-ser/lib/libsuperlu_4.0.a(dldperm.o):
>>>>>>>> In function `dldperm':
>>>>>>>> /gpfs/home/cary/facetspkgs/builds/petsc-3.1-p4/ser/externalpackages/SuperLU_4.0/SRC/dldperm.c:127:
>>>>>>>> undefined reference to `mc64id_'
>>>>>>>> /gpfs/home/cary/facetspkgs/builds/petsc-3.1-p4/ser/externalpackages/SuperLU_4.0/SRC/dldperm.c:134:
>>>>>>>> undefined reference to `mc64ad_'
>>>>>>>> 
>>>>>>>> which indicates that the SuperLU compiled with PETSc did
>>>>>>>> not get the fortran underscoring flag correct (which should
>>>>>>>> be no underscore with xlf).  nm shows
>>>>>>>> 
>>>>>>>> login1.surveyor$ nm
>>>>>>>> /gpfs/home/projects/facets/surveyor/contrib-xlc-9.0/petsc-3.1-p4-ser/lib/libsuperlu_4.0.a
>>>>>>>> | grep mc64
>>>>>>>>               U mc64ad_
>>>>>>>>               U mc64id_
>>>>>>>> mc64ad.o:
>>>>>>>> 0000000000000018 D mc64ad
>>>>>>>> 0000000000000030 D mc64bd
>>>>>>>> 0000000000000048 D mc64dd
>>>>>>>> 0000000000000060 D mc64ed
>>>>>>>> 0000000000000078 D mc64fd
>>>>>>>> 0000000000000000 D mc64id
>>>>>>>> 00000000000000c0 D mc64qd
>>>>>>>> 0000000000000090 D mc64rd
>>>>>>>> 00000000000000a8 D mc64sd
>>>>>>>> 00000000000000d8 D mc64ud
>>>>>>>> 00000000000000f0 D mc64wd
>>>>>>>>               U mc64ad_
>>>>>>>>               U mc64id_
>>>>>>>> 
>>>>>>>> that the underscored symbol is being called, but the
>>>>>>>> underscore-free symbol is what was defined.
>>>>>>>> 
>>>>>>>> My PETSc configure line was
>>>>>>>> 
>>>>>>>> #!/bin/sh
>>>>>>>> /gpfs/home/cary/facetspkgs/builds-surveyor-xlc/facetspkgs/petsc-3.1-p4/ser/configure
>>>>>>>> \
>>>>>>>> --prefix=/gpfs/home/projects/facets/surveyor/contrib-xlc-9.0/petsc-3.1-p4-ser
>>>>>>>> \
>>>>>>>> --with-mpi=0 \
>>>>>>>> --with-debugging=0 \
>>>>>>>> --with-x=0 \
>>>>>>>> --with-cc='xlc_r' \
>>>>>>>> --with-cxx='xlC_r' \
>>>>>>>> --with-fc='xlf_r' \
>>>>>>>> --COPTFLAGS='-O2 -g' \
>>>>>>>> --download-superlu \
>>>>>>>> --with-lapack-lib=/home/projects/facets/intrepid/contrib/lapack-ser/lib/liblapack.a
>>>>>>>> \
>>>>>>>> --with-blas-lib=/home/projects/facets/intrepid/contrib/lapack-ser/lib/libblas.a
>>>>>>>> \
>>>>>>>> PETSC_DIR=/gpfs/home/cary/facetspkgs/builds-surveyor-xlc/facetspkgs/petsc-3.1-p4/ser
>>>>>>>> \
>>>>>>>> PETSC_ARCH=facets-ser \
>>>>>>>> --CFLAGS='-q64 -qlanglvl=redefmac' \
>>>>>>>> --CXXFLAGS='-q64 -qlanglvl=redefmac' \
>>>>>>>> --FFLAGS='-q64 -qextname=flush' \
>>>>>>>> --with-shared=1
>>>>>>>> 
>>>>>>>> so I think that PETSc had enough info to figure out the underscoring.
>>>>>>>> Perhaps this is a bug.
>>>>>>>> 
>>>>>>>> But regardless, is there a workaround?
>>>>>>>> 
>>>>>>>> Thx....John
>>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>> 
>> 
> 
> --------------------------------------------------------------
> William (Bill) E. Allcock
> allcock at alcf.anl.gov
> Office 1123, Bldg 240
> 9700 S. Cass Ave
> Argonne, IL 60439
> Office: 630-252-7573
> Fax: 630-252-6585
> Cell: 630-854-2842
> 
> The test of courage comes when we are in the minority.
> The test of tolerance comes when we are in the majority.
>  - Ralph W. Sockman
> 
> 
> 
> 
> 
> 
> 
>

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