[petsc-users] FETI-DP implementation and call sequence

Fri Sep 5 18:44:48 CDT 2014

perhaps unrelated - but are you sure you had the latest master?

>>>>
PETSC_VERSION_RELEASE    0
PETSC_VERSION_MAJOR      3
PETSC_VERSION_MINOR      5
PETSC_VERSION_SUBMINOR   0
PETSC_VERSION_PATCH      0
<<<<<<<

PETSC_VERSION_PATCH should be 1

>>>>>
     CLINKER /home/alp/petsc/arch-mswin-c-debug/lib/libpetsc.so.3.05.0
Warning: corrupt .drectve at end of def file
Warning: corrupt .drectve at end of def file
Warning: corrupt .drectve at end of def file

rch-mswin-c-debug/obj/src/sys/utils/mpiu.o:(.text+0xdd2): undefined reference to `__security_cookie'
arch-mswin-c-debug/obj/src/sys/utils/mpiu.o:(.text+0xdd2): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `__security_cookie'
<<<<<<

Hm - must be related to --with-shared-libraries option you are
specifying. This is untested on windows.

Can you remove it and retry?

Satish

On Fri, 5 Sep 2014, Alp Kalpalp wrote:

> Hi,
> 
> Sorry for the late response. I tried the same sequence. But I need to say
> that I use git pull before it. Error is now during make all
> 
> you may find the logs in the attachment.
> 
> thanks beforehand
> 
> regards,
> 
> 
> On Fri, Sep 5, 2014 at 2:51 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> > Please send your configure.log and make.log
> >
> >   Thanks,
> >
> >     Matt
> >
> >
> > On Fri, Sep 5, 2014 at 4:27 AM, Alp Kalpalp <alpkalpalp at gmail.com> wrote:
> >
> >> As I said before, I have checked out "master" branch and merged with your
> >> stefano_zampini/pcbddc-primalfixe branch. configured, compiled successfully.
> >> I have used --with-pcbddc option in configure as Barry suggested.
> >>
> >> However, tests are failed with following reason:
> >>
> >> akalpalp at a-kalpalp ~/petsc
> >> $ make PETSC_DIR=/home/akalpalp/petsc PETSC_ARCH=arch-mswin-c-debug test
> >> Running test examples to verify correct installation
> >> Using PETSC_DIR=/home/akalpalp/petsc and PETSC_ARCH=arch-mswin-c-debug
> >> *******************Error detected during compile or
> >> link!*******************
> >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >> /home/akalpalp/petsc/src/snes/examples/tutorials ex19
> >>
> >> *********************************************************************************
> >> /home/akalpalp/petsc/arch-mswin-c-debug/bin/mpicc -o ex19.o -c -Wall
> >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0
> >> -I/home/akalpalp/petsc/include
> >> -I/home/akalpalp/petsc/arch-mswin-c-debug/include    `pwd`/ex19.c
> >> /home/akalpalp/petsc/arch-mswin-c-debug/bin/mpicc -Wall -Wwrite-strings
> >> -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0  -o ex19  ex19.o
> >> -L/home/akalpalp/petsc/arch-mswin-c-debug/lib  -lpetsc
> >> -Wl,-rpath,/home/akalpalp/petsc/arch-mswin-c-debug/lib -lf2clapack
> >> -lf2cblas -lpthread -lgdi32 -luser32 -ladvapi32 -lkernel32 -ldl
> >> /home/akalpalp/petsc/arch-mswin-c-debug/lib/libpetsc.a(pcregis.o):pcregis.c:(.rdata$.refptr.PCCreate_BDDC[.refptr.PCCreate_BDDC]+0x0):
> >> undefined reference to `PCCreate_BDDC'
> >> collect2: error: ld returned 1 exit status
> >> makefile:108: recipe for target 'ex19' failed
> >> make[3]: [ex19] Error 1 (ignored)
> >> /usr/bin/rm -f ex19.o
> >> Completed test examples
> >> =========================================
> >> Now to evaluate the computer systems you plan use - do:
> >> make PETSC_DIR=/home/akalpalp/petsc PETSC_ARCH=arch-mswin-c-debug streams
> >> NPMAX=<number of MPI processes you intend to use>
> >>
> >>
> >>
> >> On Thu, Sep 4, 2014 at 5:37 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >>
> >>>
> >>>    This is likely due to the horrible horrible fact that some of the
> >>> bddc files only get compiled if ./configure is run with the option
> >>> --with-pcbddc you will need to rerun ./configure and then make with that
> >>> option.
> >>>
> >>>    I pray that someone removes that horrible confusing configure option.
> >>>
> >>>    Barry
> >>>
> >>> On Sep 4, 2014, at 8:52 AM, Alp Kalpalp <alpkalpalp at gmail.com> wrote:
> >>>
> >>> > Dear Stefano,
> >>> >
> >>> > I have checked out "master" branch and merged with your
> >>> stefano_zampini/pcbddc-primalfixe branch. configured, compiled and all
> >>> tests are completed successfully.
> >>> > Then, I tried to compile ex59 with make ex59, it results in unresolved
> >>> external error. I believe your bddc_feti files are not included in
> >>> compilation.
> >>> > Since I am not experienced on how to solve issues in Petsc, I need to
> >>> ask several questions;
> >>> >
> >>> > 1-) Are there any global settings to add additonal directories to
> >>> compilation  (src\ksp\pc\impls\bddc)
> >>> > 2-) or should I include these files on top of ex59 (AFAIK, including
> >>> .c files is not a good thing)
> >>> > 3-) and finally what is the better way of helping you (creating
> >>> another branch from yours or what)
> >>> >
> >>> > Thanks in advance
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > On Wed, Sep 3, 2014 at 6:18 PM, Stefano Zampini <
> >>> stefano.zampini at gmail.com> wrote:
> >>> > FETIDP is in PETSc as a byproduct of the BDDC preconditioner (one is
> >>> the dual of the other) and it does not have its own classes so far.
> >>> >
> >>> > That said, you can experiment with FETI-DP only after having setup a
> >>> BDDC preconditioner with the options and customization you prefer.
> >>> > Use
> >>> http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/KSP/index.html
> >>> for manual pages.
> >>> >
> >>> > For an 'how to' with FETIDP, please see
> >>> src/ksp/ksp/examples/tutorials/ex.59.c as Jed told you, specifically look
> >>> at ComputeKSPFETIDP for obtaining the FETIDP matrix F (implemented
> >>> Matrix-free) and the optimal FETIDP dirichlet preconditioner. Once you have
> >>> F, you can use PCBDDCMatFETIDPGetRHS and PCBDDCMatFetiDPGetSolution to
> >>> obtain a right-hand side for the FETIDP system and a physical solution from
> >>> the solution of the FETIDP system.
> >>> >
> >>> > I would recommend you to use the development version of the library
> >>> and either use the ‘next’ branch or the ‘master' branch after having merged
> >>> in the branch stefano_zampini/pcbddc-primalfixes. Note that ‘next’ also
> >>> contains the new deluxe scaling operator for BDDC which is not available to
> >>> use with FETI-DP.
> >>> >
> >>> > If you have any other questions which can be useful for other PETSc
> >>> users, please use the mailing list; otherwise you can contact me personally.
> >>> >
> >>> > Stefano
> >>> >
> >>> >
> >>> > On Sep 3, 2014, at 5:19 PM, Jed Brown <jed at jedbrown.org> wrote:
> >>> >
> >>> >> Matthew Knepley <knepley at gmail.com> writes:
> >>> >>>> 1- Is it possible to complete a FETI-DP solution with the provided
> >>> >>>> functions in current PetSc release?
> >>> >>>>
> >>> >>>
> >>> >>> There is no FETI-DP in PETSc.
> >>> >>
> >>> >> Wrong.  There is PCBDDC, which has the same eigenvalues as FETI-DP.
> >>> You
> >>> >> can enable it by configuring --with-pcbddc.  This will be turned on by
> >>> >> default soon.  It is fairly new, so you should use the branch 'master'
> >>> >> instead of the release.  It has an option to do FETI-DP instead of
> >>> BDDC.
> >>> >> See src/ksp/ksp/examples/tutorials/ex59.c.
> >>> >>
> >>> >> For either of these methods, you have to assemble a MATIS.  If you use
> >>> >> MatSetValuesLocal, most of your assembly code can stay the same.
> >>> >>
> >>> >> Hopefully we can get better examples before the next release.  Stefano
> >>> >> (the author of PCBDDC, Cc'd) tests mostly with external packages, but
> >>> we
> >>> >> really need more complete tests within PETSc.
> >>> >
> >>> >
> >>>
> >>>
> >>
> >
> >
> > --
> > What most experimenters take for granted before they begin their
> > experiments is infinitely more interesting than any results to which their
> > experiments lead.
> > -- Norbert Wiener
> >
> 