[petsc-users] Install PETSc with option `--with-shared-libraries=1` failed on MacOS
Satish Balay
balay at mcs.anl.gov
Mon Mar 18 13:59:34 CDT 2024
On Mon, 18 Mar 2024, Satish Balay via petsc-users wrote:
> On Mon, 18 Mar 2024, Pierre Jolivet wrote:
>
> >
> >
> > > On 18 Mar 2024, at 5:13 PM, Satish Balay via petsc-users <petsc-users at mcs.anl.gov> wrote:
> > >
> > > 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.
> >
> > Well, that’s easy to see it is _still_ broken: https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/jobs/6419779589__;!!G_uCfscf7eWS!f4svx7Rv1mmcLfy5l0C9bXXrw9gwb49ykkTb28IAtZW0VgZ8vgdD8exUOZSL0TCEqqP5X-p-0ll6TetPkw$
> > The infamous gcc segfault that can’t let us run the pipeline, but that builds fine when it’s you that connect to the machine (I bothered you about this a couple of months ago in case you don’t remember, see https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7143__;!!G_uCfscf7eWS!f4svx7Rv1mmcLfy5l0C9bXXrw9gwb49ykkTb28IAtZW0VgZ8vgdD8exUOZSL0TCEqqP5X-p-0llrLiE4GQ$ ).
>
> > make[2]: *** [../../Makefile.tail:46: libs] Bus error (core dumped)
>
> Ah - ok - that's a strange error. I'm not sure how to debug it. [it fails when the build is invoked from configure - but not when its invoked directly from bash/shell.]
Pushed a potential workaround to jolivet/test-openblas
Note: The failure comes up on same OS (Fedora 39) on X64 aswell.
Satish
>
> Satish
>
> >
> > Thanks,
> > Pierre
> >
> > >
> > > 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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