[petsc-dev] [petsc-maint #40976] convert a matrix from CSR format to BCSR format

Satish Balay petsc-maint at mcs.anl.gov
Tue Feb 16 20:55:27 CST 2010 

For one - the interface most users are looking for is
--with-sequential - or --without-mpi - which '-with-mpi=0'
represents.. They don't know are care about mpiuni [so download-mpiuni
is not really better]

Also mpiuni is not distributed or built separately from petsc
sources/makefiles - and is akin to --with-sieve=1

Blas/lapack is not optional - hence no --with-blas-lapack=0 support.

Satish

On Tue, 16 Feb 2010, Barry Smith wrote:

> 
>    --download-c-blas-lapack puts "bad" Blas/LAPACK into its own  
> library. There is no --with-blaslapack=0
> 
>    Shouldn't  we eliminate -with-mpi=0 and instead have --download- 
> mpiuni
> 
>     Barry
> 
>     Removes one more special case, and special cases are BAD! So  
> obviously it is a good idea, let's see if anyone has a legitimate  
> reason for rejecting it instead of knee-jerk conservatism.
> 
> 
> 
> On Feb 16, 2010, at 8:31 PM, Satish Balay wrote:
> 
> > This is a conflict with --with-mpi=0 and the curent default
> > --with-single-library=1
> >
> > Ideally we should create libmpiuni.a [and a .so] even with
> > --with-single-library=1 - but I'm not sure how to do that cleanly. So
> > my current fix is to remove libmpiuni.a for
> > --with-single-library=1. [i.e libpetsc.a will have the mpiuni stuff as
> > well]
> >
> > Testing this change - and will push once I verify.
> >
> > Satish
> >
> > On Tue, 16 Feb 2010, Matthew Knepley wrote:
> >
> >> On Tue, Feb 16, 2010 at 8:16 PM, Dahai Guo <dhguo at ncsa.uiuc.edu>  
> >> wrote:
> >>
> >>>
> >>>
> >>> Thanks, Barry.
> >>>
> >>>
> >>>
> >>> I tried to configure and built petsc-dev on AIX with the following  
> >>> options,
> >>> but failed when "make test" as follow "ld: 0706-006 Cannot find or  
> >>> open
> >>> library file: -l mpiuni". I  used the same options for petsc-3.0,  
> >>> everything
> >>> is fine. Would you tell me how to fix it?
> >>>
> >>
> >> Always send configure.log
> >>
> >>  Matt
> >>
> >>
> >>> Dahai
> >>>
> >>>
> >>>
> >>> export OBJECT_MODE=64  # for 64/32-bit ar
> >>> export PETSC_DIR=$PWD
> >>>
> >>> config/configure.py  --with-mpi=0 --with-64-bit-pointers=1  --with- 
> >>> cc=xlc_r
> >>> --with-cxx=xlC_r --with-fc=xlf_r COPTFLAGS='-q64 -O3 -qstrict - 
> >>> qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6' FOPTFLAGS='-q64 -O3 -qstrict -qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6' CXXOPTFLAGS='-q64 -O3 -qstrict -qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6'
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> bash-3.1$ make test
> >>> Running test examples to verify correct installation
> >>> --------------Error detected during compile or  
> >>> link!-----------------------
> >>> See
> >>> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
> >>> xlc_r -o ex19.o -c -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include -I/blhome/dhguo/petsc-dev/ 
> >>> include/mpiuni
> >>> -D__SDIR__="src/snes/examples/tutorials/" ex19.c
> >>>        xlc_r -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6  -o
> >>> ex19  ex19.o -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lpetsc  -lX11 - 
> >>> lessl
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lmpiuni -lm -ldl
> >>> -L/usr/vac/lib -lxlopt -lxl -lpthreads -lxlf90 -L/usr/lpp/xlf/lib - 
> >>> lxlf
> >>> -lxlomp_ser -lm -ldl -lxlopt -lxl -lpthreads -ldl
> >>> ld: 0706-006 Cannot find or open library file: -l mpiuni
> >>>        ld:open(): No such file or directory
> >>> make: The error code from the last command is 255.
> >>> make: Ignored error code 255 from last command.
> >>>        /usr/linux/bin/rm -f ex19.o
> >>> --------------Error detected during compile or  
> >>> link!-----------------------
> >>> See
> >>> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
> >>>        xlf_r -c  -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include -I/blhome/dhguo/petsc-dev/ 
> >>> include/mpiuni
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include/mpiuni    -o ex5f.o ex5f.F
> >>> ** main   === End of Compilation 1 ===
> >>> ** forminitialguess   === End of Compilation 2 ===
> >>> ** initialguesslocal   === End of Compilation 3 ===
> >>> ** formfunctionlocal   === End of Compilation 4 ===
> >>> ** formjacobianlocal   === End of Compilation 5 ===
> >>> 1501-510  Compilation successful for file ex5f.F.
> >>>        xlf_r -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6   -o
> >>> ex5f ex5f.o -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lpetsc  -lX11 - 
> >>> lessl
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lmpiuni -lm -ldl
> >>> -L/usr/vac/lib -lxlopt -lxl -lpthreads -lxlf90 -L/usr/lpp/xlf/lib - 
> >>> lxlf
> >>> -lxlomp_ser -lm -ldl -lxlopt -lxl -lpthreads -ldl
> >>> ld: 0706-006 Cannot find or open library file: -l mpiuni
> >>>        ld:open(): No such file or directory
> >>> make: The error code from the last command is 255.
> >>> make: Ignored error code 255 from last command.
> >>>        /usr/linux/bin/rm -f ex5f.o
> >>> Completed test examples
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ----- Original Message -----
> >>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>> Sent: Tuesday, February 16, 2010 1:40:53 PM GMT -06:00 Central  
> >>> America
> >>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format  
> >>> to BCSR
> >>> format
> >>>
> >>>
> >>>   Sorry, I forgot to check the code last weekend.
> >>>
> >>>   I cannot reproduce your problem.
> >>>
> >>>   Looks like you are using petsc 3.0.0. That is completely insane!
> >>> This problem has been fixed for a year. You should be using petsc- 
> >>> dev
> >>> http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html
> >>>  it will make your live much easier.
> >>>
> >>>
> >>>    Barry
> >>>
> >>> On Feb 15, 2010, at 10:38 AM, Dahai Guo wrote:
> >>>
> >>>>
> >>>>
> >>>> Barry:
> >>>>
> >>>>
> >>>>
> >>>> In the function “MatGetFactor” in src/mat/interface/matrix.c, it
> >>>> only checks if the matsolver is available for subclass, but NOT
> >>>> further check for the AIJ/BAIJ.    I think it is one of the reasons
> >>>> that a subclass(e.g. crl ) inherited from AIJ/BAIJ can not inherit
> >>>> "MatGetFactor" from AIJ/BAIJ.
> >>>>
> >>>> Is there some special reason for designing it in this way? Or it is
> >>>> just a bug? How to improve it? Please advise.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Dahai
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>>> Sent: Thursday, February 11, 2010 9:45:24 PM GMT -06:00 US/Canada
> >>>> Central
> >>>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format
> >>>> to BCSR format
> >>>>
> >>>>
> >>>>   Dahai,
> >>>>
> >>>>     You have to switch to a decent email client. Stuff you send is
> >>>> never in attachments, it is always crammed into the message as one
> >>>> long piece of text.
> >>>>
> >>>>     I'll try to reproduce the problem tomorrow,
> >>>>
> >>>>    Barry
> >>>>
> >>>> On Feb 11, 2010, at 8:01 PM, Dahai Guo wrote:
> >>>>
> >>>>> tried CSR format, it showed the similar problem as follow.??? I
> >>>>> attached the test code and datafile.
> >>>>
> >>>>
> >>>> Barry:
> >>>>
> >>>> In the function “MatGetFactor” in src/mat/interface/matrix.c, it
> >>>> only checks if the matsolver is available for subclass, but NOT
> >>>> further check for the AIJ/BAIJ.   I think it is one of the reasons
> >>>> that a subclass(e.g. crl ) inherited from AIJ/BAIJ can not inherit
> >>>> "MatGetFactor" from AIJ/BAIJ.
> >>>>
> >>>> Is there some special reason for designing it in this way? Or it is
> >>>> just a bug? How to improve it? Please advise.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Dahai
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>>> Sent: Thursday, February 11, 2010 9:45:24 PM GMT -06:00 US/Canada
> >>>> Central
> >>>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format
> >>>> to BCSR format
> >>>>
> >>>>
> >>>>   Dahai,
> >>>>
> >>>>     You have to switch to a decent email client. Stuff you send is
> >>>> never in attachments, it is always crammed into the message as one
> >>>> long piece of text.
> >>>>
> >>>>     I'll try to reproduce the problem tomorrow,
> >>>>
> >>>>    Barry
> >>>>
> >>>> On Feb 11, 2010, at 8:01 PM, Dahai Guo wrote:
> >>>>
> >>>>> tried CSR format, it showed the similar problem as follow.??? I
> >>>>> attached the test code and datafile.
> >>>>
> >>>
> >>>
> >>>
> >>> Thanks, Barry.
> >>>
> >>>
> >>>
> >>> I tried to configure and built petsc-dev on AIX with the following  
> >>> options,
> >>> but failed when "make test" as follow "ld: 0706-006 Cannot find or  
> >>> open
> >>> library file: -l mpiuni". I  used the same options for petsc-3.0,  
> >>> everything
> >>> is fine. Would you tell me how to fix it?
> >>>
> >>>
> >>>
> >>> Dahai
> >>>
> >>>
> >>>
> >>> export OBJECT_MODE=64  # for 64/32-bit ar
> >>> export PETSC_DIR=$PWD
> >>>
> >>> config/configure.py  --with-mpi=0 --with-64-bit-pointers=1  --with- 
> >>> cc=xlc_r
> >>> --with-cxx=xlC_r --with-fc=xlf_r COPTFLAGS='-q64 -O3 -qstrict - 
> >>> qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6' FOPTFLAGS='-q64 -O3 -qstrict -qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6' CXXOPTFLAGS='-q64 -O3 -qstrict -qmaxmem=-1
> >>> -qarch=pwr6 -qtune=pwr6'
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> bash-3.1$ make test
> >>> Running test examples to verify correct installation
> >>> --------------Error detected during compile or  
> >>> link!-----------------------
> >>> See
> >>> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
> >>> xlc_r -o ex19.o -c -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include -I/blhome/dhguo/petsc-dev/ 
> >>> include/mpiuni
> >>> -D__SDIR__="src/snes/examples/tutorials/" ex19.c
> >>>        xlc_r -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6  -o
> >>> ex19  ex19.o -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lpetsc  -lX11 - 
> >>> lessl
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lmpiuni -lm -ldl
> >>> -L/usr/vac/lib -lxlopt -lxl -lpthreads -lxlf90 -L/usr/lpp/xlf/lib - 
> >>> lxlf
> >>> -lxlomp_ser -lm -ldl -lxlopt -lxl -lpthreads -ldl
> >>> ld: 0706-006 Cannot find or open library file: -l mpiuni
> >>>        ld:open(): No such file or directory
> >>> make: The error code from the last command is 255.
> >>> make: Ignored error code 255 from last command.
> >>>        /usr/linux/bin/rm -f ex19.o
> >>> --------------Error detected during compile or  
> >>> link!-----------------------
> >>> See
> >>> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
> >>>        xlf_r -c  -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include -I/blhome/dhguo/petsc-dev/ 
> >>> include/mpiuni
> >>> -I/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/include
> >>> -I/blhome/dhguo/petsc-dev/include/mpiuni    -o ex5f.o ex5f.F
> >>> ** main   === End of Compilation 1 ===
> >>> ** forminitialguess   === End of Compilation 2 ===
> >>> ** initialguesslocal   === End of Compilation 3 ===
> >>> ** formfunctionlocal   === End of Compilation 4 ===
> >>> ** formjacobianlocal   === End of Compilation 5 ===
> >>> 1501-510  Compilation successful for file ex5f.F.
> >>>        xlf_r -q64 -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 - 
> >>> qtune=pwr6   -o
> >>> ex5f ex5f.o -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lpetsc  -lX11 - 
> >>> lessl
> >>> -L/blhome/dhguo/petsc-dev/aix5.3.0.0-c-debug/lib -lmpiuni -lm -ldl
> >>> -L/usr/vac/lib -lxlopt -lxl -lpthreads -lxlf90 -L/usr/lpp/xlf/lib - 
> >>> lxlf
> >>> -lxlomp_ser -lm -ldl -lxlopt -lxl -lpthreads -ldl
> >>> ld: 0706-006 Cannot find or open library file: -l mpiuni
> >>>        ld:open(): No such file or directory
> >>> make: The error code from the last command is 255.
> >>> make: Ignored error code 255 from last command.
> >>>        /usr/linux/bin/rm -f ex5f.o
> >>> Completed test examples
> >>>
> >>>
> >>>
> >>>
> >>> ----- Original Message -----
> >>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>> Sent: Tuesday, February 16, 2010 1:40:53 PM GMT -06:00 Central  
> >>> America
> >>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format  
> >>> to BCSR
> >>> format
> >>>
> >>>
> >>>   Sorry, I forgot to check the code last weekend.
> >>>
> >>>   I cannot reproduce your problem.
> >>>
> >>>   Looks like you are using petsc 3.0.0. That is completely insane!
> >>> This problem has been fixed for a year. You should be using petsc- 
> >>> dev
> >>> http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html
> >>>  it will make your live much easier.
> >>>
> >>>
> >>>    Barry
> >>>
> >>> On Feb 15, 2010, at 10:38 AM, Dahai Guo wrote:
> >>>
> >>>>
> >>>>
> >>>> Barry:
> >>>>
> >>>>
> >>>>
> >>>> In the function “MatGetFactor” in src/mat/interface/matrix.c, it
> >>>> only checks if the matsolver is available for subclass, but NOT
> >>>> further check for the AIJ/BAIJ.    I think it is one of the reasons
> >>>> that a subclass(e.g. crl ) inherited from AIJ/BAIJ can not inherit
> >>>> "MatGetFactor" from AIJ/BAIJ.
> >>>>
> >>>> Is there some special reason for designing it in this way? Or it is
> >>>> just a bug? How to improve it? Please advise.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Dahai
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>>> Sent: Thursday, February 11, 2010 9:45:24 PM GMT -06:00 US/Canada
> >>>> Central
> >>>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format
> >>>> to BCSR format
> >>>>
> >>>>
> >>>>   Dahai,
> >>>>
> >>>>     You have to switch to a decent email client. Stuff you send is
> >>>> never in attachments, it is always crammed into the message as one
> >>>> long piece of text.
> >>>>
> >>>>     I'll try to reproduce the problem tomorrow,
> >>>>
> >>>>    Barry
> >>>>
> >>>> On Feb 11, 2010, at 8:01 PM, Dahai Guo wrote:
> >>>>
> >>>>> tried CSR format, it showed the similar problem as follow.??? I
> >>>>> attached the test code and datafile.
> >>>>
> >>>>
> >>>> Barry:
> >>>>
> >>>> In the function “MatGetFactor” in src/mat/interface/matrix.c, it
> >>>> only checks if the matsolver is available for subclass, but NOT
> >>>> further check for the AIJ/BAIJ.   I think it is one of the reasons
> >>>> that a subclass(e.g. crl ) inherited from AIJ/BAIJ can not inherit
> >>>> "MatGetFactor" from AIJ/BAIJ.
> >>>>
> >>>> Is there some special reason for designing it in this way? Or it is
> >>>> just a bug? How to improve it? Please advise.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Dahai
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>> From: "Barry Smith" <bsmith at mcs.anl.gov>
> >>>> To: petsc-maint at mcs.anl.gov, "Dahai Guo" <dhguo at ncsa.uiuc.edu>
> >>>> Sent: Thursday, February 11, 2010 9:45:24 PM GMT -06:00 US/Canada
> >>>> Central
> >>>> Subject: Re: [petsc-maint #40976] convert a matrix from CSR format
> >>>> to BCSR format
> >>>>
> >>>>
> >>>>   Dahai,
> >>>>
> >>>>     You have to switch to a decent email client. Stuff you send is
> >>>> never in attachments, it is always crammed into the message as one
> >>>> long piece of text.
> >>>>
> >>>>     I'll try to reproduce the problem tomorrow,
> >>>>
> >>>>    Barry
> >>>>
> >>>> On Feb 11, 2010, at 8:01 PM, Dahai Guo wrote:
> >>>>
> >>>>> tried CSR format, it showed the similar problem as follow.??? I
> >>>>> attached the test code and datafile.
> >>>>
> >>>
> >>>
> >>>
> >>
> >>
> >>
> >
> 
> 
>

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