April 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Fortran macOS Linkage Warning
by Barry Smith 16 Apr '21

16 Apr '21

If I had understand from the beginning this was merely a bug report we could have processed it much quicker and easier. Hopefully this will resolve the problem and can get into the release branch soon. https://gitlab.com/petsc/petsc/-/merge_requests/3884 <https://gitlab.com/petsc/petsc/-/merge_requests/3884> > On Apr 16, 2021, at 3:23 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com> wrote: > >> I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? > > At least on my end, none of them are possible without setting MAOSX_DEPLOYMENT_TARGET or --LDFLAGS=-mmacosx-version-min=11.2. Configure fails when it tests fortran linkage capability. > > <configure.log> > > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > >> On Apr 16, 2021, at 15:03, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >> >> >> I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? >> >> If so that should clearly be reported as a bug with all relevant information supplied. >> >> No, we have never and do not ever intend for PETSc users even developers to know or care about MACOSX_DEPLOYMENT_TARGET >> >> Anyways if you are reporting a bug and I am guess the bug correctly the fix is to add "was built for newer macOS version" to the list of filtered link warnings. There will be a bunch of such warnings that will need to be added to the filtering in the next few months but once they are in place the filtering should not be an issue. >> >> >> Barry >> >> >> >>> On Apr 16, 2021, at 6:20 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >>> >>> Barry, >>> That issue + this commit: >>> $ git bisect bad >>> 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit >>> commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 >>> Author: Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> >>> Date: Sat Apr 10 13:40:10 2021 -0500 >>> makes it actually impossible to ./configure on macOS. >>> Do we really expect all macOS users to know about the variable MACOSX_DEPLOYMENT_TARGET? >>> >>> Thanks, >>> Pierre >>> >>> $ ./configure >>> =============================================================================== >>> Configuring PETSc to compile on your system >>> =============================================================================== >>> TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) >>> ******************************************************************************* >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >>> ------------------------------------------------------------------------------- >>> Fortran libraries cannot be used with C as linker >>> ******************************************************************************* >>> >>> Executing: mpicc -o /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm >>> Possible ERROR while running linker: >>> stderr: >>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> compilers: Cannot compile/link C with mpicc. >>> >>>> On 12 Mar 2021, at 6:16 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>>> >>>> >>>> You should be able to edit lib/petsc/conf/rules and add it to the filter for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc .F90.PETSc: >>>> >>>> I think it is fine to hide this warning; it is impossible for me to understand anyway :-(. >>>> >>>> Barry >>>> >>>> >>>> >>>> >>>>> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >>>>> >>>>> Sorry to dig up this old thread, but this is triggering false positives while make checking for people who don’t want to toy around with MACOSX_DEPLOYMENT_TARGET. >>>>> Could/should we filter this somehow, or have BuildSystem tinker with the environment variable itself? >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> $ make check >>>>> Running check examples to verify correct installation >>>>> Using PETSC_DIR=/Users/jolivet/repo/petsc and PETSC_ARCH=arch-darwin-c-debug-real >>>>> *******************Error detected during compile or link!******************* >>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> >>>>> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >>>>> ********************************************************************************* >>>>> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g -I/Users/jolivet/repo/petsc/include -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include -I/opt/intel/mkl/include ex19.c -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >>>>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.1) than being linked (11.0) >>>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>>>> >>>>> >>>>>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>>> >>>>>> Yes, this also seems to work on my end. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Jacob Faibussowitsch >>>>>> (Jacob Fai - booss - oh - vitch) >>>>>> Cell: (312) 694-3391 >>>>>> >>>>>>> On Feb 15, 2021, at 12:05, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: >>>>>>> >>>>>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>>>>> >>>>>>> Satish >>>>>>> >>>>>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>> >>>>>>>> I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: >>>>>>>> >>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>>> >>>>>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Jacob Faibussowitsch >>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>> Cell: (312) 694-3391 >>>>>>>> >>>>>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>>> >>>>>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> Jacob Faibussowitsch >>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>> Cell: (312) 694-3391 >>>>>>>>> >>>>>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>>> >>>>>>>>>> I can reproduce the warning compiling just that simple code you listed. This is the compile command: >>>>>>>>>> >>>>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>>>>> >>>>>>>>>> And error: >>>>>>>>>> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> >>>>>>>>>> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. >>>>>>>>>> >>>>>>>>>> Best regards, >>>>>>>>>> >>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>> Cell: (312) 694-3391 >>>>>>>>>> >>>>>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>>>> >>>>>>>>>>> Here is the compile command and the warning: >>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>> ===== Checking linker >>>>>>>>>>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>>>>> Successful compile: >>>>>>>>>>> Source: >>>>>>>>>>> function foo(a) >>>>>>>>>>> real:: a,x,bar >>>>>>>>>>> common /xx/ x >>>>>>>>>>> x=a >>>>>>>>>>> foo = bar(x) >>>>>>>>>>> end >>>>>>>>>>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>>>> Possible ERROR while running linker: >>>>>>>>>>> stderr: >>>>>>>>>>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>>>>> ============================================================================================= >>>>>>>>>>> <<<<<< >>>>>>>>>>> >>>>>>>>>>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. >>>>>>>>>>> >>>>>>>>>>> There is a related issue at: >>>>>>>>>>> >>>>>>>>>>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> <https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644>> >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello All, >>>>>>>>>>>> >>>>>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. >>>>>>>>>>>> >>>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>>> >>>>>>>>>>>> Best regards, >>>>>>>>>>>> >>>>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>>>> Cell: (312) 694-3391 >>>>>> >>>>> >>>> >>> >> >

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Re: [petsc-dev] p4est w/o MPI
by Isaac, Tobin G 16 Apr '21

16 Apr '21

Understandable, p4est has its own minimal pseudo-mpi interface, I'll work with Satish and the other p4est devs to a simple way to keep the MPIUNI / MPIP4EST from colliding. ________________________________________ From: Barry Smith <bsmith(a)petsc.dev> Sent: Friday, April 16, 2021 16:10 To: Isaac, Tobin G Cc: petsc-dev Subject: Re: [petsc-dev] p4est w/o MPI Toby, It was never our intention that MPIUNI support any other packages besides PETSc/SLEPc as an "mpi substitute". There are just so many fragile aspects to it. I think it is is best if p4est maintains its own non-MPI version (if it wants to have such as thing) and does not have it involve MPIUNI. Barry On Apr 16, 2021, at 12:53 PM, Isaac, Tobin G <tisaac(a)cc.gatech.edu<mailto:[email protected]>> wrote: Hmm. So if petsc always compiles mpiuni if --with-mpi=0, then it makes me think it should be possible to drop requires(MPI) from p4est, while still passing `--enable-mpi` to p4est. Maybe: if mpiuni doesn't provide some esoteric part of MPI that p4est uses, it will break. Toby Isaac, Assistant Professor, GTCSE ________________________________ From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> Sent: Friday, April 16, 2021 1:03:55 PM To: Isaac, Tobin G <tisaac(a)cc.gatech.edu<mailto:[email protected]>> Cc: petsc-dev <petsc-dev(a)mcs.anl.gov<mailto:[email protected]>> Subject: Re: [petsc-dev] p4est w/o MPI Thanks! Another issue: mpiuni provides mpi.h. And I get the following errors when building PETSc. /home/balay/petsc/arch-linux-c-debug/include/sc.h:87:2: error: #error "mpi.h is included. Use --enable-mpi." 87 | #error "mpi.h is included. Use --enable-mpi." | ^~~~~ etc.. Satish On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > Yes, `--disable-mpi` should be accepted by p4est. > > ________________________________________ > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > Sent: Friday, April 16, 2021 11:47 > To: Satish Balay via petsc-dev > Cc: Isaac, Tobin G > Subject: Re: [petsc-dev] p4est w/o MPI > > BTW: Is there no --disable-mpi option? > > Satish > > On Fri, 16 Apr 2021, Satish Balay via petsc-dev wrote: > > > MPI pacakge is a bit weird compared to others [as it does this funny thing with MPIUNI]. > > > > For regular packages - I guess I would use 'if package.found' > > > > I guess I should create an MR with this diff. > > > > Satish > > > > ---- > > > > diff --git a/config/BuildSystem/config/packages/p4est.py b/config/BuildSystem/config/packages/p4est.py > > index e7108b0ab8..40d6797f02 100644 > > --- a/config/BuildSystem/config/packages/p4est.py > > +++ b/config/BuildSystem/config/packages/p4est.py > > @@ -24,14 +24,16 @@ class Configure(config.package.GNUPackage): > > self.blasLapack = framework.require('config.packages.BlasLapack',self) > > self.zlib = framework.require('config.packages.zlib',self) > > self.memalign = framework.argDB['with-memalign'] > > - self.deps = [self.mpi,self.blasLapack,self.zlib] > > + self.deps = [self.blasLapack,self.zlib] > > + self.odeps = [self.mpi] > > return > > > > def formGNUConfigureArgs(self): > > args = config.package.GNUPackage.formGNUConfigureArgs(self) > > if self.argDB['with-p4est-debugging']: > > args.append('--enable-debug') > > - args.append('--enable-mpi') > > + if not self.mpi.usingMPIUni: > > + args.append('--enable-mpi') > > args.append('CPPFLAGS="'+self.headers.toStringNoDupes(self.dinclude)+'"') > > args.append('LIBS="'+self.libraries.toString(self.dlib)+'"') > > args.append('--enable-memalign='+self.memalign) > > > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > > > Matt, this is the configure logic I would like, but I don't know how to do it: > > > - configure p4est after MPI, but do not require MPI > > > - if MPI is present, add the '--enable-mpi' flack in formGNUConfigureArgs(), otherwise omit it. > > > > > > ________________________________________ > > > From: Isaac, Tobin G <tisaac(a)cc.gatech.edu<mailto:[email protected]>> > > > Sent: Friday, April 16, 2021 11:03 > > > To: Mark Adams; For users of the development version of PETSc > > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > > > p4est has a mode where it can compile without MPI, I don't know if PETSc is using it, will check. > > > > > > ________________________________________ > > > From: petsc-dev <petsc-dev-bounces(a)mcs.anl.gov<mailto:[email protected]>> on behalf of Mark Adams <mfadams(a)lbl.gov<mailto:[email protected]>> > > > Sent: Friday, April 16, 2021 10:23 > > > To: For users of the development version of PETSc > > > Subject: [petsc-dev] p4est w/o MPI > > > > > > I don't have MPI (Fugaku w/ gcc) and p4est seems to need it. Is there a work around? > > > Thanks, > > > Mark > > > > > >

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Jacob Faibussowitsch 16 Apr '21

16 Apr '21

> I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? At least on my end, none of them are possible without setting MAOSX_DEPLOYMENT_TARGET or --LDFLAGS=-mmacosx-version-min=11.2. Configure fails when it tests fortran linkage capability. Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) > On Apr 16, 2021, at 15:03, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? > > If so that should clearly be reported as a bug with all relevant information supplied. > > No, we have never and do not ever intend for PETSc users even developers to know or care about MACOSX_DEPLOYMENT_TARGET > > Anyways if you are reporting a bug and I am guess the bug correctly the fix is to add "was built for newer macOS version" to the list of filtered link warnings. There will be a bunch of such warnings that will need to be added to the filtering in the next few months but once they are in place the filtering should not be an issue. > > > Barry > > > >> On Apr 16, 2021, at 6:20 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >> >> Barry, >> That issue + this commit: >> $ git bisect bad >> 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit >> commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 >> Author: Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> >> Date: Sat Apr 10 13:40:10 2021 -0500 >> makes it actually impossible to ./configure on macOS. >> Do we really expect all macOS users to know about the variable MACOSX_DEPLOYMENT_TARGET? >> >> Thanks, >> Pierre >> >> $ ./configure >> =============================================================================== >> Configuring PETSc to compile on your system >> =============================================================================== >> TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) >> ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >> ------------------------------------------------------------------------------- >> Fortran libraries cannot be used with C as linker >> ******************************************************************************* >> >> Executing: mpicc -o /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm >> Possible ERROR while running linker: >> stderr: >> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> compilers: Cannot compile/link C with mpicc. >> >>> On 12 Mar 2021, at 6:16 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>> >>> >>> You should be able to edit lib/petsc/conf/rules and add it to the filter for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc .F90.PETSc: >>> >>> I think it is fine to hide this warning; it is impossible for me to understand anyway :-(. >>> >>> Barry >>> >>> >>> >>> >>>> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >>>> >>>> Sorry to dig up this old thread, but this is triggering false positives while make checking for people who don’t want to toy around with MACOSX_DEPLOYMENT_TARGET. >>>> Could/should we filter this somehow, or have BuildSystem tinker with the environment variable itself? >>>> >>>> Thanks, >>>> Pierre >>>> >>>> $ make check >>>> Running check examples to verify correct installation >>>> Using PETSC_DIR=/Users/jolivet/repo/petsc and PETSC_ARCH=arch-darwin-c-debug-real >>>> *******************Error detected during compile or link!******************* >>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> >>>> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >>>> ********************************************************************************* >>>> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g -I/Users/jolivet/repo/petsc/include -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include -I/opt/intel/mkl/include ex19.c -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >>>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.1) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>>> >>>> >>>>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>> >>>>> Yes, this also seems to work on my end. >>>>> >>>>> Best regards, >>>>> >>>>> Jacob Faibussowitsch >>>>> (Jacob Fai - booss - oh - vitch) >>>>> Cell: (312) 694-3391 >>>>> >>>>>> On Feb 15, 2021, at 12:05, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: >>>>>> >>>>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>>>> >>>>>> Satish >>>>>> >>>>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>>>> >>>>>>> I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: >>>>>>> >>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>> >>>>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> Jacob Faibussowitsch >>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>> Cell: (312) 694-3391 >>>>>>> >>>>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>> >>>>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Jacob Faibussowitsch >>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>> Cell: (312) 694-3391 >>>>>>>> >>>>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>> >>>>>>>>> I can reproduce the warning compiling just that simple code you listed. This is the compile command: >>>>>>>>> >>>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>>>> >>>>>>>>> And error: >>>>>>>>> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> >>>>>>>>> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> Jacob Faibussowitsch >>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>> Cell: (312) 694-3391 >>>>>>>>> >>>>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is the compile command and the warning: >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>> ===== Checking linker >>>>>>>>>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>>>> Successful compile: >>>>>>>>>> Source: >>>>>>>>>> function foo(a) >>>>>>>>>> real:: a,x,bar >>>>>>>>>> common /xx/ x >>>>>>>>>> x=a >>>>>>>>>> foo = bar(x) >>>>>>>>>> end >>>>>>>>>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>>> Possible ERROR while running linker: >>>>>>>>>> stderr: >>>>>>>>>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>>>> ============================================================================================= >>>>>>>>>> <<<<<< >>>>>>>>>> >>>>>>>>>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. >>>>>>>>>> >>>>>>>>>> There is a related issue at: >>>>>>>>>> >>>>>>>>>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> <https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644>> >>>>>>>>>> >>>>>>>>>> Satish >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>>>> >>>>>>>>>>> Hello All, >>>>>>>>>>> >>>>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. >>>>>>>>>>> >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> >>>>>>>>>>> Best regards, >>>>>>>>>>> >>>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>>> Cell: (312) 694-3391 >>>>> >>>> >>> >> >

1 0

Re: [petsc-dev] Fortran macOS Linkage Warning
by Pierre Jolivet 16 Apr '21

16 Apr '21

> On 16 Apr 2021, at 10:03 PM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? I’m unable to configure. $ git clone https://gitlab.com/petsc/petsc Cloning into 'petsc'... warning: redirecting to https://gitlab.com/petsc/petsc.git/ remote: Enumerating objects: 64141, done. remote: Counting objects: 100% (64141/64141), done. remote: Compressing objects: 100% (7098/7098), done. remote: Total 939408 (delta 62202), reused 57532 (delta 57038), pack-reused 875267 Receiving objects: 100% (939408/939408), 267.66 MiB | 1.07 MiB/s, done. Resolving deltas: 100% (720467/720467), done. Updating files: 100% (9849/9849), done. $ cd petsc $ export PETSC_DIR=`pwd` $ ./configure =============================================================================== Configuring PETSc to compile on your system =============================================================================== TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran libraries cannot be used with C as linker ******************************************************************************* configure.log is there: http://joliv.et/configure_broken_fortran_filter.log <http://joliv.et/configure_broken_fortran_filter.log> Workaround is: MACOSX_DEPLOYMENT_TARGET=11.2 ./configure FFLAGS="-mmacosx-version-min=11.2" I tried setting one and not the other additional flag but I respectively had failures re-compiling ParMETIS or Elemental. Thanks, Pierre > > If so that should clearly be reported as a bug with all relevant information supplied. > > No, we have never and do not ever intend for PETSc users even developers to know or care about MACOSX_DEPLOYMENT_TARGET > > Anyways if you are reporting a bug and I am guess the bug correctly the fix is to add "was built for newer macOS version" to the list of filtered link warnings. There will be a bunch of such warnings that will need to be added to the filtering in the next few months but once they are in place the filtering should not be an issue. > > > Barry > > > >> On Apr 16, 2021, at 6:20 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >> >> Barry, >> That issue + this commit: >> $ git bisect bad >> 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit >> commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 >> Author: Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> >> Date: Sat Apr 10 13:40:10 2021 -0500 >> makes it actually impossible to ./configure on macOS. >> Do we really expect all macOS users to know about the variable MACOSX_DEPLOYMENT_TARGET? >> >> Thanks, >> Pierre >> >> $ ./configure >> =============================================================================== >> Configuring PETSc to compile on your system >> =============================================================================== >> TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) >> ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >> ------------------------------------------------------------------------------- >> Fortran libraries cannot be used with C as linker >> ******************************************************************************* >> >> Executing: mpicc -o /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm >> Possible ERROR while running linker: >> stderr: >> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >> compilers: Cannot compile/link C with mpicc. >> >>> On 12 Mar 2021, at 6:16 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >>> >>> >>> You should be able to edit lib/petsc/conf/rules and add it to the filter for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc .F90.PETSc: >>> >>> I think it is fine to hide this warning; it is impossible for me to understand anyway :-(. >>> >>> Barry >>> >>> >>> >>> >>>> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >>>> >>>> Sorry to dig up this old thread, but this is triggering false positives while make checking for people who don’t want to toy around with MACOSX_DEPLOYMENT_TARGET. >>>> Could/should we filter this somehow, or have BuildSystem tinker with the environment variable itself? >>>> >>>> Thanks, >>>> Pierre >>>> >>>> $ make check >>>> Running check examples to verify correct installation >>>> Using PETSC_DIR=/Users/jolivet/repo/petsc and PETSC_ARCH=arch-darwin-c-debug-real >>>> *******************Error detected during compile or link!******************* >>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> >>>> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >>>> ********************************************************************************* >>>> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g -I/Users/jolivet/repo/petsc/include -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include -I/opt/intel/mkl/include ex19.c -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >>>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.1) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) was built for newer macOS version (11.2) than being linked (11.0) >>>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>>> >>>> >>>>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>> >>>>> Yes, this also seems to work on my end. >>>>> >>>>> Best regards, >>>>> >>>>> Jacob Faibussowitsch >>>>> (Jacob Fai - booss - oh - vitch) >>>>> Cell: (312) 694-3391 >>>>> >>>>>> On Feb 15, 2021, at 12:05, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: >>>>>> >>>>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>>>> >>>>>> Satish >>>>>> >>>>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>>>> >>>>>>> I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: >>>>>>> >>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>> >>>>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> Jacob Faibussowitsch >>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>> Cell: (312) 694-3391 >>>>>>> >>>>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>>> >>>>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Jacob Faibussowitsch >>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>> Cell: (312) 694-3391 >>>>>>>> >>>>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>> >>>>>>>>> I can reproduce the warning compiling just that simple code you listed. This is the compile command: >>>>>>>>> >>>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>>>> >>>>>>>>> And error: >>>>>>>>> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> >>>>>>>>> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> Jacob Faibussowitsch >>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>> Cell: (312) 694-3391 >>>>>>>>> >>>>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>>> >>>>>>>>>> Here is the compile command and the warning: >>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>> ===== Checking linker >>>>>>>>>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>>>> Successful compile: >>>>>>>>>> Source: >>>>>>>>>> function foo(a) >>>>>>>>>> real:: a,x,bar >>>>>>>>>> common /xx/ x >>>>>>>>>> x=a >>>>>>>>>> foo = bar(x) >>>>>>>>>> end >>>>>>>>>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>>> Possible ERROR while running linker: >>>>>>>>>> stderr: >>>>>>>>>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>>>> ============================================================================================= >>>>>>>>>> <<<<<< >>>>>>>>>> >>>>>>>>>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. >>>>>>>>>> >>>>>>>>>> There is a related issue at: >>>>>>>>>> >>>>>>>>>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> <https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644>> >>>>>>>>>> >>>>>>>>>> Satish >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>>>> >>>>>>>>>>> Hello All, >>>>>>>>>>> >>>>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. >>>>>>>>>>> >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>>> >>>>>>>>>>> Best regards, >>>>>>>>>>> >>>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>>> Cell: (312) 694-3391 >>>>> >>>> >>> >> >

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Re: [petsc-dev] p4est w/o MPI
by Satish Balay 16 Apr '21

16 Apr '21

On Fri, 16 Apr 2021, Matthew Knepley wrote: > Hmm, this looks like an MPIUNI memory leak with split collectives. I will > have to spin up that configuration and track it down. with mpich: Breakpoint 2, PetscSplitReductionDestroy (sr=sr@entry=0xd457d0) at /home/balay/petsc/src/vec/vec/utils/comb.c:267 267 { (gdb) where #0 PetscSplitReductionDestroy (sr=sr@entry=0xd457d0) at /home/balay/petsc/src/vec/vec/utils/comb.c:267 #1 0x00007ffff66f0a3a in Petsc_DelReduction (comm=<optimized out>, keyval=<optimized out>, attr_val=0xd457d0, extra_state=<optimized out>) at /home/balay/petsc/src/vec/vec/utils/comb.c:291 #2 0x00007ffff53dec55 in MPII_Attr_delete_c_proxy (user_function=0x7ffff66f095e <Petsc_DelReduction>, handle=-2080374784, keyval=-1539309563, attrib_type=MPIR_ATTR_PTR, attrib=0xd457d0, extra_state=0x0) at src/mpi/attr/attrutil.c:347 #3 0x00007ffff53de385 in MPIR_Call_attr_delete (handle=-2080374784, attr_p=0x7ffff56dd5e8 <MPID_Attr_direct+392>) at src/mpi/attr/attrutil.c:95 #4 0x00007ffff53de6ea in MPIR_Attr_delete_list (handle=-2080374784, attr=0x7ffff56de208 <MPIR_Comm_direct+72>) at src/mpi/attr/attrutil.c:266 #5 0x00007ffff545208b in MPIR_Comm_delete_internal (comm_ptr=0x7ffff56de1c0 <MPIR_Comm_direct>) at src/mpi/comm/commutil.c:756 #6 0x00007ffff5331000 in MPIR_Comm_release (comm_ptr=0x7ffff56de1c0 <MPIR_Comm_direct>) at ./src/include/mpir_comm.h:233 #7 0x00007ffff53310a1 in MPIR_Comm_free_impl (comm_ptr=0x7ffff56de1c0 <MPIR_Comm_direct>) at src/mpi/comm/comm_free.c:35 #8 0x00007ffff53314a0 in PMPI_Comm_free (comm=0x7fffffffa178) at src/mpi/comm/comm_free.c:127 #9 0x00007ffff65401fa in PetscCommDestroy (comm=comm@entry=0x625920) at /home/balay/petsc/src/sys/objects/tagm.c:217 #10 0x00007ffff6547c48 in PetscHeaderDestroy_Private (h=0x6258e0) at /home/balay/petsc/src/sys/objects/inherit.c:121 #11 0x00007ffff7017f3e in PetscP4estFinalize () at /home/balay/petsc/src/dm/impls/forest/p4est/petsc_p4est_package.c:47 #12 0x00007ffff6543270 in PetscRegisterFinalizeAll () at /home/balay/petsc/src/sys/objects/destroy.c:389 #13 0x00007ffff657b7b1 in PetscFinalize () at /home/balay/petsc/src/sys/objects/pinit.c:1476 #14 0x000000000040b51a in main (argc=<optimized out>, argv=<optimized out>) at ex12.c:1249 (gdb) with mpiuni - there is no call to PetscSplitReductionDestroy() I guess this mechanism doesn't work with mpiuni Satish ------ PETSC_EXTERN void petsc_mpi_comm_free_(int *comm,int *ierr) { *ierr = MPI_SUCCESS; }

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Re: [petsc-dev] p4est w/o MPI
by Barry Smith 16 Apr '21

16 Apr '21

Toby, It was never our intention that MPIUNI support any other packages besides PETSc/SLEPc as an "mpi substitute". There are just so many fragile aspects to it. I think it is is best if p4est maintains its own non-MPI version (if it wants to have such as thing) and does not have it involve MPIUNI. Barry > On Apr 16, 2021, at 12:53 PM, Isaac, Tobin G <tisaac(a)cc.gatech.edu> wrote: > > Hmm. So if petsc always compiles mpiuni if --with-mpi=0, then it makes me think it should be possible to drop requires(MPI) from p4est, while still passing `--enable-mpi` to p4est. > > Maybe: if mpiuni doesn't provide some esoteric part of MPI that p4est uses, it will break. > > Toby Isaac, Assistant Professor, GTCSE > > From: Satish Balay <balay(a)mcs.anl.gov> > Sent: Friday, April 16, 2021 1:03:55 PM > To: Isaac, Tobin G <tisaac(a)cc.gatech.edu> > Cc: petsc-dev <petsc-dev(a)mcs.anl.gov> > Subject: Re: [petsc-dev] p4est w/o MPI > > Thanks! Another issue: > > mpiuni provides mpi.h. And I get the following errors when building PETSc. > > /home/balay/petsc/arch-linux-c-debug/include/sc.h:87:2: error: #error "mpi.h is included. Use --enable-mpi." > 87 | #error "mpi.h is included. Use --enable-mpi." > | ^~~~~ > > etc.. > > Satish > > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > Yes, `--disable-mpi` should be accepted by p4est. > > > > ________________________________________ > > From: Satish Balay <balay(a)mcs.anl.gov> > > Sent: Friday, April 16, 2021 11:47 > > To: Satish Balay via petsc-dev > > Cc: Isaac, Tobin G > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > BTW: Is there no --disable-mpi option? > > > > Satish > > > > On Fri, 16 Apr 2021, Satish Balay via petsc-dev wrote: > > > > > MPI pacakge is a bit weird compared to others [as it does this funny thing with MPIUNI]. > > > > > > For regular packages - I guess I would use 'if package.found' > > > > > > I guess I should create an MR with this diff. > > > > > > Satish > > > > > > ---- > > > > > > diff --git a/config/BuildSystem/config/packages/p4est.py b/config/BuildSystem/config/packages/p4est.py > > > index e7108b0ab8..40d6797f02 100644 > > > --- a/config/BuildSystem/config/packages/p4est.py > > > +++ b/config/BuildSystem/config/packages/p4est.py > > > @@ -24,14 +24,16 @@ class Configure(config.package.GNUPackage): > > > self.blasLapack = framework.require('config.packages.BlasLapack',self) > > > self.zlib = framework.require('config.packages.zlib',self) > > > self.memalign = framework.argDB['with-memalign'] > > > - self.deps = [self.mpi,self.blasLapack,self.zlib] > > > + self.deps = [self.blasLapack,self.zlib] > > > + self.odeps = [self.mpi] > > > return > > > > > > def formGNUConfigureArgs(self): > > > args = config.package.GNUPackage.formGNUConfigureArgs(self) > > > if self.argDB['with-p4est-debugging']: > > > args.append('--enable-debug') > > > - args.append('--enable-mpi') > > > + if not self.mpi.usingMPIUni: > > > + args.append('--enable-mpi') > > > args.append('CPPFLAGS="'+self.headers.toStringNoDupes(self.dinclude)+'"') > > > args.append('LIBS="'+self.libraries.toString(self.dlib)+'"') > > > args.append('--enable-memalign='+self.memalign) > > > > > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > > > > > Matt, this is the configure logic I would like, but I don't know how to do it: > > > > - configure p4est after MPI, but do not require MPI > > > > - if MPI is present, add the '--enable-mpi' flack in formGNUConfigureArgs(), otherwise omit it. > > > > > > > > ________________________________________ > > > > From: Isaac, Tobin G <tisaac(a)cc.gatech.edu> > > > > Sent: Friday, April 16, 2021 11:03 > > > > To: Mark Adams; For users of the development version of PETSc > > > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > > > > > p4est has a mode where it can compile without MPI, I don't know if PETSc is using it, will check. > > > > > > > > ________________________________________ > > > > From: petsc-dev <petsc-dev-bounces(a)mcs.anl.gov> on behalf of Mark Adams <mfadams(a)lbl.gov> > > > > Sent: Friday, April 16, 2021 10:23 > > > > To: For users of the development version of PETSc > > > > Subject: [petsc-dev] p4est w/o MPI > > > > > > > > I don't have MPI (Fugaku w/ gcc) and p4est seems to need it. Is there a work around? > > > > Thanks, > > > > Mark > > > > > > > > > >

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Re: [petsc-dev] Fortran macOS Linkage Warning
by Barry Smith 16 Apr '21

16 Apr '21

I am not sure what the point is here. Are you unable to configure? or make all? or make check PETSc? If so that should clearly be reported as a bug with all relevant information supplied. No, we have never and do not ever intend for PETSc users even developers to know or care about MACOSX_DEPLOYMENT_TARGET Anyways if you are reporting a bug and I am guess the bug correctly the fix is to add "was built for newer macOS version" to the list of filtered link warnings. There will be a bunch of such warnings that will need to be added to the filtering in the next few months but once they are in place the filtering should not be an issue. Barry > On Apr 16, 2021, at 6:20 AM, Pierre Jolivet <pierre(a)joliv.et> wrote: > > Barry, > That issue + this commit: > $ git bisect bad > 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit > commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 > Author: Barry Smith <bsmith(a)mcs.anl.gov <mailto:[email protected]>> > Date: Sat Apr 10 13:40:10 2021 -0500 > makes it actually impossible to ./configure on macOS. > Do we really expect all macOS users to know about the variable MACOSX_DEPLOYMENT_TARGET? > > Thanks, > Pierre > > $ ./configure > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > Fortran libraries cannot be used with C as linker > ******************************************************************************* > > Executing: mpicc -o /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm > Possible ERROR while running linker: > stderr: > ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) > ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) > compilers: Cannot compile/link C with mpicc. > >> On 12 Mar 2021, at 6:16 PM, Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: >> >> >> You should be able to edit lib/petsc/conf/rules and add it to the filter for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc .F90.PETSc: >> >> I think it is fine to hide this warning; it is impossible for me to understand anyway :-(. >> >> Barry >> >> >> >> >>> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>> wrote: >>> >>> Sorry to dig up this old thread, but this is triggering false positives while make checking for people who don’t want to toy around with MACOSX_DEPLOYMENT_TARGET. >>> Could/should we filter this somehow, or have BuildSystem tinker with the environment variable itself? >>> >>> Thanks, >>> Pierre >>> >>> $ make check >>> Running check examples to verify correct installation >>> Using PETSC_DIR=/Users/jolivet/repo/petsc and PETSC_ARCH=arch-darwin-c-debug-real >>> *******************Error detected during compile or link!******************* >>> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> >>> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >>> ********************************************************************************* >>> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -Wall -g -Wall -g -I/Users/jolivet/repo/petsc/include -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include -I/opt/intel/mkl/include ex19.c -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >>> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.1) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) was built for newer macOS version (11.2) than being linked (11.0) >>> ld: warning: object file (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) was built for newer macOS version (11.2) than being linked (11.0) >>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>> >>> >>>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>> >>>> Yes, this also seems to work on my end. >>>> >>>> Best regards, >>>> >>>> Jacob Faibussowitsch >>>> (Jacob Fai - booss - oh - vitch) >>>> Cell: (312) 694-3391 >>>> >>>>> On Feb 15, 2021, at 12:05, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]>> wrote: >>>>> >>>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>>> >>>>> Satish >>>>> >>>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>>> >>>>>> I think this problem ultimately stems from the fact that gcc/g++ and gfortran are not from the same people on macOS. It seems like clang is configured to build for 11.0 target, whilst gcc defaults to newest available target. And indeed if I change my compile command there is no warning: >>>>>> >>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>> >>>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not clang in a trench coat). >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Jacob Faibussowitsch >>>>>> (Jacob Fai - booss - oh - vitch) >>>>>> Cell: (312) 694-3391 >>>>>> >>>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]>> wrote: >>>>>>> >>>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning disappears... >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> Jacob Faibussowitsch >>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>> Cell: (312) 694-3391 >>>>>>> >>>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob.fai(a)gmail.com <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>> >>>>>>>> I can reproduce the warning compiling just that simple code you listed. This is the compile command: >>>>>>>> >>>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined dynamic_lookup && rm -rf ./build >>>>>>>> >>>>>>>> And error: >>>>>>>> ld: warning: object file (./build/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>> >>>>>>>> Note I recently uninstalled and reinstalled command line tools too, which does not seem to have fixed it. >>>>>>>> >>>>>>>> Best regards, >>>>>>>> >>>>>>>> Jacob Faibussowitsch >>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>> Cell: (312) 694-3391 >>>>>>>> >>>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <balay(a)mcs.anl.gov <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: >>>>>>>>> >>>>>>>>> Here is the compile command and the warning: >>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>> ===== Checking linker >>>>>>>>> Executing: gfortran -c -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>>> Successful compile: >>>>>>>>> Source: >>>>>>>>> function foo(a) >>>>>>>>> real:: a,x,bar >>>>>>>>> common /xx/ x >>>>>>>>> x=a >>>>>>>>> foo = bar(x) >>>>>>>>> end >>>>>>>>> Executing: gcc -o /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib -dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>>> Possible ERROR while running linker: >>>>>>>>> stderr: >>>>>>>>> ld: warning: object file (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>>> ============================================================================================= >>>>>>>>> <<<<<< >>>>>>>>> >>>>>>>>> Its likely due to the way brew built gfortran. You can try compiling a simple test code and see if you can reproduce this warning. >>>>>>>>> >>>>>>>>> There is a related issue at: >>>>>>>>> >>>>>>>>> https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644> <https://github.com/spack/spack/issues/21644 <https://github.com/spack/spack/issues/21644>> >>>>>>>>> >>>>>>>>> Satish >>>>>>>>> >>>>>>>>> >>>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>>> >>>>>>>>>> Hello All, >>>>>>>>>> >>>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it was due to gfortran brew package not being updated for Big Sur, but since it has persisted through a few gfortran brew updates I’m thinking it may be petsc related. This is on clean build on master. >>>>>>>>>> >>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> ld: warning: object file (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>>> >>>>>>>>>> Best regards, >>>>>>>>>> >>>>>>>>>> Jacob Faibussowitsch >>>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>>> Cell: (312) 694-3391 >>>> >>> >> >

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Re: [petsc-dev] p4est w/o MPI
by Matthew Knepley 16 Apr '21

16 Apr '21

On Fri, Apr 16, 2021 at 2:06 PM Satish Balay via petsc-dev < petsc-dev(a)mcs.anl.gov> wrote: > Sure that might work. Also just commenting out the 3 lines for that check > got the build going for me. > > Or a simple change (but a bit intrusive): > > [balay@pj01 petsc]$ diff -Nru ./arch-linux-c-debug/include/sc.h~ > ./arch-linux-c-debug/include/sc.h > --- ./arch-linux-c-debug/include/sc.h~ 2021-04-16 12:59:20.803995227 -0500 > +++ ./arch-linux-c-debug/include/sc.h 2021-04-16 13:00:06.490993496 -0500 > @@ -83,7 +83,7 @@ > #ifdef SC_ENABLE_MPI > #include <mpi.h> > #else > -#ifdef MPI_SUCCESS > +#if defined(MPI_SUCCESS) && !defined(MPIUNI_H) > #error "mpi.h is included. Use --enable-mpi." > #endif > #endif > > Also getting test suite errors - Matt might have to check on. [attaching > log] > Hmm, this looks like an MPIUNI memory leak with split collectives. I will have to spin up that configuration and track it down. Matt > Satish > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > Hmm. So if petsc always compiles mpiuni if --with-mpi=0, then it makes > me think it should be possible to drop requires(MPI) from p4est, while > still passing `--enable-mpi` to p4est. > > > > Maybe: if mpiuni doesn't provide some esoteric part of MPI that p4est > uses, it will break. > > > > Toby Isaac, Assistant Professor, GTCSE > > > > ________________________________ > > From: Satish Balay <balay(a)mcs.anl.gov> > > Sent: Friday, April 16, 2021 1:03:55 PM > > To: Isaac, Tobin G <tisaac(a)cc.gatech.edu> > > Cc: petsc-dev <petsc-dev(a)mcs.anl.gov> > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > Thanks! Another issue: > > > > mpiuni provides mpi.h. And I get the following errors when building > PETSc. > > > > /home/balay/petsc/arch-linux-c-debug/include/sc.h:87:2: error: #error > "mpi.h is included. Use --enable-mpi." > > 87 | #error "mpi.h is included. Use --enable-mpi." > > | ^~~~~ > > > > etc.. > > > > Satish > > > > > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > > > Yes, `--disable-mpi` should be accepted by p4est. > > > > > > ________________________________________ > > > From: Satish Balay <balay(a)mcs.anl.gov> > > > Sent: Friday, April 16, 2021 11:47 > > > To: Satish Balay via petsc-dev > > > Cc: Isaac, Tobin G > > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > > > BTW: Is there no --disable-mpi option? > > > > > > Satish > > > > > > On Fri, 16 Apr 2021, Satish Balay via petsc-dev wrote: > > > > > > > MPI pacakge is a bit weird compared to others [as it does this funny > thing with MPIUNI]. > > > > > > > > For regular packages - I guess I would use 'if package.found' > > > > > > > > I guess I should create an MR with this diff. > > > > > > > > Satish > > > > > > > > ---- > > > > > > > > diff --git a/config/BuildSystem/config/packages/p4est.py > b/config/BuildSystem/config/packages/p4est.py > > > > index e7108b0ab8..40d6797f02 100644 > > > > --- a/config/BuildSystem/config/packages/p4est.py > > > > +++ b/config/BuildSystem/config/packages/p4est.py > > > > @@ -24,14 +24,16 @@ class Configure(config.package.GNUPackage): > > > > self.blasLapack = > framework.require('config.packages.BlasLapack',self) > > > > self.zlib = framework.require('config.packages.zlib',self) > > > > self.memalign = framework.argDB['with-memalign'] > > > > - self.deps = [self.mpi,self.blasLapack,self.zlib] > > > > + self.deps = [self.blasLapack,self.zlib] > > > > + self.odeps = [self.mpi] > > > > return > > > > > > > > def formGNUConfigureArgs(self): > > > > args = config.package.GNUPackage.formGNUConfigureArgs(self) > > > > if self.argDB['with-p4est-debugging']: > > > > args.append('--enable-debug') > > > > - args.append('--enable-mpi') > > > > + if not self.mpi.usingMPIUni: > > > > + args.append('--enable-mpi') > > > > > args.append('CPPFLAGS="'+self.headers.toStringNoDupes(self.dinclude)+'"') > > > > args.append('LIBS="'+self.libraries.toString(self.dlib)+'"') > > > > args.append('--enable-memalign='+self.memalign) > > > > > > > > On Fri, 16 Apr 2021, Isaac, Tobin G wrote: > > > > > > > > > Matt, this is the configure logic I would like, but I don't know > how to do it: > > > > > - configure p4est after MPI, but do not require MPI > > > > > - if MPI is present, add the '--enable-mpi' flack in > formGNUConfigureArgs(), otherwise omit it. > > > > > > > > > > ________________________________________ > > > > > From: Isaac, Tobin G <tisaac(a)cc.gatech.edu> > > > > > Sent: Friday, April 16, 2021 11:03 > > > > > To: Mark Adams; For users of the development version of PETSc > > > > > Subject: Re: [petsc-dev] p4est w/o MPI > > > > > > > > > > p4est has a mode where it can compile without MPI, I don't know if > PETSc is using it, will check. > > > > > > > > > > ________________________________________ > > > > > From: petsc-dev <petsc-dev-bounces(a)mcs.anl.gov> on behalf of Mark > Adams <mfadams(a)lbl.gov> > > > > > Sent: Friday, April 16, 2021 10:23 > > > > > To: For users of the development version of PETSc > > > > > Subject: [petsc-dev] p4est w/o MPI > > > > > > > > > > I don't have MPI (Fugaku w/ gcc) and p4est seems to need it. Is > there a work around? > > > > > Thanks, > > > > > Mark > > > > > > > > > > > > > > > > > -- 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 https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] [EXTERNAL] Re: building on Fugaku
by Sreepathi, Sarat 16 Apr '21

16 Apr '21

It’s 48 cores but there are 4 NUMA domains (CMGs). So, you may want to experiment in hybrid mode (4x12 etc.) if possible. -Sarat. From: Mark Adams <mfadams(a)lbl.gov> Sent: Friday, April 16, 2021 2:10 PM To: petsc-dev <petsc-dev(a)mcs.anl.gov> Cc: Satish Balay <balay(a)mcs.anl.gov>; Sreepathi, Sarat <sarat(a)ornl.gov> Subject: Re: [petsc-dev] [EXTERNAL] Re: building on Fugaku Sarat, is there anything special that you do for Kokkos - OpenMP? Just set OMP_NUM_THREADS=48 ? Also, I am confused about the number of cores here. Is 48 or 64 per node/socket? On Fri, Apr 16, 2021 at 2:03 PM Mark Adams <mfadams(a)lbl.gov<mailto:[email protected]>> wrote: Cool, I have it running too. Need to add Sarat's flags and test ex2. On Fri, Apr 16, 2021 at 1:57 PM Satish Balay via petsc-dev <petsc-dev(a)mcs.anl.gov<mailto:[email protected]>> wrote: Mark, The following build works for me: Satish ---- pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L "elapse=1:00:00" --sparam "wait-time=1200" . /vol0004/apps/oss/spack/share/spack/setup-env.sh spack load fujitsu-mpi%gcc spack load gcc(a)10.2.0<mailto:[email protected]> arch=linux-rhel8-a64fx ./configure COPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' CXXOPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' FOPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' --with-openmp=1 --download-p4est --download-zlib --download-kokkos --download-kokkos-kernels --download-kokkos-commit=origin/develop --download-kokkos-kernels-commit=origin/develop '--download-kokkos-cmake-arguments=-DBUILD_TESTING=OFF -DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON' --download-cmake=https://github.com/Kitware/CMake/releases/download/v3.20.1/cmake-3.20.1.tar.gz --download-fblaslapack=1 make PETSC_DIR=/vol0004/ra010009/a04201/petsc.z PETSC_ARCH=arch-linux-c-debug all To test - redo job allocation using max-proc-per-node: login6$ pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L "elapse=1:00:00" --sparam "wait-time=1200" --mpi "max-proc-per-node=16" [a04201@c31-3201c petsc.z]$ . /vol0004/apps/oss/spack/share/spack/setup-env.sh [a04201@c31-3201c petsc.z]$ spack load fujitsu-mpi%gcc [a04201@c31-3201c petsc.z]$ spack load gcc(a)10.2.0<mailto:[email protected]> arch=linux-rhel8-a64fx [a04201@c31-3201c petsc.z]$ make check Running check examples to verify correct installation Using PETSC_DIR=/vol0004/ra010009/a04201/petsc.z and PETSC_ARCH=arch-linux-c-debug C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process Completed test examples [a04201@c31-3201c petsc.z]$

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Re: [petsc-dev] [EXTERNAL] Re: building on Fugaku
by Mark Adams 16 Apr '21

16 Apr '21

Sarat, is there anything special that you do for Kokkos - OpenMP? Just set OMP_NUM_THREADS=48 ? Also, I am confused about the number of cores here. Is 48 or 64 per node/socket? On Fri, Apr 16, 2021 at 2:03 PM Mark Adams <mfadams(a)lbl.gov> wrote: > Cool, I have it running too. Need to add Sarat's flags and test ex2. > > On Fri, Apr 16, 2021 at 1:57 PM Satish Balay via petsc-dev < > petsc-dev(a)mcs.anl.gov> wrote: > >> Mark, >> >> The following build works for me: >> >> Satish >> >> ---- >> >> pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L >> "elapse=1:00:00" --sparam "wait-time=1200" >> >> . /vol0004/apps/oss/spack/share/spack/setup-env.sh >> spack load fujitsu-mpi%gcc >> spack load gcc(a)10.2.0 arch=linux-rhel8-a64fx >> ./configure COPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' >> CXXOPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' >> FOPTFLAGS='-Ofast -march=armv8.2-a+sve -msve-vector-bits=512' >> --with-openmp=1 --download-p4est --download-zlib --download-kokkos >> --download-kokkos-kernels --download-kokkos-commit=origin/develop >> --download-kokkos-kernels-commit=origin/develop >> '--download-kokkos-cmake-arguments=-DBUILD_TESTING=OFF >> -DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON' >> --download-cmake= >> https://github.com/Kitware/CMake/releases/download/v3.20.1/cmake-3.20.1.tar… >> --download-fblaslapack=1 >> make PETSC_DIR=/vol0004/ra010009/a04201/petsc.z >> PETSC_ARCH=arch-linux-c-debug all >> >> >> To test - redo job allocation using max-proc-per-node: >> >> login6$ pjsub --interact -L "node=1" -L "rscunit=rscunit_ft01" -L >> "elapse=1:00:00" --sparam "wait-time=1200" --mpi "max-proc-per-node=16" >> >> [a04201@c31-3201c petsc.z]$ . >> /vol0004/apps/oss/spack/share/spack/setup-env.sh >> [a04201@c31-3201c petsc.z]$ spack load fujitsu-mpi%gcc >> [a04201@c31-3201c petsc.z]$ spack load gcc(a)10.2.0 arch=linux-rhel8-a64fx >> [a04201@c31-3201c petsc.z]$ make check >> Running check examples to verify correct installation >> Using PETSC_DIR=/vol0004/ra010009/a04201/petsc.z and >> PETSC_ARCH=arch-linux-c-debug >> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI >> processes >> C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels >> Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI >> process >> Completed test examples >> [a04201@c31-3201c petsc.z]$ >> >

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