[CIG-LONG] Gale 2.0.1 install problem with PETSc
Feng Lin
rimbong at gmail.com
Tue Jan 29 14:44:32 PST 2013
Hi Walter,
I still couldn't install Gale2.0.1.
I think I am facing at the same problem with Frank.
I installed the Gale2.0.0 without any problem last fall. So I did some test here:
I compared the config.cfg files between Gale2.0.0(configured with petsc 3.0) and Gale2.0.1(configured with petsc 3.2）
I noticed that the config.cfg in Gale2.0.1 contains much less LIB and LIBPATH...etc than in Gale2.0.0
Then I tried to configure Gale2.0.1 with petsc 3.0. I went through the configure part and I got a config.cfg similar with Gale2.0.0(configured with petsc 3.0).
However I couldn't finish the installation with ./scons.
file attached is cfg files for Gale2.0.1/petsc3.0(config10.cfg) Gale2.0.0/petsc3.0(config00.cfg) Gale2.0.1/petsc3.2(config12.cfg)
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Does this mean I did something wrong when I installed petsc3.2 ?
Sincerely,
Feng Lin
On Jan 26, 2013, at 4:46 PM, "Morgan, Frank" <Frank.Morgan at jhuapl.edu> wrote:
> Hi Walter,
>
> That didn't fix it. petsc-3.2-p7/linux-gnu-c-debug/lib was already in the
> LIBPATH. I added 'fblas', 'flapack' to LIBS ('lapack' wasn't there). And I
> still get the undefined references to blas/lapack routines.
>
> I'm attaching the Gale config.cfg file (as modified), the PETSc config log,
> and the console output from scons.
>
> The undefined routines do appear in
> petsc-3.2-p7/externalpackages/fblaslapack-3.1.1/lapack or .../blas
>
> As far as I can tell all the undefined references are calls from LAPACK
> routines to BLAS routines. Except the undefined "gfortran_*" routines, I'm
> not sure where they're supposed to be.
>
> Thanks-
> Frank
>
>
>
> On 1/26/13 3:00 PM, "cig-long-request at geodynamics.org"
> <cig-long-request at geodynamics.org> wrote:
>
>> Send CIG-LONG mailing list submissions to
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>> Today's Topics:
>>
>> 1. Re: CIG-LONG Digest, Vol 73, Issue 5 (Morgan, Frank)
>> 2. Re: CIG-LONG Digest, Vol 73, Issue 5 (Walter Landry)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 25 Jan 2013 18:23:02 -0500
>> From: "Morgan, Frank" <Frank.Morgan at jhuapl.edu>
>> Subject: Re: [CIG-LONG] CIG-LONG Digest, Vol 73, Issue 5
>> To: "cig-long at geodynamics.org" <cig-long at geodynamics.org>
>> Message-ID: <CD287E06.CF30%Frank.Morgan at jhuapl.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Thanks Walter - configuring PETSc without X11 got me past the Gale config.
>>
>> But I'm getting the same errors on scons as Feng Lin. I configured PETSc
>> with:
>> --download-f-blas-lapack=/home/morgamf1/Applications/tmp/fblaslapack-3.1.1.t
>> ar.gz
>> (pointing to the LAPACK package previously downloaded)
>>
>> ...and I have libfblas.a, libflapack.a in
>> /petsc-3.2-p7/linux-gnu-c-debug/lib/
>>
>> Is there possibly a version requirement on the LAPACK/BLAS package Gale
>> 2.0.1 needs? Is 3.1.1 maybe the wrong version? Looks like LAPACK routines
>> get moved around on occasion...
>>
>> Frank
>>
>>
>> On 1/25/13 7:49 AM, "cig-long-request at geodynamics.org"
>> <cig-long-request at geodynamics.org> wrote:
>>
>>> Send CIG-LONG mailing list submissions to
>>> cig-long at geodynamics.org
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long
>>> or, via email, send a message with subject or body 'help' to
>>> cig-long-request at geodynamics.org
>>>
>>> You can reach the person managing the list at
>>> cig-long-owner at geodynamics.org
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of CIG-LONG digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>> 1. Re: Gale 2.0.1 install problem with PETSc libraries
>>> (Walter Landry)
>>> 2. Re: Gale 2.0.1 install problem with PETSc libraries (Feng Lin)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Thu, 24 Jan 2013 14:41:41 -0800 (PST)
>>> From: Walter Landry <wlandry at caltech.edu>
>>> Subject: Re: [CIG-LONG] Gale 2.0.1 install problem with PETSc
>>> libraries
>>> To: cig-long at geodynamics.org
>>> Message-ID: <20130124.144141.967880878673273828.wlandry at caltech.edu>
>>> Content-Type: Text/Plain; charset=us-ascii
>>>
>>> feng lin <rimbong at gmail.com> wrote:
>>>> I had the same problem with your first and second time. And I haven't fixed
>>>> it yet. Even I config and make with flag --with-single-library=1, I still
>>>> keep getting the message: Static missing:
>>>> ['petscsnes', 'petscksp', 'petscdm', 'petscmat', 'petscvec']
>>>> Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
>>>> 'petscvec', 'petsc']
>>>> Looked in: ['/home/feng/Gale2.0.1/petsc-3.2-p7/lib',
>>>> '/home/feng/Gale2.0.1/petsc-3.2-p7/arch-linux2-c-debug/lib']
>>>>
>>>>
>>>>
>>>> Any one can tell me the possible reason?
>>>
>>> You have the same issue. You need to build Petsc without X11 support.
>>>
>>> Cheers,
>>> Walter Landry
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Fri, 25 Jan 2013 06:48:50 -0600
>>> From: Feng Lin <rimbong at gmail.com>
>>> Subject: Re: [CIG-LONG] Gale 2.0.1 install problem with PETSc
>>> libraries
>>> To: cig-long at geodynamics.org
>>> Message-ID: <008F74E7-DC55-4FD8-848F-254F66394CED at gmail.com>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> Walter,
>>>
>>> I've done with configure, but I couldn't install by using ./scons
>>>
>>> there's error coming out.
>>> It looks like :
>>>
>>> build/lib/libUnderworld.a(REP_Algorithm.os): In function
>>> `_REP_Algorithm_Solver(double**, double*, int)':
>>> /home/feng/Gale2.0.1/Gale-2_0_1/Underworld/Utils/src/REP_Algorithm.cxx:523:
>>> undefined reference to `dgesv_'
>>>
> /home/feng/Gale2.0.1/petsc-3.2-p7/arch-linux2-c-debug/lib/libpetsc.a(bvec2.o)>>
> :
>>> In function `VecSwap_Seq':
>>> /home/feng/Gale2.0.1/petsc-3.2-p7/src/vec/vec/impls/seq/bvec2.c:219:
>>> undefined
>>> reference to `dswap_'
>>>
>>>
>>> file attached is the log file of ./scons
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>>>
>>>
>>> Thanks!
>>>
>>> Regards,
>>>
>>>
>>> Feng Lin
>>>
>>> On Jan 24, 2013, at 4:41 PM, Walter Landry <wlandry at caltech.edu> wrote:
>>>
>>>> feng lin <rimbong at gmail.com> wrote:
>>>>> I had the same problem with your first and second time. And I haven't fixed
>>>>> it yet. Even I config and make with flag --with-single-library=1, I still
>>>>> keep getting the message: Static missing:
>>>>> ['petscsnes', 'petscksp', 'petscdm', 'petscmat', 'petscvec']
>>>>> Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
>>>>> 'petscvec', 'petsc']
>>>>> Looked in: ['/home/feng/Gale2.0.1/petsc-3.2-p7/lib',
>>>>> '/home/feng/Gale2.0.1/petsc-3.2-p7/arch-linux2-c-debug/lib']
>>>>>
>>>>>
>>>>>
>>>>> Any one can tell me the possible reason?
>>>>
>>>> You have the same issue. You need to build Petsc without X11 support.
>>>>
>>>> Cheers,
>>>> Walter Landry
>>>> _______________________________________________
>>>> CIG-LONG mailing list
>>>> CIG-LONG at geodynamics.org
>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> CIG-LONG mailing list
>>> CIG-LONG at geodynamics.org
>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long
>>>
>>> End of CIG-LONG Digest, Vol 73, Issue 5
>>> ***************************************
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 25 Jan 2013 19:37:33 -0800 (PST)
>> From: Walter Landry <wlandry at caltech.edu>
>> Subject: Re: [CIG-LONG] CIG-LONG Digest, Vol 73, Issue 5
>> To: cig-long at geodynamics.org
>> Message-ID: <20130125.193733.601209235165056426.wlandry at caltech.edu>
>> Content-Type: Text/Plain; charset=us-ascii
>>
>> "Morgan, Frank" <Frank.Morgan at jhuapl.edu> wrote:
>>> Thanks Walter - configuring PETSc without X11 got me past the Gale config.
>>>
>>> But I'm getting the same errors on scons as Feng Lin. I configured PETSc
>>> with:
>>> --download-f-blas-lapack=/home/morgamf1/Applications/tmp/fblaslapack-3.1.1.t
>>> ar.gz
>>> (pointing to the LAPACK package previously downloaded)
>>>
>>> ...and I have libfblas.a, libflapack.a in
>>> /petsc-3.2-p7/linux-gnu-c-debug/lib/
>>
>> This is good. In the Gale directory, try modifying "config.cfg" by
>> modifying the line with
>>
>> LIBPATH
>>
>> to add the directory
>>
>> /petsc-3.2-p7/linux-gnu-c-debug/lib/
>>
>> Then change the line with
>>
>> LIBS
>>
>> to remove "lapack" and add "flapack" and "fblas".
>>
>> Cheers,
>> Walter Landry
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> CIG-LONG mailing list
>> CIG-LONG at geodynamics.org
>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-long
>>
>> End of CIG-LONG Digest, Vol 73, Issue 7
>> ***************************************
>
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