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Error building tensorflow-gpu #104801

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locallycompact opened this issue Nov 24, 2020 · 2 comments · Fixed by #107944
Closed

Error building tensorflow-gpu #104801

locallycompact opened this issue Nov 24, 2020 · 2 comments · Fixed by #107944
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0.kind: bug Something is broken

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@locallycompact
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Hi, I get this error when building tensorflowWithCuda.

ERROR: /build/output/external/hwloc/BUILD.bazel:229:1: C++ compilation of rule '@hwloc//:hwloc' failed (Exit 1)
[7,212 / 12,420] 31 actions running
    Compiling external/mkl_dnn/src/cpu/cpu_engine.cpp; 42s local
    @mkl_dnn//:mkldnn_single_threaded; 42s local
    @mkl_dnn//:mkldnn_single_threaded; 28s local
    @mkl_dnn//:mkldnn_single_threaded; 25s local
    Compiling external/mkl_dnn/src/cpu/cpu_reorder.cpp; 23s local
    Compiling external/mkl_dnn/src/cpu/rnn/ref_rnn.cpp; 14s local
    Compiling .../xla/service/cpu/runtime_single_threaded_conv2d.cc; 9s local
    Compiling .../service/cpu/runtime_single_threaded_matmul.cc; 9s local ...
external/hwloc/hwloc/topology.c:45:10: fatal error: sys/sysctl.h: No such file or directory
 #include <sys/sysctl.h>

Steps to reproduce:

nix-shell -p python37Packages.tensorflowWithCuda
@locallycompact locallycompact added the 0.kind: bug Something is broken label Nov 24, 2020
@avdv
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avdv commented Nov 26, 2020

Same problem when trying to build python36Packages.dm-sonnet which depends on tensorflow:

ERROR: /build/output/external/hwloc/BUILD.bazel:229:1: C++ compilation of rule '@hwloc//:hwloc' failed (Exit 1)
[4,944 / 5,456] 7 actions running
    Compiling tensorflow/core/util/batch_util.cc [for host]; 24s local
    Compiling .../core/framework/graph_to_functiondef.cc [for host]; 4s local
    Compiling tensorflow/core/framework/dataset.cc [for host]; 2s local
    Compiling .../core/common_runtime/bfc_allocator.cc [for host]; 0s local
    Compiling tensorflow/core/framework/collective.cc [for host]; 0s local
    Compiling .../core/common_runtime/allocator_retry.cc [for host]; 0s local
    Compiling external/hwloc/hwloc/topology-linux.c [for host]; 0s local
external/hwloc/hwloc/topology.c:45:10: fatal error: sys/sysctl.h: No such file or directory
   45 | #include <sys/sysctl.h>
      |          ^~~~~~~~~~~~~~
compilation terminated.

@avdv avdv mentioned this issue Nov 30, 2020
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matthewbauer added a commit to matthewbauer/nixpkgs that referenced this issue Dec 30, 2020
@matthewbauer
tensorflow1: disable sysctl.h in hwloc
a9ecac2 
We need to override tensorflow's hwloc configuration, since it forces
sysctl.h usage which is removed since glibc 2.31. This does not appear
to effect tensorflow2.

See also tensorflow/tensorflow#45861

Fixes NixOS#104801
@matthewbauer matthewbauer mentioned this issue Dec 30, 2020
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@matthewbauer
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Should be fixed with #107944

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tensorflow1: disable sysctl.h in hwloc matthewbauer/nixpkgs
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@matthewbauer @locallycompact @avdv