njzjz
commented
2 years ago Please apply #1275 to the code - or downgrade the TensorFlow version.
Closed CompRhys closed 2 years ago
njzjz
commented
2 years ago Please apply #1275 to the code - or downgrade the TensorFlow version.
CompRhys
commented
2 years ago @njzjz I tried the alternative of using main and pinning the tensorflow version to 2.6 and it doesn't resolve the issues.
Do you have a pip freeze of an environment and shell variable that work with the latest release?
Processing /Users/comprhys/deepmd-kit
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting python-hostlist>=1.21
Using cached python_hostlist-1.21-py3-none-any.whl
Collecting pyyaml
Using cached PyYAML-6.0-cp38-cp38-macosx_10_9_x86_64.whl (192 kB)
Requirement already satisfied: h5py in ./deep_env/lib/python3.8/site-packages (from deepmd-kit==2.0.3) (3.1.0)
Collecting wcmatch
Using cached wcmatch-8.3-py3-none-any.whl (42 kB)
Collecting scipy
Using cached scipy-1.8.0-cp38-cp38-macosx_12_0_universal2.macosx_10_9_x86_64.whl (55.3 MB)
Requirement already satisfied: numpy in ./deep_env/lib/python3.8/site-packages (from deepmd-kit==2.0.3) (1.19.5)
Collecting dargs>=0.2.6
Using cached dargs-0.2.8-py3-none-any.whl (11 kB)
Collecting bracex>=2.1.1
Using cached bracex-2.2.1-py3-none-any.whl (12 kB)
Building wheels for collected packages: deepmd-kit
Building wheel for deepmd-kit (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for deepmd-kit (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [179 lines of output]
Not searching for unused variables given on the command line.
-- The C compiler identification is AppleClang 12.0.5.12050022
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- The CXX compiler identification is AppleClang 12.0.5.12050022
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/comprhys/deepmd-kit/_cmake_test_compile/build
-- The C compiler identification is AppleClang 12.0.5.12050022
-- The CXX compiler identification is AppleClang 12.0.5.12050022
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/local/bin/git (found version "2.35.1")
-- Supported model version: 1.0
-- Will not build nv GPU support
-- Will not build AMD GPU support
-- Disabled cpp interface build, looking for tensorflow_framework
-- Found TensorFlow: /Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/include, , /Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/libtensorflow_framework.dylib in /Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow;/Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/../tensorflow_core;/Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow;/Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/../tensorflow_core;/usr/;/usr/local/ (found version "2.6.0")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Automatically determined OP_CXX_ABI=0
-- Set GLIBCXX_USE_CXX_ABI=0 when compiling ops
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- /Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/libtensorflow_framework.dylib
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
PYTHON_INCLUDE_DIR
PYTHON_LIBRARY
PYTHON_VERSION_STRING
SKBUILD
-- Build files have been written to: /Users/comprhys/deepmd-kit/_skbuild/macosx-11.0-x86_64-3.8/cmake-build
[1/55] Building CXX object op/CMakeFiles/op_abi.dir/ewald_recp.cc.o
FAILED: op/CMakeFiles/op_abi.dir/ewald_recp.cc.o
/Library/Developer/CommandLineTools/usr/bin/c++ -Dop_abi_EXPORTS -I/Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow/include -I/Users/comprhys/deepmd-kit/source/lib/include -std=c++11 -Wno-ignored-attributes -O3 -DNDEBUG -arch x86_64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk -mmacosx-version-min=11.0 -fPIC -D_GLIBCXX_USE_CXX11_ABI=0 -MD -MT op/CMakeFiles/op_abi.dir/ewald_recp.cc.o -MF op/CMakeFiles/op_abi.dir/ewald_recp.cc.o.d -o op/CMakeFiles/op_abi.dir/ewald_recp.cc.o -c /Users/comprhys/deepmd-kit/source/op/ewald_recp.cc
In file included from /Users/comprhys/deepmd-kit/source/op/ewald_recp.cc:2:
/Users/comprhys/deepmd-kit/source/lib/include/ewald.h:5:9: fatal error: 'omp.h' file not found
#include<omp.h>
^~~~~~~
1 error generated.
[2/55] Building CXX object op/CMakeFiles/op_abi.dir/custom_op.cc.o
[3/55] Building CXX object op/CMakeFiles/op_abi.dir/map_aparam.cc.o
[4/55] Building CXX object op/CMakeFiles/op_abi.dir/soft_min_force.cc.o
[5/55] Building CXX object op/CMakeFiles/op_abi.dir/soft_min_virial.cc.o
[6/55] Building CXX object op/CMakeFiles/op_abi.dir/prod_force.cc.o
[7/55] Building CXX object op/CMakeFiles/op_abi.dir/prod_force_multi_device.cc.o
[8/55] Building CXX object op/CMakeFiles/op_abi.dir/prod_virial.cc.o
[9/55] Building CXX object op/CMakeFiles/op_abi.dir/soft_min.cc.o
In file included from /Users/comprhys/deepmd-kit/source/op/soft_min.cc:2:
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:787:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized std::vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:896:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:1004:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
[10/55] Building CXX object op/CMakeFiles/op_abi.dir/pair_tab.cc.o
[11/55] Building CXX object op/CMakeFiles/op_abi.dir/gelu_multi_device.cc.o
[12/55] Building CXX object op/CMakeFiles/op_abi.dir/prod_virial_multi_device.cc.o
[13/55] Building CXX object op/CMakeFiles/op_abi.dir/neighbor_stat.cc.o
[14/55] Building CXX object op/CMakeFiles/op_abi.dir/descrpt_se_a_ef_para.cc.o
In file included from /Users/comprhys/deepmd-kit/source/op/descrpt_se_a_ef_para.cc:2:
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:787:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized std::vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:896:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:1004:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
[15/55] Building CXX object op/CMakeFiles/op_abi.dir/descrpt_se_a_ef.cc.o
In file included from /Users/comprhys/deepmd-kit/source/op/descrpt_se_a_ef.cc:3:
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:787:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized std::vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:896:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:1004:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
[16/55] Building CXX object op/CMakeFiles/op_abi.dir/descrpt_se_a_ef_vert.cc.o
In file included from /Users/comprhys/deepmd-kit/source/op/descrpt_se_a_ef_vert.cc:2:
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:787:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized std::vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:896:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:1004:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
[17/55] Building CXX object op/CMakeFiles/op_abi.dir/prod_env_mat_multi_device.cc.o
[18/55] Building CXX object op/CMakeFiles/op_abi.dir/descrpt.cc.o
In file included from /Users/comprhys/deepmd-kit/source/op/descrpt.cc:2:
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:787:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized std::vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:896:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/comprhys/deepmd-kit/source/lib/include/ComputeDescriptor.h:1004:55: warning: expression result unused [-Wunused-value]
assert( fabs(deepmd::dot3(ef, ef) - 1.0) < 1e-12 ), "ef should be a normalized vector";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
ninja: build stopped: subcommand failed.
File "/private/var/folders/yh/fjbfn5h91dgc6p34j72mzq_r0000gn/T/pip-build-env-yjp0bu53/overlay/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 595, in setup
cmkr.make(make_args, env=env)
File "/private/var/folders/yh/fjbfn5h91dgc6p34j72mzq_r0000gn/T/pip-build-env-yjp0bu53/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 609, in make
raise SKBuildError(
--------------------------------------------------------------------------------
-- Trying "Ninja" generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying "Ninja" generator - success
--------------------------------------------------------------------------------
Configuring Project
Working directory:
/Users/comprhys/deepmd-kit/_skbuild/macosx-11.0-x86_64-3.8/cmake-build
Command:
cmake /Users/comprhys/deepmd-kit/source -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/Users/comprhys/deepmd-kit/_skbuild/macosx-11.0-x86_64-3.8/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/Users/comprhys/deepmd-kit/deep_env/bin/python -DPYTHON_VERSION_STRING:STRING=3.8.6 -DPYTHON_INCLUDE_DIR:PATH=/Users/comprhys/.pyenv/versions/3.8.6/include/python3.8 -DPYTHON_LIBRARY:FILEPATH=/Users/comprhys/.pyenv/versions/3.8.6/lib/libpython3.8.a -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/private/var/folders/yh/fjbfn5h91dgc6p34j72mzq_r0000gn/T/pip-build-env-yjp0bu53/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DCMAKE_MAKE_PROGRAM:FILEPATH=/private/var/folders/yh/fjbfn5h91dgc6p34j72mzq_r0000gn/T/pip-build-env-yjp0bu53/overlay/lib/python3.8/site-packages/ninja/data/bin/ninja -DTENSORFLOW_ROOT:STRING=/Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages/tensorflow -DBUILD_PY_IF:BOOL=TRUE -DBUILD_CPP_IF:BOOL=FALSE -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=11.0 -DCMAKE_OSX_ARCHITECTURES:STRING=x86_64
Traceback (most recent call last):
An error occurred while building with CMake.
Command:
cmake --build . --target install --config Release --
Source directory:
/Users/comprhys/deepmd-kit
Working directory:
/Users/comprhys/deepmd-kit/_skbuild/macosx-11.0-x86_64-3.8/cmake-build
Please see CMake's output for more information.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for deepmd-kit
Failed to build deepmd-kit
ERROR: Could not build wheels for deepmd-kit, which is required to install pyproject.toml-based projects
(deep_env) ➜ deepmd-kit git:(master) pip show tensorflow-cpu
Name: tensorflow-cpu
Version: 2.6.0
Summary: TensorFlow is an open source machine learning framework for everyone.
Home-page: https://www.tensorflow.org/
Author: Google Inc.
Author-email: packages@tensorflow.org
License: Apache 2.0
Location: /Users/comprhys/deepmd-kit/deep_env/lib/python3.8/site-packages
Requires: absl-py, astunparse, clang, flatbuffers, gast, google-pasta, grpcio, h5py, keras, keras-preprocessing, numpy, opt-einsum, protobuf, six, tensorboard, tensorflow-estimator, termcolor, typing-extensions, wheel, wrapt
Required-by: It looks like you didn't install OpenMP, so the error happened.
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
Although, I think OpenMP should be an optional dependency instead of the mandatory dependency. I will try to fix it.
When trying to follow the instructions at https://github.com/deepmodeling/deepmd-kit/blob/master/doc/install/install-from-source.md the build fails both on the macOS and linux machines I have tested it on.
After following the instructions up to
pip install .I get the following stack trace: