June 2014 - petsc-dev - mailman3.cels.anl.gov

Runs PETSc solvers on both iOS and Android
by Barry Smith 29 Jun '14

29 Jun '14

I’ve installed it, have you ? :-) http://onelab.info/wiki/Main_Page

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Re: [petsc-dev] problem building on Mira
by Barry Smith 28 Jun '14

28 Jun '14

On Jun 28, 2014, at 11:50 AM, Brian Van Straalen <bvstraalen(a)lbl.gov> wrote: > the warnings for Chombo has to do with the C++11 standard and that the trunk is not compliant with a very specific and amazingly annoying new aspect of the language. I fixed this in the 3.2 release but haven’t back ported these changes to the development trunk. I will work on that this week, but that is not what’s stopping you. > > The PETSc Syntax error seems to be related to > >> petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h > > where there are new definitions for things that live inside the C standard libraries. My guess is that PETSc’s configure was run with a different compiler than you are compiling with. The quick fix is to edit the petscfix.h file and remove the extra definitions. Then run the make again. Barry On some very obscure systems these definitions need to be added, we are not sure why configure has added them for the BlueGene and will track down why and fix it. > > > > > On Jun 28, 2014, at 7:48 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > >> PETSc, >> >> I am trying to build a code with PETSc on Mira and I seem to be getting some conflicting declarations. >> I have pulled from dev and reconfigured PETSc today. Any ideas? >> >> Mark >> >> mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools -DCH_LANG_CC -c PetscCompGrid.cpp -o o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a default argument expression and is not a definition. >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h". >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a default argument expression and is not a definition. >> gmake[2]: *** [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error 1 >> gmake[1]: *** [AMRElliptic] Error 2 >> make: *** [AMRElliptic] Error 2 >> [adams@miralac1 execBCG]$ > > Brian Van Straalen Lawrence Berkeley Lab > BVStraalen(a)lbl.gov Computational Research > (510) 486-4976 Division (crd.lbl.gov) > > > >

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nightly build error please fix!
by Barry Smith 28 Jun '14

28 Jun '14

http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2014/06/28/filtered-ma…

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Re: [petsc-dev] problem building on Mira
by Barry Smith 28 Jun '14

28 Jun '14

Jed and Matt, stop bickering and actual look through the configure.log to determine how this is happening and how to fix it. The first time _GNU_SOURCE is used in TEST configureFeatureTestMacros from PETSc.utilities.featureTestMacros Executing: mpixlc_r -c -o /tmp/petsc-ByVZS6/PETSc.utilities.featureTestMacros/conftest.o -I/tmp/petsc-ByVZS6/config.libraries -I/tmp/petsc-ByVZS6/config.compilers -I/tmp/petsc-ByVZS6/config.setCompilers -I/tmp/petsc-ByVZS6/config.headers -I/tmp/petsc-ByVZS6/PETSc.utilities.cacheDetails -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/PETSc.utilities.featureTestMacros -O5 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict -qstrict_induction /tmp/petsc-ByVZS6/PETSc.utilities.featureTestMacros/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _GNU_SOURCE #include <sched.h> int main() { cpu_set_t mset; CPU_ZERO(&mset);; return 0; } Defined "_GNU_SOURCE" to “1" it does not complain about _GNU_SOURCE already being defined. but the next time TEST configureMissingGetdomainnamePrototype from PETSc.utilities.missing(/gpfs/mira-home/adams/petsc_public/config/PETSc/utilities/missing.py:92) TESTING: configureMissingGetdomainnamePrototype from PETSc.utilities.missing(config/PETSc/utilities/missing.py:92) Executing: mpixlc_r -c -o /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o -I/tmp/petsc-ByVZS6/config.compilers -I/tmp/petsc-ByVZS6/config.setCompilers -I/tmp/petsc-ByVZS6/config.headers -I/tmp/petsc-ByVZS6/PETSc.utilities.cacheDetails -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/PETSc.utilities.featureTestMacros -I/tmp/petsc-ByVZS6/config.libraries -I/tmp/petsc-ByVZS6/config.types -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict -qstrict_induction /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.c Successful compile: Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #define _GNU_SOURCE it does complain "/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a different definition. So either _GNU_SOURCE is now being defined in “confdefs.h” or “conffix.h” which it should not be or something is different about this compile to get it to be defined. What is different about this compile? Well the #define _BSD_SOURCE Could they be doing something so perverse as automatically setting _GNU_SOURCE if _BSD_SOURCE is being defined? Someone with an account on that machine needs to log in and try to manually reproduce the problem. Barry On Jun 28, 2014, at 10:55 AM, Jed Brown <jed(a)jedbrown.org> wrote: > Matthew Knepley <knepley(a)gmail.com> writes: > >> On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <mfadams(a)lbl.gov> wrote: >> >>> And this is the configure log. >>> >> >> Here is the problem: >> >> Executing: mpixlcxx_r -c -o >> /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o >> -I/tmp/petsc-ByVZS6/config.compilers >> -I/tmp/petsc-ByVZS6/config.setCompilers >> -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/config.types >> -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto >> -qmaxmem=-1 -qstrict -qstrict_induction -+ >> /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc >> Possible ERROR while running compiler: exit code 256 >> stderr: >> "/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: >> 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a >> different definition. >> Source: >> #include "confdefs.h" >> #include "conffix.h" >> #define _BSD_SOURCE >> #define _GNU_SOURCE >> >> #ifdef PETSC_HAVE_UNISTD_H >> #include <unistd.h> >> #endif >> #ifdef PETSC_HAVE_NETDB_H >> #include <netdb.h> >> #endif >> >> int main() { >> >> int (*getdomainname_ptr)(char*,size_t) = getdomainname; >> char test[10]; >> if (getdomainname_ptr(test,10)) return 1; >> ; >> return 0; >> } >> Compile failed inside link >> >> Jed, what is going on with the _GNU_SOURCE crap? > > Who defined it before us? The man page for getdomainname says that > _BSD_SOURCE must be defined. Some other functions we look for require > _GNU_SOURCE. > > The problem with skipping the feature test macros is that we fail to > detect something that actually exists, and may cause problems later. > This is especially annoying when we test for a function using the > linker, then fail to find it in the header because it is only defined > when suitable feature test macros are defined.

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Re: [petsc-dev] problem building on Mira
by Brian Van Straalen 28 Jun '14

28 Jun '14

the warnings for Chombo has to do with the C++11 standard and that the trunk is not compliant with a very specific and amazingly annoying new aspect of the language. I fixed this in the 3.2 release but haven’t back ported these changes to the development trunk. I will work on that this week, but that is not what’s stopping you. The PETSc Syntax error seems to be related to > petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h where there are new definitions for things that live inside the C standard libraries. My guess is that PETSc’s configure was run with a different compiler than you are compiling with. On Jun 28, 2014, at 7:48 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > PETSc, > > I am trying to build a code with PETSc on Mira and I seem to be getting some conflicting declarations. > I have pulled from dev and reconfigured PETSc today. Any ideas? > > Mark > > mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools -DCH_LANG_CC -c PetscCompGrid.cpp -o o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a default argument expression and is not a definition. > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h". > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a default argument expression and is not a definition. > gmake[2]: *** [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error 1 > gmake[1]: *** [AMRElliptic] Error 2 > make: *** [AMRElliptic] Error 2 > [adams@miralac1 execBCG]$ Brian Van Straalen Lawrence Berkeley Lab BVStraalen(a)lbl.gov Computational Research (510) 486-4976 Division (crd.lbl.gov)

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Re: [petsc-dev] problem building on Mira
by Jed Brown 28 Jun '14

28 Jun '14

Matthew Knepley <knepley(a)gmail.com> writes: > On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > >> And this is the configure log. >> > > Here is the problem: > > Executing: mpixlcxx_r -c -o > /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o > -I/tmp/petsc-ByVZS6/config.compilers > -I/tmp/petsc-ByVZS6/config.setCompilers > -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/config.types > -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto > -qmaxmem=-1 -qstrict -qstrict_induction -+ > /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc > Possible ERROR while running compiler: exit code 256 > stderr: > "/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: > 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a > different definition. > Source: > #include "confdefs.h" > #include "conffix.h" > #define _BSD_SOURCE > #define _GNU_SOURCE > > #ifdef PETSC_HAVE_UNISTD_H > #include <unistd.h> > #endif > #ifdef PETSC_HAVE_NETDB_H > #include <netdb.h> > #endif > > int main() { > > int (*getdomainname_ptr)(char*,size_t) = getdomainname; > char test[10]; > if (getdomainname_ptr(test,10)) return 1; > ; > return 0; > } > Compile failed inside link > > Jed, what is going on with the _GNU_SOURCE crap? Who defined it before us? The man page for getdomainname says that _BSD_SOURCE must be defined. Some other functions we look for require _GNU_SOURCE. The problem with skipping the feature test macros is that we fail to detect something that actually exists, and may cause problems later. This is especially annoying when we test for a function using the linker, then fail to find it in the header because it is only defined when suitable feature test macros are defined.

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Re: [petsc-dev] problem building on Mira
by Matthew Knepley 28 Jun '14

28 Jun '14

On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > And this is the configure log. > Here is the problem: Executing: mpixlcxx_r -c -o /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o -I/tmp/petsc-ByVZS6/config.compilers -I/tmp/petsc-ByVZS6/config.setCompilers -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/config.types -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict -qstrict_induction -+ /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc Possible ERROR while running compiler: exit code 256 stderr: "/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a different definition. Source: #include "confdefs.h" #include "conffix.h" #define _BSD_SOURCE #define _GNU_SOURCE #ifdef PETSC_HAVE_UNISTD_H #include <unistd.h> #endif #ifdef PETSC_HAVE_NETDB_H #include <netdb.h> #endif int main() { int (*getdomainname_ptr)(char*,size_t) = getdomainname; char test[10]; if (getdomainname_ptr(test,10)) return 1; ; return 0; } Compile failed inside link Jed, what is going on with the _GNU_SOURCE crap? Matt > Mark > > > > On Sat, Jun 28, 2014 at 4:48 PM, Mark Adams <mfadams(a)lbl.gov> wrote: > >> PETSc, >> >> I am trying to build a code with PETSc on Mira and I seem to be getting >> some conflicting declarations. >> I have pulled from dev and reconfigured PETSc today. Any ideas? >> >> Mark >> >> mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI >> -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL >> -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE >> -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include >> -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include >> -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include >> -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include >> -I/bgsys/drivers/V1R2M1/ppc64/comm/include >> -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 >> -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include >> -I/bgsys/drivers/V1R2M1/ppc64/spi/include >> -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE >> -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools >> -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools >> -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools >> -DCH_LANG_CC -c PetscCompGrid.cpp -o >> o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", >> line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a >> default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", >> line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a >> default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", >> line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a >> default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", >> line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a >> default argument expression and is not a definition. >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", >> line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting >> declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", >> line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h". >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", >> line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", >> line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". >> "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", >> line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration. >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", >> line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of >> "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", >> line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a >> default argument expression and is not a definition. >> "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", >> line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a >> default argument expression and is not a definition. >> gmake[2]: *** >> [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error >> 1 >> gmake[1]: *** [AMRElliptic] Error 2 >> make: *** [AMRElliptic] Error 2 >> [adams@miralac1 execBCG]$ >> > > -- 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

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Re: [petsc-dev] problem building on Mira
by Mark Adams 28 Jun '14

28 Jun '14

And this is the configure log. Mark On Sat, Jun 28, 2014 at 4:48 PM, Mark Adams <mfadams(a)lbl.gov> wrote: > PETSc, > > I am trying to build a code with PETSc on Mira and I seem to be getting > some conflicting declarations. > I have pulled from dev and reconfigured PETSc today. Any ideas? > > Mark > > mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI > -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL > -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE > -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include > -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include > -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include > -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include > -I/bgsys/drivers/V1R2M1/ppc64/comm/include > -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 > -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include > -I/bgsys/drivers/V1R2M1/ppc64/spi/include > -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE > -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools > -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools > -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools > -DCH_LANG_CC -c PetscCompGrid.cpp -o > o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", > line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a > default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", > line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a > default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", > line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a > default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", > line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a > default argument expression and is not a definition. > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line > 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting > declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", > line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h". > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line > 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", > line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". > "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line > 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration. > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", > line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of > "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", > line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a > default argument expression and is not a definition. > "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", > line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a > default argument expression and is not a definition. > gmake[2]: *** > [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error > 1 > gmake[1]: *** [AMRElliptic] Error 2 > make: *** [AMRElliptic] Error 2 > [adams@miralac1 execBCG]$ >

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problem building on Mira
by Mark Adams 28 Jun '14

28 Jun '14

PETSc, I am trying to build a code with PETSc on Mira and I seem to be getting some conflicting declarations. I have pulled from dev and reconfigured PETSc today. Any ideas? Mark mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools -DCH_LANG_CC -c PetscCompGrid.cpp -o o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a default argument expression and is not a definition. "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a default argument expression and is not a definition. "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a default argument expression and is not a definition. "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a default argument expression and is not a definition. "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting declaration. "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h". "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration. "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". "/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration. "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h". "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a default argument expression and is not a definition. "/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a default argument expression and is not a definition. gmake[2]: *** [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error 1 gmake[1]: *** [AMRElliptic] Error 2 make: *** [AMRElliptic] Error 2 [adams@miralac1 execBCG]$

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Re: [petsc-dev] mkl_pardiso test
by Hong Zhang 26 Jun '14

26 Jun '14

Jose, > > You can use any example in PETSc that generates matrices to run with mkl-paridiso you don’t need to read from a file. You may look at petsc/src/ksp/ksp/examples/tutorials/ex52.c Hong > > Barry > > On Jun 26, 2014, at 8:54 PM, José David Bermeo López <jdbermeol(a)gmail.com> wrote: > >> So I was adding a new test in src/mat/examples/tests/ using the file ex125.c, this test required data from ftp.mcs.anl.gov:/pub/petsc/matrices, I download the data, but I get the following error: >> >> > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >> > [0]PETSC ERROR: Read from file failed >> > [0]PETSC ERROR: Read past end of file >> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. >> > [0]PETSC ERROR: Petsc Development GIT revision: GIT Date: >> > [0]PETSC ERROR: ./ex125 on a linux-complex named conte-fe00.rcac.purdue.edu by jbermeol Thu Jun 26 21:36:20 2014 >> > [0]PETSC ERROR: Configure options CC=mpiicc CXX=mpiicpc FC=mpiifort COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --with-scalar-type=complex --with-shared-libraries=0 --with-debugging=1 --with-pic=1 --with-clanguage=C++ --with-fortran=1 --with-fortran-kernels=0 --download-mumps --download-metis --download-parmetis --with-scalapack-lib="-L/apps/rhel6/intel/composer_xe_2013.3.163/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/apps/rhel6/intel/composer_xe_2013.3.163/mkl/include --with-blas-lapack-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl --with-mkl-pardiso-dir=/apps/rhel6/intel/composer_xe_2013.3.163/mkl >> > [0]PETSC ERROR: #1 PetscBinaryRead() line 274 in /home/jbermeol/software/petsc_cplx/src/sys/fileio/sysio.c >> > [0]PETSC ERROR: #2 MatLoad_SeqAIJ() line 4312 in /home/jbermeol/software/petsc_cplx/src/mat/impls/aij/seq/aij.c >> > [0]PETSC ERROR: #3 MatLoad() line 997 in /home/jbermeol/software/petsc_cplx/src/mat/interface/matrix.c >> > [0]PETSC ERROR: #4 main() line 36 in ex125.c >> > [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- >> > application called MPI_Abort(MPI_COMM_WORLD, 66) - process 0 >> >> Not sure if the file is corrupted, could you please help me with that. Thanks >> >> >> On Thu, Jun 26, 2014 at 3:38 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: >> On Thu, 26 Jun 2014, José David Bermeo López wrote: >> >> > Hi, I would like to add a test to the repository for mkl_pardiso, looking >> > for mumps test, I sow test ex125.c that uses MUMPS or other solvers >> > depending on the option, so i have some questions: >> > >> > 1. Would be a good idea to add mkl_pardiso in that test(ex125.c) >> >> I've added one test. But more tests would be good. >> [check runex2_mkl_pardiso in src/ksp/ksp/examples/tutorials/makefile] >> >> > 2. For that test you load matrix A, is it a distributed matrix or a >> > sequential matrix. >> >> Hm - this example appears to also test Superlu [which is sequential] - >> so adding mkl_pardiso similarly might work.. >> >> [Hong might have better suggestions] >> >> >> > 3. You had html pages, for documentation of each solver, is this >> > automatically generated base on comments, or do I had to added my self. >> >> Ah - I didn't check that. You can look at the end of >> mat/impls/aij/mpi/superlu_dist/superlu_dist.c for its >> documentation. If you add something similar to mkl_pardiso.c - the >> docs for it will get autogenerated. >> >> Satish >> >

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