docker pull from google/deepvariant:1.6.0-gpu ,but the python version is 3.11 and the proto file cannot import about deepvariant

[kishwarshafin]

Hi @one-matrix ,

Are you trying to build deepvariant locally? If that's the case, then please follow the steps here: https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-build-test.md

[one-matrix]

i have excute build_and_test.sh but the other error come.
`
(py38) root@30634345fd4a:/deepvariant# ./build_and_test.sh

• source settings.sh
  ++ export DV_USE_PREINSTALLED_TF=0
  ++ DV_USE_PREINSTALLED_TF=0
  ++ export TF_NEED_GCP=1
  ++ TF_NEED_GCP=1
  ++ export CUDNN_INSTALL_PATH=/usr/lib/x86_64-linux-gnu
  ++ CUDNN_INSTALL_PATH=/usr/lib/x86_64-linux-gnu
  ++ DV_BAZEL_VERSION=5.3.0
  ++ export PATH=/root/bin:/root/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/bin/remote-cli:/opt/conda/envs/py38/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin:/root/bin
  ++ PATH=/root/bin:/root/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/bin/remote-cli:/opt/conda/envs/py38/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin:/root/bin
  ++ export DEEPVARIANT_BUCKET=gs://deepvariant
  ++ DEEPVARIANT_BUCKET=gs://deepvariant
  ++ export DV_PACKAGE_BUCKET_PATH=gs://deepvariant/packages
  ++ DV_PACKAGE_BUCKET_PATH=gs://deepvariant/packages
  ++ export DV_PACKAGE_CURL_PATH=https://storage.googleapis.com/deepvariant/packages
  ++ DV_PACKAGE_CURL_PATH=https://storage.googleapis.com/deepvariant/packages
  ++ export DV_TF_NIGHTLY_BUILD=0
  ++ DV_TF_NIGHTLY_BUILD=0
  ++ [[ 0 = \1 ]]
  ++ export DV_CPP_TENSORFLOW_TAG=v2.11.0
  ++ DV_CPP_TENSORFLOW_TAG=v2.11.0
  ++ export DV_GCP_OPTIMIZED_TF_WHL_VERSION=2.11.0
  ++ DV_GCP_OPTIMIZED_TF_WHL_VERSION=2.11.0
  ++ export DV_TENSORFLOW_STANDARD_GPU_WHL_VERSION=2.11.0
  ++ DV_TENSORFLOW_STANDARD_GPU_WHL_VERSION=2.11.0
  ++ export DV_TENSORFLOW_STANDARD_CPU_WHL_VERSION=2.11.0
  ++ DV_TENSORFLOW_STANDARD_CPU_WHL_VERSION=2.11.0
  ++ export DV_GPU_BUILD=1
  ++ DV_GPU_BUILD=1
  ++ export DV_USE_GCP_OPTIMIZED_TF_WHL=1
  ++ DV_USE_GCP_OPTIMIZED_TF_WHL=1
  ++ export GCP_OPTIMIZED_TF_WHL_FILENAME=tensorflow-2.11.0.deepvariant_gcp-cp27-none-linux_x86_64.whl
  ++ GCP_OPTIMIZED_TF_WHL_FILENAME=tensorflow-2.11.0.deepvariant_gcp-cp27-none-linux_x86_64.whl
  ++ export GCP_OPTIMIZED_TF_WHL_PATH=gs://deepvariant/packages/tensorflow
  ++ GCP_OPTIMIZED_TF_WHL_PATH=gs://deepvariant/packages/tensorflow
  ++ export GCP_OPTIMIZED_TF_WHL_CURL_PATH=https://storage.googleapis.com/deepvariant/packages/tensorflow
  ++ GCP_OPTIMIZED_TF_WHL_CURL_PATH=https://storage.googleapis.com/deepvariant/packages/tensorflow
  ++ export DV_TF_NUMPY_VERSION=1.19.2
  ++ DV_TF_NUMPY_VERSION=1.19.2
  ++ export DV_INSTALL_GPU_DRIVERS=0
  ++ DV_INSTALL_GPU_DRIVERS=0
  ++ export PYTHON_VERSION=3.8
  ++ PYTHON_VERSION=3.8
  +++ which python3.8
  ++ export PYTHON_BIN_PATH=/opt/conda/envs/py38/bin/python3.8
  ++ PYTHON_BIN_PATH=/opt/conda/envs/py38/bin/python3.8
  ++ export PYTHON_LIB_PATH=/usr/local/lib/python3.8/dist-packages
  ++ PYTHON_LIB_PATH=/usr/local/lib/python3.8/dist-packages
  ++ export USE_DEFAULT_PYTHON_LIB_PATH=1
  ++ USE_DEFAULT_PYTHON_LIB_PATH=1
  ++ export 'DV_COPT_FLAGS=--copt=-march=corei7 --copt=-Wno-sign-compare --copt=-Wno-write-strings --experimental_build_setting_api --java_runtime_version=remotejdk_11'
  ++ DV_COPT_FLAGS='--copt=-march=corei7 --copt=-Wno-sign-compare --copt=-Wno-write-strings --experimental_build_setting_api --java_runtime_version=remotejdk_11'
• bazel
  [bazel release 5.3.0]
  Usage: bazel ...

Available commands:
analyze-profile Analyzes build profile data.
aquery Analyzes the given targets and queries the action graph.
build Builds the specified targets.
canonicalize-flags Canonicalizes a list of bazel options.
clean Removes output files and optionally stops the server.
coverage Generates code coverage report for specified test targets.
cquery Loads, analyzes, and queries the specified targets w/ configurations.
dump Dumps the internal state of the bazel server process.
fetch Fetches external repositories that are prerequisites to the targets.
help Prints help for commands, or the index.
info Displays runtime info about the bazel server.
license Prints the license of this software.
mobile-install Installs targets to mobile devices.
print_action Prints the command line args for compiling a file.
query Executes a dependency graph query.
run Runs the specified target.
shutdown Stops the bazel server.
sync Syncs all repositories specified in the workspace file
test Builds and runs the specified test targets.
version Prints version information for bazel.

Getting more help:
bazel help
Prints help and options for .
bazel help startup_options
Options for the JVM hosting bazel.
bazel help target-syntax
Explains the syntax for specifying targets.
bazel help info-keys
Displays a list of keys used by the info command.

• [[ 1 = \1 ]]
• bazel test -c opt --local_test_jobs=1 --copt=-march=corei7 --copt=-Wno-sign-compare --copt=-Wno-write-strings --experimental_build_setting_api --java_runtime_version=remotejdk_11 deepvariant/...
  (05:40:22) INFO: Options provided by the client:
  Inherited 'common' options: --isatty=1 --terminal_columns=166
  (05:40:22) INFO: Reading rc options for 'test' from /tensorflow/.bazelrc:
  Inherited 'common' options: --experimental_repo_remote_exec
  (05:40:22) INFO: Reading rc options for 'test' from /tensorflow/.bazelrc:
  Inherited 'build' options: --define framework_shared_object=true --define tsl_protobuf_header_only=true --define=use_fast_cpp_protos=true --define=allow_oversize_protos=true --spawn_strategy=standalone -c opt --announce_rc --define=grpc_no_ares=true --noincompatible_remove_legacy_whole_archive --enable_platform_specific_config --define=with_xla_support=true --config=short_logs --config=v2 --define=no_aws_support=true --define=no_hdfs_support=true --experimental_cc_shared_library --experimental_link_static_libraries_once=false --deleted_packages=tensorflow/compiler/mlir/tfrt,tensorflow/compiler/mlir/tfrt/benchmarks,tensorflow/compiler/mlir/tfrt/jit/python_binding,tensorflow/compiler/mlir/tfrt/jit/transforms,tensorflow/compiler/mlir/tfrt/python_tests,tensorflow/compiler/mlir/tfrt/tests,tensorflow/compiler/mlir/tfrt/tests/ir,tensorflow/compiler/mlir/tfrt/tests/analysis,tensorflow/compiler/mlir/tfrt/tests/jit,tensorflow/compiler/mlir/tfrt/tests/lhlo_to_tfrt,tensorflow/compiler/mlir/tfrt/tests/lhlo_to_jitrt,tensorflow/compiler/mlir/tfrt/tests/tf_to_corert,tensorflow/compiler/mlir/tfrt/tests/tf_to_tfrt_data,tensorflow/compiler/mlir/tfrt/tests/saved_model,tensorflow/compiler/mlir/tfrt/transforms/lhlo_gpu_to_tfrt_gpu,tensorflow/core/runtime_fallback,tensorflow/core/runtime_fallback/conversion,tensorflow/core/runtime_fallback/kernel,tensorflow/core/runtime_fallback/opdefs,tensorflow/core/runtime_fallback/runtime,tensorflow/core/runtime_fallback/util,tensorflow/core/tfrt/common,tensorflow/core/tfrt/eager,tensorflow/core/tfrt/eager/backends/cpu,tensorflow/core/tfrt/eager/backends/gpu,tensorflow/core/tfrt/eager/core_runtime,tensorflow/core/tfrt/eager/cpp_tests/core_runtime,tensorflow/core/tfrt/gpu,tensorflow/core/tfrt/run_handler_thread_pool,tensorflow/core/tfrt/runtime,tensorflow/core/tfrt/saved_model,tensorflow/core/tfrt/graph_executor,tensorflow/core/tfrt/saved_model/tests,tensorflow/core/tfrt/tpu,tensorflow/core/tfrt/utils
  (05:40:22) INFO: Reading rc options for 'test' from /tensorflow/.tf_configure.bazelrc:
  Inherited 'build' options: --action_env PYTHON_BIN_PATH=/opt/conda/envs/py38/bin/python3.8 --action_env PYTHON_LIB_PATH=/usr/local/lib/python3.8/dist-packages --python_path=/opt/conda/envs/py38/bin/python3.8
  (05:40:22) INFO: Reading rc options for 'test' from /deepvariant/.bazelrc:
  Inherited 'build' options: --jobs 128 --config=monolithic --show_timestamps --verbose_failures --define=use_fast_cpp_protos=true --copt=-Wno-maybe-uninitialized --copt=-Wno-unused-function --cxxopt=-std=c++17 --python_top=//:deepvariant_python_runtime --incompatible_use_python_toolchains=false
  (05:40:22) INFO: Reading rc options for 'test' from /tensorflow/.tf_configure.bazelrc:
  'test' options: --flaky_test_attempts=3 --test_size_filters=small,medium
  (05:40:22) INFO: Reading rc options for 'test' from /deepvariant/.bazelrc:
  'test' options: --test_output=errors
  (05:40:22) INFO: Found applicable config definition build:short_logs in file /tensorflow/.bazelrc: --output_filter=DONT_MATCH_ANYTHING
  (05:40:22) INFO: Found applicable config definition build:v2 in file /tensorflow/.bazelrc: --define=tf_api_version=2 --action_env=TF2_BEHAVIOR=1
  (05:40:22) INFO: Found applicable config definition test:v2 in file /tensorflow/.tf_configure.bazelrc: --test_tag_filters=-benchmark-test,-no_oss,-gpu,-oss_serial,-v1only --build_tag_filters=-benchmark-test,-no_oss,-gpu,-v1only
  (05:40:22) INFO: Found applicable config definition build:monolithic in file /tensorflow/.bazelrc: --define framework_shared_object=false --define tsl_protobuf_header_only=false --experimental_link_static_libraries_once=false
  (05:40:22) INFO: Found applicable config definition build:linux in file /tensorflow/.bazelrc: --host_copt=-w --copt=-Wno-all --copt=-Wno-extra --copt=-Wno-deprecated --copt=-Wno-deprecated-declarations --copt=-Wno-ignored-attributes --copt=-Wno-unknown-warning --copt=-Wno-array-parameter --copt=-Wno-stringop-overflow --copt=-Wno-array-bounds --copt=-Wunused-result --copt=-Werror=unused-result --define=PREFIX=/usr --define=LIBDIR=$(PREFIX)/lib --define=INCLUDEDIR=$(PREFIX)/include --define=PROTOBUF_INCLUDE_PATH=$(PREFIX)/include --cxxopt=-std=c++17 --host_cxxopt=-std=c++17 --config=dynamic_kernels --distinct_host_configuration=false --experimental_guard_against_concurrent_changes
  (05:40:22) INFO: Found applicable config definition build:dynamic_kernels in file /tensorflow/.bazelrc: --define=dynamic_loaded_kernels=true --copt=-DAUTOLOAD_DYNAMIC_KERNELS
  (05:40:23) INFO: Current date is 2023-12-18
  (05:40:23) DEBUG: /root/.cache/bazel/_bazel_root/18a0a1d061f0109a3b92fbdafbaf1bbd/external/org_tensorflow/third_party/repo.bzl:132:14:
  Warning: skipping import of repository 'com_google_protobuf' because it already exists.
  (05:40:23) INFO: Analyzed 189 targets (0 packages loaded, 0 targets configured).
  (05:40:23) INFO: Found 141 targets and 48 test targets...
  (05:40:24) ERROR: /deepvariant/third_party/nucleus/util/python/BUILD:13:11: CLIF wrapping third_party/nucleus/util/python/math.clif failed: (Exit 3): pyclif failed: error executing command
  (cd /root/.cache/bazel/_bazel_root/18a0a1d061f0109a3b92fbdafbaf1bbd/execroot/com_google_deepvariant &&
  exec env -
  bazel-out/k8-opt-exec-50AE0418/bin/external/clif/pyclif --modname third_party.nucleus.util.python.math -c bazel-out/k8-opt/bin/third_party/nucleus/util/python/math.cc -g bazel-out/k8-opt/bin/third_party/nucleus/util/python/math.h -i bazel-out/k8-opt/bin/third_party/nucleus/util/python/math_init.cc --prepend clif/python/types.h -I. -Ibazel-out/k8-opt/bin -Iexternal/com_google_absl -Ibazel-out/k8-opt/bin/external/com_google_absl -Iexternal/clif -Ibazel-out/k8-opt/bin/external/clif -Iexternal/com_google_glog -Ibazel-out/k8-opt/bin/external/com_google_glog -Iexternal/com_github_gflags_gflags -Ibazel-out/k8-opt/bin/external/com_github_gflags_gflags -Iexternal/com_google_protobuf -Ibazel-out/k8-opt/bin/external/com_google_protobuf -Iexternal/zlib -Ibazel-out/k8-opt/bin/external/zlib -Iexternal/local_config_python -Ibazel-out/k8-opt/bin/external/local_config_python -Iexternal/com_google_protobuf/src -Ibazel-out/k8-opt/bin/external/com_google_protobuf/src -Iexternal/local_config_python/python_include -Ibazel-out/k8-opt/bin/external/local_config_python/python_include -Iexternal/local_config_cc '-f-I. -Ibazel-out/k8-opt/bin -Iexternal/com_google_absl -Ibazel-out/k8-opt/bin/external/com_google_absl -Iexternal/clif -Ibazel-out/k8-opt/bin/external/clif -Iexternal/com_google_glog -Ibazel-out/k8-opt/bin/external/com_google_glog -Iexternal/com_github_gflags_gflags -Ibazel-out/k8-opt/bin/external/com_github_gflags_gflags -Iexternal/com_google_protobuf -Ibazel-out/k8-opt/bin/external/com_google_protobuf -Iexternal/zlib -Ibazel-out/k8-opt/bin/external/zlib -Iexternal/local_config_python -Ibazel-out/k8-opt/bin/external/local_config_python -Iexternal/com_google_protobuf/src -Ibazel-out/k8-opt/bin/external/com_google_protobuf/src -Iexternal/local_config_python/python_include -Ibazel-out/k8-opt/bin/external/local_config_python/python_include -Iexternal/local_config_cc -std=c++17' third_party/nucleus/util/python/math.clif)

Configuration: dc5f3e671e47dda93c7e5877bba31e0dc0cd0cda8bb0d2473db6563f34168f46

Execution platform: @local_execution_config_platform//:platform

Line .123456789.123456789.123456789.123456789
1:# Copyright 2018 Google LLC.\n
2:#\n
3:# Redistribution and use in source and binary forms, with or without\n
4:# modification, are permitted provided that the following conditions\n
5:# are met:\n
6:#\n
7:# 1. Redistributions of source code must retain the above copyright notice,\n
8:# this list of conditions and the following disclaimer.\n
9:#\n
10:# 2. Redistributions in binary form must reproduce the above copyright\n
11:# notice, this list of conditions and the following disclaimer in the\n
12:# documentation and/or other materials provided with the distribution.\n
13:#\n
14:# 3. Neither the name of the copyright holder nor the names of its\n
15:# contributors may be used to endorse or promote products derived from this\n
16:# software without specific prior written permission.\n
17:#\n
18:# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"\n
19:# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n
20:# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n
21:# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE\n
22:# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n
23:# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n
24:# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n
25:# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n
26:# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n
27:# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE\n
28:# POSSIBILITY OF SUCH DAMAGE.\n
29:\n
30:from "third_party/nucleus/util/math.h":\n
31: namespace nucleus:\n
32: def Log10PTrueToPhred as log10_ptrue_to_phred(\n
33: log10_ptrue: float, value_if_not_finite: float) -> float\n
34: def PhredToPError as phred_to_perror(phred: int) -> float\n
35: def PhredToLog10PError as phred_to_log10_perror(phred: int) -> float\n
36: def PErrorToLog10PError as perror_to_log10_perror(perror: float) -> float\n
37: def PErrorToPhred as perror_to_phred(perror: float) -> float\n
38: def Log10PErrorToPhred as log10_perror_to_phred(log10_perror: float) -> float\n
39: def PErrorToRoundedPhred as perror_to_rounded_phred(perror: float) -> int\n
40: def Log10PErrorToRoundedPhred as log10_perror_to_rounded_phred(log10_perror: float) -> int\n
41: def Log10ToReal as log10_perror_to_perror(log10_perror: float) -> float\n
42: def ZeroShiftLikelihoods as zero_shift_log10_probs(log10_probs: list) -> list\n
_ParseError: include "clif/python/types.h" not found
`