[petsc-users] Install PETSc with option `--with-shared-libraries=1` failed on MacOS
Zongze Yang
yangzongze at gmail.com
Mon Mar 18 00:26:46 CDT 2024
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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