BTW: You could also instal lapack (liblapack-devel), openmpi (openmpi-devel) packages from cygwin - and avoid --download-f2cblaslapack and --download-mpich
Satish On Sat, 6 Sep 2014, Satish Balay wrote: > On Sat, 6 Sep 2014, Alp Kalpalp wrote: > > > Hi, > > > > I switched back to master again and PETSC_VERSION_SUBMINOR is equal to 1 > > again. I think with the merge of stefano_zampini/pcbddc-primalfixe > > it is changing to 0. > > the merge won't change PETSC_VERSION_SUBMINOR > > > > > As you suggested I removed --with-shared-libraries option, but although > > make all seems working make test is failed with attached errors. > > I'll suggest "rm -rf /home/alp/petsc/arch-mswin-c-debug/" and then retry > > or if you could clean the git repo with: > git reset --hard > git clean -f -d -x > > And then rerun configure > > Satish > > > > > thanks > > > > > > On Sat, Sep 6, 2014 at 2:44 AM, Satish Balay <[email protected]> wrote: > > > > > 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 <[email protected]> > > > wrote: > > > > > > > > > Please send your configure.log and make.log > > > > > > > > > > Thanks, > > > > > > > > > > Matt > > > > > > > > > > > > > > > On Fri, Sep 5, 2014 at 4:27 AM, Alp Kalpalp <[email protected]> > > > 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@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 <[email protected]> > > > 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 <[email protected]> > > > 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 < > > > > >>> [email protected]> 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 <[email protected]> wrote: > > > > >>> > > > > > >>> >> Matthew Knepley <[email protected]> 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 > > > > > > > > > > > > > > >
