[petsc-users] Install PETSc with option `--with-shared-libraries=1` failed on MacOS
Satish Balay
balay at mcs.anl.gov
Mon Mar 18 11:13:02 CDT 2024
Ah - the compiler did flag code bugs.
> (current version is 0.3.26 but we can’t update because there is a huge performance regression which makes the pipeline timeout)
maybe we should retry - updating to the latest snapshot and see if this issue persists.
Satish
On Mon, 18 Mar 2024, Zongze Yang wrote:
> The issue of openblas was resolved by this pr https://urldefense.us/v3/__https://github.com/OpenMathLib/OpenBLAS/pull/4565__;!!G_uCfscf7eWS!b09n5clcTFuLceLY_9KfqtSsgmmCIBLFbqciRVCKvnvFw9zTaNF8ssK0MiQlBOXUJe7H88nl-7ExdfhB-cMXLQ2d$
>
> Best wishes,
> Zongze
>
> > On 18 Mar 2024, at 00:50, Zongze Yang <yangzongze at gmail.com> wrote:
> >
> > It can be resolved by adding CFLAGS=-Wno-int-conversion. Perhaps the default behaviour of the new version compiler has been changed?
> >
> > Best wishes,
> > Zongze
> >> On 18 Mar 2024, at 00:23, Satish Balay <balay at mcs.anl.gov> wrote:
> >>
> >> Hm - I just tried a build with balay/xcode15-mpich - and that goes through fine for me. So don't know what the difference here is.
> >>
> >> One difference is - I have a slightly older xcode. However your compiler appears to behave as using -Werror. Perhaps CFLAGS=-Wno-int-conversion will help here?
> >>
> >> Satish
> >>
> >> ----
> >> Executing: gcc --version
> >> stdout:
> >> Apple clang version 15.0.0 (clang-1500.3.9.4)
> >>
> >> Executing: /Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/bin/mpicc -show
> >> stdout: gcc -fPIC -fno-stack-check -Qunused-arguments -g -O0 -Wno-implicit-function-declaration -fno-common -I/Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/include -L/Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/lib -lmpi -lpmpi
> >>
> >> /Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/bin/mpicc -O2 -DMAX_STACK_ALLOC=2048 -Wall -DF_INTERFACE_GFORT -fPIC -DNO_WARMUP -DMAX_CPU_NUMBER=12 -DMAX_PARALLEL_NUMBER=1 -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.21\" -march=armv8-a -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_lapack_wrappers -DASMFNAME=_lapack_wrappers_ -DNAME=lapack_wrappers_ -DCNAME=lapack_wrappers -DCHAR_NAME=\"lapack_wrappers_\" -DCHAR_CNAME=\"lapack_wrappers\" -DNO_AFFINITY -I.. -c src/lapack_wrappers.c -o src/lapack_wrappers.o
> >> src/lapack_wrappers.c:570:81: error: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >> RELAPACK_sgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >> ^~~~
> >> &
> >>
> >> vs:
> >> Executing: gcc --version
> >> stdout:
> >> Apple clang version 15.0.0 (clang-1500.1.0.2.5)
> >>
> >> Executing: /Users/balay/petsc/arch-darwin-c-debug/bin/mpicc -show
> >> stdout: gcc -fPIC -fno-stack-check -Qunused-arguments -g -O0 -Wno-implicit-function-declaration -fno-common -I/Users/balay/petsc/arch-darwin-c-debug/include -L/Users/balay/petsc/arch-darwin-c-debug/lib -lmpi -lpmpi
> >>
> >>
> >> /Users/balay/petsc/arch-darwin-c-debug/bin/mpicc -O2 -DMAX_STACK_ALLOC=2048 -Wall -DF_INTERFACE_GFORT -fPIC -DNO_WARMUP -DMAX_CPU_NUMBER=24 -DMAX_PARALLEL_NUMBER=1 -DBUILD_SINGLE=1 -DBUILD_DOUBLE=1 -DBUILD_COMPLEX=1 -DBUILD_COMPLEX16=1 -DVERSION=\"0.3.21\" -march=armv8-a -UASMNAME -UASMFNAME -UNAME -UCNAME -UCHAR_NAME -UCHAR_CNAME -DASMNAME=_lapack_wrappers -DASMFNAME=_lapack_wrappers_ -DNAME=lapack_wrappers_ -DCNAME=lapack_wrappers -DCHAR_NAME=\"lapack_wrappers_\" -DCHAR_CNAME=\"lapack_wrappers\" -DNO_AFFINITY -I.. -c src/lapack_wrappers.c -o src/lapack_wrappers.o
> >> src/lapack_wrappers.c:570:81: warning: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >> RELAPACK_sgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >> ^~~~
> >> &
> >>
> >>
> >>
> >>
> >> On Sun, 17 Mar 2024, Pierre Jolivet wrote:
> >>
> >>> Ah, my bad, I misread linux-opt-arm as a macOS runner, no wonder the option is not helping…
> >>> Take Barry’s advice.
> >>> Furthermore, it looks like OpenBLAS people are steering in the opposite direction as us, by forcing the use of ld-classic https://urldefense.us/v3/__https://github.com/OpenMathLib/OpenBLAS/commit/103d6f4e42fbe532ae4ea48e8d90d7d792bc93d2__;!!G_uCfscf7eWS!bY2l3X9Eb5PRzNQYrfPFXhgcUodHCiDinhQYga0PeQn1IQzJYD376fk-pZfktGAkpTvBmzy7BFDc9SrazFoooQ$ , so that’s another good argument in favor of -framework Accelerate.
> >>>
> >>> Thanks,
> >>> Pierre
> >>>
> >>> PS: anyone benchmarked those https://urldefense.us/v3/__https://developer.apple.com/documentation/accelerate/sparse_solvers__;!!G_uCfscf7eWS!bY2l3X9Eb5PRzNQYrfPFXhgcUodHCiDinhQYga0PeQn1IQzJYD376fk-pZfktGAkpTvBmzy7BFDc9SrpnDvT5g$ ? I didn’t even know they existed.
> >>>
> >>>> On 17 Mar 2024, at 3:06 PM, Zongze Yang <yangzongze at gmail.com <mailto:yangzongze at gmail.com>> wrote:
> >>>>
> >>>> This Message Is From an External Sender
> >>>> This message came from outside your organization.
> >>>> Understood. Thank you for your advice.
> >>>>
> >>>> Best wishes,
> >>>> Zongze
> >>>>
> >>>>> On 17 Mar 2024, at 22:04, Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev> <mailto:bsmith at petsc.dev>> wrote:
> >>>>>
> >>>>>
> >>>>> I would just avoid the --download-openblas option. The BLAS/LAPACK provided by Apple should perform fine, perhaps even better than OpenBLAS on your system.
> >>>>>
> >>>>>
> >>>>>> On Mar 17, 2024, at 9:58 AM, Zongze Yang <yangzongze at gmail.com <mailto:yangzongze at gmail.com> <mailto:yangzongze at gmail.com>> wrote:
> >>>>>>
> >>>>>> This Message Is From an External Sender
> >>>>>> This message came from outside your organization.
> >>>>>> Adding the flag `--download-openblas-make-options=TARGET=GENERIC` did not resolve the issue. The same error persisted.
> >>>>>>
> >>>>>> Best wishes,
> >>>>>> Zongze
> >>>>>>
> >>>>>>> On 17 Mar 2024, at 20:58, Pierre Jolivet <pierre at joliv.et <mailto:pierre at joliv.et> <mailto:pierre at joliv.et>> wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> On 17 Mar 2024, at 1:04 PM, Zongze Yang <yangzongze at gmail.com <mailto:yangzongze at gmail.com> <mailto:yangzongze at gmail.com>> wrote:
> >>>>>>>>
> >>>>>>>> Thank you for providing the instructions. I try the first option.
> >>>>>>>>
> >>>>>>>> Now, the error of the configuration is related to OpenBLAS.
> >>>>>>>> Add `--CFLAGS=-Wno-int-conversion` to configure command resolve this. Should this be reported to OpenBLAS? Or need to fix the configure in petsc?
> >>>>>>>
> >>>>>>> I see our linux-opt-arm runner is using the additional flag '--download-openblas-make-options=TARGET=GENERIC', could you maybe try to add that as well?
> >>>>>>> I don’t think there is much to fix on our end, OpenBLAS has been very broken lately on arm (current version is 0.3.26 but we can’t update because there is a huge performance regression which makes the pipeline timeout).
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>> Pierre
> >>>>>>>
> >>>>>>>>
> >>>>>>>> The configure.log is attached. The errors are show below:
> >>>>>>>> ```
> >>>>>>>> src/lapack_wrappers.c:570:81: error: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >>>>>>>> RELAPACK_sgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >>>>>>>> ^~~~
> >>>>>>>> &
> >>>>>>>> src/../inc/relapack.h:74:216: note: passing argument to parameter here
> >>>>>>>> void RELAPACK_sgemmt(const char *, const char *, const char *, const blasint *, const blasint *, const float *, const float *, const blasint *, const float *, const blasint *, const float *, float *, const blasint *);
> >>>>>>>> ^
> >>>>>>>> src/lapack_wrappers.c:583:81: error: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >>>>>>>> RELAPACK_dgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >>>>>>>> ^~~~
> >>>>>>>> &
> >>>>>>>> src/../inc/relapack.h:75:221: note: passing argument to parameter here
> >>>>>>>> void RELAPACK_dgemmt(const char *, const char *, const char *, const blasint *, const blasint *, const double *, const double *, const blasint *, const double *, const blasint *, const double *, double *, const blasint *);
> >>>>>>>> ^
> >>>>>>>> src/lapack_wrappers.c:596:81: error: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >>>>>>>> RELAPACK_cgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >>>>>>>> ^~~~
> >>>>>>>> &
> >>>>>>>> src/../inc/relapack.h:76:216: note: passing argument to parameter here
> >>>>>>>> void RELAPACK_cgemmt(const char *, const char *, const char *, const blasint *, const blasint *, const float *, const float *, const blasint *, const float *, const blasint *, const float *, float *, const blasint *);
> >>>>>>>> ^
> >>>>>>>> src/lapack_wrappers.c:609:81: error: incompatible integer to pointer conversion passing 'blasint' (aka 'int') to parameter of type 'const blasint *' (aka 'const int *'); take the address with & [-Wint-conversion]
> >>>>>>>> RELAPACK_zgemmt(uplo, transA, transB, n, k, alpha, A, ldA, B, ldB, beta, C, info);
> >>>>>>>> ^~~~
> >>>>>>>> &
> >>>>>>>> src/../inc/relapack.h:77:221: note: passing argument to parameter here
> >>>>>>>> void RELAPACK_zgemmt(const char *, const char *, const char *, const blasint *, const blasint *, const double *, const double *, const blasint *, const double *, const blasint *, const double *, double *, const blasint *);
> >>>>>>>> ^
> >>>>>>>> 4 errors generated.
> >>>>>>>> ```
> >>>>>>>>
> >>>>>>>> Best wishes,
> >>>>>>>> Zongze
> >>>>>>>>
> >>>>>>>> <configure.log.tar.gz>
> >>>>>>>>
> >>>>>>>>> On 17 Mar 2024, at 18:48, Pierre Jolivet <pierre at joliv.et <mailto:pierre at joliv.et> <mailto:pierre at joliv.et>> wrote:
> >>>>>>>>>
> >>>>>>>>> You need this MR https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7365__;!!G_uCfscf7eWS!bY2l3X9Eb5PRzNQYrfPFXhgcUodHCiDinhQYga0PeQn1IQzJYD376fk-pZfktGAkpTvBmzy7BFDc9SqG8HOUGQ$ <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7365__;!!G_uCfscf7eWS!eCQRfbol7FDQiO0o78iDit2saij_ydIUtCfRQnsQAt-h_YcXr2Yi2BFnFnqHZp0FO3Lhpyr2RKdHZ-T-OF94HpwQ$>
> >>>>>>>>> main has been broken for macOS since https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7341__;!!G_uCfscf7eWS!bY2l3X9Eb5PRzNQYrfPFXhgcUodHCiDinhQYga0PeQn1IQzJYD376fk-pZfktGAkpTvBmzy7BFDc9Soe8Kh_uQ$ <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7341__;!!G_uCfscf7eWS!eCQRfbol7FDQiO0o78iDit2saij_ydIUtCfRQnsQAt-h_YcXr2Yi2BFnFnqHZp0FO3Lhpyr2RKdHZ-T-OIhlJwLx$>, so the alternative is to revert to the commit prior.
> >>>>>>>>> It should work either way.
> >>>>>>>>>
> >>>>>>>>> Thanks,
> >>>>>>>>> Pierre
> >>>>>>>>>
> >>>>>>>>>> On 17 Mar 2024, at 11:31 AM, Zongze Yang <yangzongze at gmail.com <mailto:yangzongze at gmail.com> <mailto:yangzongze at gmail.com>> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> This Message Is From an External Sender
> >>>>>>>>>> This message came from outside your organization.
> >>>>>>>>>> Hi, PETSc Team,
> >>>>>>>>>>
> >>>>>>>>>> I am trying to install petsc with the following configuration
> >>>>>>>>>> ```
> >>>>>>>>>> ./configure \
> >>>>>>>>>> --download-bison \
> >>>>>>>>>> --download-mpich \
> >>>>>>>>>> --download-mpich-configure-arguments=--disable-opencl \
> >>>>>>>>>> --download-hwloc \
> >>>>>>>>>> --download-hwloc-configure-arguments=--disable-opencl \
> >>>>>>>>>> --download-openblas \
> >>>>>>>>>> --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" \
> >>>>>>>>>> --with-shared-libraries=1 \
> >>>>>>>>>> --with-fortran-bindings=0 \
> >>>>>>>>>> --with-zlib \
> >>>>>>>>>> LDFLAGS=-Wl,-ld_classic
> >>>>>>>>>> ```
> >>>>>>>>>>
> >>>>>>>>>> The log shows that
> >>>>>>>>>> ```
> >>>>>>>>>> Exhausted all shared linker guesses. Could not determine how to create a shared library!
> >>>>>>>>>> ```
> >>>>>>>>>>
> >>>>>>>>>> I recently updated the system and Xcode, as well as homebrew.
> >>>>>>>>>>
> >>>>>>>>>> The configure.log is attached.
> >>>>>>>>>>
> >>>>>>>>>> Thanks for your attention to this matter.
> >>>>>>>>>>
> >>>>>>>>>> Best wishes,
> >>>>>>>>>> Zongze
> >>>>>>>>>> <configure.log.tar.gz>
> >>>
> >> <configure.log.gz>
> >
>
>
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