Issue 1:
Hi! While installing jaxlib from sources on macos 11.2.2. by following docs the installation fails with ld: 2 duplicate symbols error that points to output in bazel-out/. The log below is taken from rerunning python3 build/build.py (fails with same error). Thank you for any tips what I can be missing!

Following the install from sources instructions:

git clone https://github.com/google/jax; cd jax

running installation (without cuda): python3 build/build.py

$ python3 build/build.py

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Bazel binary path: ./bazel-3.7.2-darwin-x86_64
Python binary path: /usr/local/opt/python@3.8/bin/python3.8
Python version: 3.8
MKL-DNN enabled: yes
Target CPU features: release
CUDA enabled: no
ROCm enabled: no

Building XLA and installing it in the jaxlib source tree...
./bazel-3.7.2-darwin-x86_64 run --verbose_failures=true --config=short_logs --config=avx_posix --config=mkl_open_source_only :build_wheel -- --output_path=/Users/mateusz/PycharmProjects/jax/dist
INFO: Options provided by the client:
Inherited 'common' options: --isatty=0 --terminal_columns=80
INFO: Reading rc options for 'run' from /Users/mateusz/PycharmProjects/jax/.bazelrc:
Inherited 'common' options: --experimental_repo_remote_exec
INFO: Reading rc options for 'run' from /Users/mateusz/PycharmProjects/jax/.bazelrc:
Inherited 'build' options: --repo_env PYTHON_BIN_PATH=/usr/local/opt/python@3.8/bin/python3.8 --action_env=PYENV_ROOT --python_path=/usr/local/opt/python@3.8/bin/python3.8 --repo_env TF_NEED_CUDA=0 --action_env TF_CUDA_COMPUTE_CAPABILITIES=3.5,5.2,6.0,6.1,7.0 --repo_env TF_NEED_ROCM=0 --action_env TF_ROCM_AMDGPU_TARGETS=gfx803,gfx900,gfx906,gfx1010 --distinct_host_configuration=false -c opt --apple_platform_type=macos --macos_minimum_os=10.9 --announce_rc --define open_source_build=true --define=no_kafka_support=true --define=no_ignite_support=true --define=grpc_no_ares=true --spawn_strategy=standalone --strategy=Genrule=standalone --enable_platform_specific_config --define=with_tpu_support=true
INFO: Found applicable config definition build:short_logs in file /Users/mateusz/PycharmProjects/jax/.bazelrc: --output_filter=DONT_MATCH_ANYTHING
INFO: Found applicable config definition build:avx_posix in file /Users/mateusz/PycharmProjects/jax/.bazelrc: --copt=-mavx --host_copt=-mavx
INFO: Found applicable config definition build:mkl_open_source_only in file /Users/mateusz/PycharmProjects/jax/.bazelrc: --define=tensorflow_mkldnn_contraction_kernel=1
INFO: Found applicable config definition build:macos in file /Users/mateusz/PycharmProjects/jax/.bazelrc: --config=posix
INFO: Found applicable config definition build:posix in file /Users/mateusz/PycharmProjects/jax/.bazelrc: --copt=-Wno-sign-compare --define=no_aws_support=true --define=no_gcp_support=true --define=no_hdfs_support=true --cxxopt=-std=c++14 --host_cxxopt=-std=c++14
Loading:
Loading: 0 packages loaded
Analyzing: target //build:build_wheel (0 packages loaded, 0 targets configured)
INFO: Analyzed target //build:build_wheel (0 packages loaded, 0 targets configured).
INFO: Found 1 target...
[0 / 2] [Prepa] BazelWorkspaceStatusAction stable-status.txt
[1 / 2] Linking external/org_tensorflow/tensorflow/compiler/xla/python/xla_extension.so; 1s local
ERROR: /private/var/tmp/_bazel_mateusz/b6eb44f2f011bbc7a8c2a6afe83ceb88/external/org_tensorflow/tensorflow/compiler/xla/python/BUILD:496:17: Linking of rule '@org_tensorflow//tensorflow/compiler/xla/python:xla_extension.so' failed (Exit 1): cc_wrapper.sh failed: error executing command
(cd /private/var/tmp/_bazel_mateusz/b6eb44f2f011bbc7a8c2a6afe83ceb88/execroot/__main__ && \
exec env - \
PATH=/usr/local/opt/python@3.8/bin:/Users/mateusz/.jenv/shims:/Users/mateusz/.jenv/bin:/usr/local/sbin:/usr/local/texlive/2016basic/bin/x86_64-darwin:/Users/mateusz/.cargo/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin \
PWD=/proc/self/cwd \
TF_CUDA_COMPUTE_CAPABILITIES=3.5,5.2,6.0,6.1,7.0 \
TF_ROCM_AMDGPU_TARGETS=gfx803,gfx900,gfx906,gfx1010 \
external/local_config_cc/cc_wrapper.sh -shared -o bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/xla_extension.so bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/_objs/xla_extension.so/xla.pic.o bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libdlpack.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libpmap_lib.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libjax_jit.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libops.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/client/lib/liblu_decomposition.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/client/lib/libqr.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/client/lib/libself_adjoint_eig.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/client/lib/libsorting.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/client/lib/libsvd.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libprofiler.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/internal/cpu/libhost_tracer.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/internal/cpu/libhost_tracer_utils.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libparse_annotation.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/internal/tpu/libtpu_tracer.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/tpu/libtpu_api_dlsym_initializer.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/rpc/libprofiler_server_impl.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/rpc/libprofiler_service_impl.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/lib/libprofiler_session_impl.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/lib/libprofiler_factory_impl.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/lib/libprofiler_lock.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/convert/libpost_process_single_host_xplane.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libderived_timeline.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libgroup_events.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libxplane_schema.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libtf_op_utils.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libxplane_utils.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libxplane_builder.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/utils/libxplane_visitor.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/libprofiler_service_proto_cc_impl.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/libprofiler_service_monitor_result_proto_cc_impl.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libpytree.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libpy_traceback.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/liboutfeed_receiver_py.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/liboutfeed_receiver.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libxla_compiler.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libpy_client.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libtraceback.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libpython_ref_manager.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/profiler/libprotos_all_cc_impl.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/libtypes.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/pjrt/libcpu_device.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libcpu_compiler.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libbuffer_info_util.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libconv_canonicalization.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libcpu_executable.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/libxla_debug_info_manager.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libcpu_instruction_fusion.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/libinstruction_fusion.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libcpu_layout_assignment.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libir_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libir_function.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libparallel_loop_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libalias_analysis.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libbuffer_assignment_util.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libparallel_task_assignment.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libdot_op_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libmlir_emitter.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/xla/libhlo_utils.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/libhlo.pic.lo -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/libinfer_fusibility_op_interface.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/libconvert_op_folder.pic.a -Wl,-force_load,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/liblhlo.pic.lo bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/libhlo_ops_base_enums.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/mlir/hlo/libhlo_ops_base_structs.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libTargetLLVMIR.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libLLVMAVX512ToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libLLVMArmNeonToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libLLVMArmSVEToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libLLVMToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libOpenMPToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libROCDLToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libTranslation.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libtiled_dot_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libir_emission_utils.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libshape_partition.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libdynamic_update_slice_util.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libfused_ir_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libtuple_ops.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/libfusion_node_indexing_evaluation.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/libelemental_ir_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/gpu/libparallel_loop_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/gpu/liblaunch_dimensions.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/gpu/libtarget_util.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libkernel_support_library.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libloop_emitter.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libllvm_loop.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libir_array.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libsimple_orc_jit.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libcompiler_functor.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libllvm_ir_runtime.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libvector_support_library.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/llvm_ir/libmath_ops.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/liborc_jit_memory_mapper.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_fp16.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_pow.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_conv2d_mkl.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_conv2d.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_fft.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_fork_join.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_key_value_sort.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_topk.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_matmul.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_matmul_mkl.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_single_threaded_conv2d.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libruntime_single_threaded_fft.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libOrcJIT.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libExecutionEngine.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libJITLink.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libOrcTargetProcess.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libOrcShared.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libPasses.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libCoroutines.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libObjCARC.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libRuntimeDyld.pic.a bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/service/cpu/libtarget_machine_features.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libAffineTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libAsyncTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libComplexToLLVM.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSCFToOpenMP.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libTosaToLinalg.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUToGPURuntimeTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libAsyncToLLVM.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libNVVMToLLVMIRTranslation.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libNVPTXCodeGen.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libIPO.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libIRReader.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libLinker.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libNVPTXDesc.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libNVPTXInfo.pic.a bazel-out/darwin-opt/bin/external/llvm-project/llvm/libVectorize.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUToNVVMTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUToROCDLTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUCommonTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUToSPIRV.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSCFToSPIRV.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUToVulkanTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSPIRVSerialization.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSPIRVBinaryUtils.pic.a 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bazel-out/darwin-opt/bin/external/llvm-project/mlir/libGPUTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSCFToStandard.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSCFTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSDBM.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSPIRVToLLVM.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSPIRVTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libShapeToStandard.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libShapeTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libShape.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libStandardToSPIRV.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libSPIRVUtils.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libTensorTransforms.pic.a bazel-out/darwin-opt/bin/external/llvm-project/mlir/libAsync.pic.a 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bazel-out/darwin-opt/bin/external/com_google_absl/absl/strings/libstr_format_internal.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/strings/libstrings.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/strings/libinternal.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/libbase.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/libdynamic_annotations.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/libspinlock_wait.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/libthrow_delegate.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/libraw_logging_internal.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/base/liblog_severity.pic.a bazel-out/darwin-opt/bin/external/com_google_absl/absl/numeric/libint128.pic.a -Wl,-rpath,@loader_path/,-rpath,@loader_path/..,-rpath,@loader_path/../..,-rpath,@loader_path/../../.. -Wl,-rename_section,__TEXT,text_env,__TEXT,__text -Wl,-w -Wl,-exported_symbols_list,bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/compiler/xla/python/xla_extension-exported-symbols.lds -lm -lpthread -framework IOKit -ldl -ldl -lm -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -framework CoreFoundation -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -pthread -ldl -lpthread -lm -pthread -pthread -lm -lpthread -lm -lpthread -lm -pthread -undefined dynamic_lookup -headerpad_max_install_names -lstdc++ -lm)
Execution platform: @local_execution_config_platform//:platform
duplicate symbol 'tensorflow::tpu::InitializeTpuLibrary(void*)' in:
bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/tpu/libtpu_api_dlsym_initializer.pic.lo(tpu_api_dlsym_initializer.pic.o)
bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/tpu/libtpu_executor_dlsym_initializer.pic.lo(tpu_executor_dlsym_initializer.pic.o)
duplicate symbol 'tensorflow::tpu::FindAndLoadTpuLibrary()' in:
bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/tpu/libtpu_api_dlsym_initializer.pic.lo(tpu_api_dlsym_initializer.pic.o)
bazel-out/darwin-opt/bin/external/org_tensorflow/tensorflow/core/tpu/libtpu_executor_dlsym_initializer.pic.lo(tpu_executor_dlsym_initializer.pic.o)
ld: 2 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Target //build:build_wheel failed to build
INFO: Elapsed time: 3.424s, Critical Path: 2.82s
INFO: 2 processes: 2 internal.
FAILED: Build did NOT complete successfully
ERROR: Build failed. Not running target
FAILED: Build did NOT complete successfully
Traceback (most recent call last):
File "build/build.py", line 516, in <module>
main()
File "build/build.py", line 511, in main
shell(command)
File "build/build.py", line 51, in shell
output = subprocess.check_output(cmd)
File "/usr/local/Cellar/python@3.8/3.8.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py", line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/usr/local/Cellar/python@3.8/3.8.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['./bazel-3.7.2-darwin-x86_64', 'run', '--verbose_failures=true', '--config=short_logs', '--config=avx_posix', '--config=mkl_open_source_only', ':build_wheel', '--', '--output_path=/Users/mateusz/PycharmProjects/jax/dist']' returned non-zero exit status 1.

Issue 2:
Description

The difference operation between two BCOO sparse matrices implicitly removes zeros. The behaviour is different from the one observed for the addition. Consider the example below.

import jax.experimental.sparse as jsp
import jax.numpy as jnp

a = jsp.BCOO((jnp.array([1.0]), jnp.array([[0, 0]])), shape=(3, 3))
b_values = jnp.array([0.0, 1.0, 0.0])
b_indices = jnp.array([[0, 0], [1, 1], [2, 2]])
b = jsp.BCOO((b_values, b_indices), shape=(3, 3))

print("Difference\n", (a - b).indices)
print("Addition\n", (a + b).indices)

The output is

Difference
[[0 0]
[1 1]
[3 3]
[3 3]]
Addition
[[0 0]
[0 0]
[1 1]
[2 2]]

As you can see, in the difference operation the indices associated to null values in a or b have disappeared and they have been replaced with the out-of-bounds index [3,3].

The expected behaviour can be obtained using a + (-1)*b.

What jax/jaxlib version are you using?

jax v0.3.25, jaxlib v.0.3.25

Which accelerator(s) are you using?

CPU/GPU

Additional system info

Python 3.10.8, ArchLinux

NVIDIA GPU info

NVIDIA-SMI 520.56.06 Driver Version: 520.56.06 CUDA Version: 11.8