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Installation error #39

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yongmayer opened this issue Jan 17, 2022 · 5 comments
Closed

Installation error #39

yongmayer opened this issue Jan 17, 2022 · 5 comments

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@yongmayer
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Hi Alan,

Hope all is well and glad to catch up with you on GitHub! I try to install deepwave via a clean conda environment but failed.
My setup is ubuntu=20.04, python=3.9, torch=1.10.1 with gpu. I suspect I need to switch to gcc 10 (current gcc 9) for tigerlake. Could you please shed some lights on how to specify gcc when installing deepwave if possible? The following is the error message I had.

Thank you very much for the help!

Best regards,
Yong

(seis) yma@lambda [~]$ pip install deepwave
Collecting deepwave
  Using cached deepwave-0.0.9.tar.gz (33 kB)
Requirement already satisfied: numpy in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave) (1.21.2)
Requirement already satisfied: scipy in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave) (1.7.3)
Requirement already satisfied: torch>=1.7.1 in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave) (1.10.1)
Requirement already satisfied: typing_extensions in ./anaconda3/envs/seis/lib/python3.9/site-packages (from torch>=1.7.1->deepwave) (3.10.0.2)
Building wheels for collected packages: deepwave
  Building wheel for deepwave (setup.py) ... error

  ERROR: Command errored out with exit status 1:
   command: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"'; __file__='"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-hm0_egvy
       cwd: /tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/
  Complete output (35 lines):
  Warning: 'classifiers' should be a list, got type 'tuple'
  running bdist_wheel
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:381: UserWarning: Attempted to use ninja as the BuildExtension backend but we could not find ninja.. Falling back to using the slow distutils backend.
    warnings.warn(msg.format('we could not find ninja.'))
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/wavelets.py -> build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/__init__.py -> build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/utils.py -> build/lib.linux-x86_64-3.9/deepwave
  creating build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/scalar.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/scalar_born.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  creating build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/pad.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/model.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/propagator.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/extract.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/base
  running build_ext
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:782: UserWarning: The detected CUDA version (11.1) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
    warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
  building 'scalar1d_cpu_iso_4_float' extension
  creating build/temp.linux-x86_64-3.9
  creating build/temp.linux-x86_64-3.9/deepwave
  creating build/temp.linux-x86_64-3.9/deepwave/scalar
  gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDEEPWAVE_DIM=1 -DDEEPWAVE_TYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_4_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  cc1plus: error: bad value (‘tigerlake’) for ‘-march=’ switch
  cc1plus: note: valid arguments to ‘-march=’ switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 native
  cc1plus: error: bad value (‘tigerlake’) for ‘-mtune=’ switch
  cc1plus: note: valid arguments to ‘-mtune=’ switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm intel x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 generic native
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for deepwave
  Running setup.py clean for deepwave
Failed to build deepwave
Installing collected packages: deepwave
    Running setup.py install for deepwave ... error
    ERROR: Command errored out with exit status 1:
     command: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"'; __file__='"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-c37e8b70/install-record.txt --single-version-externally-managed --compile --install-headers /home/yxm906/anaconda3/envs/seis/include/python3.9/deepwave
         cwd: /tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/
    Complete output (35 lines):
    Warning: 'classifiers' should be a list, got type 'tuple'
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/wavelets.py -> build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/__init__.py -> build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/utils.py -> build/lib.linux-x86_64-3.9/deepwave
    creating build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/scalar.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/scalar_born.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    creating build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/pad.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/model.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/propagator.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/extract.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/base
    running build_ext
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:381: UserWarning: Attempted to use ninja as the BuildExtension backend but we could not find ninja.. Falling back to using the slow distutils backend.
      warnings.warn(msg.format('we could not find ninja.'))
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:782: UserWarning: The detected CUDA version (11.1) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
      warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
    building 'scalar1d_cpu_iso_4_float' extension
    creating build/temp.linux-x86_64-3.9
    creating build/temp.linux-x86_64-3.9/deepwave
    creating build/temp.linux-x86_64-3.9/deepwave/scalar
    gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDEEPWAVE_DIM=1 -DDEEPWAVE_TYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_4_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
    cc1plus: error: bad value (‘tigerlake’) for ‘-march=’ switch
    cc1plus: note: valid arguments to ‘-march=’ switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 native
    cc1plus: error: bad value (‘tigerlake’) for ‘-mtune=’ switch
    cc1plus: note: valid arguments to ‘-mtune=’ switch are: nocona core2 nehalem corei7 westmere sandybridge corei7-avx ivybridge core-avx-i haswell core-avx2 broadwell skylake skylake-avx512 cannonlake icelake-client icelake-server cascadelake bonnell atom silvermont slm goldmont goldmont-plus tremont knl knm intel x86-64 eden-x2 nano nano-1000 nano-2000 nano-3000 nano-x2 eden-x4 nano-x4 k8 k8-sse3 opteron opteron-sse3 athlon64 athlon64-sse3 athlon-fx amdfam10 barcelona bdver1 bdver2 bdver3 bdver4 znver1 znver2 btver1 btver2 generic native
    error: command '/usr/bin/gcc' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"'; __file__='"'"'/tmp/pip-install-mo3c3l_h/deepwave_f6845b09ab8b4b499a587a516d9ff97c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-c37e8b70/install-record.txt --single-version-externally-managed --compile --install-headers /home/yxm906/anaconda3/envs/seis/include/python3.9/deepwave Check the logs for full command output.
@ar4
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ar4 commented Jan 17, 2022

Hi Yong,

It's good to hear from you again. I hope that you are well and enjoying the new job.

Compiling the native code causes trouble for so many people that I wonder whether I should just rewrite it in Python, even if it makes it a bit slower. In your case it looks like there is a compiler bug that is causing it to expand "-march=native" into "-march=tigerlake" even though the "tigerlake" option is not supported by your compiler. I thus agree with your analysis that switching to GCC 10 should solve the problem. Another solution that might be quicker is to download the Deepwave code (git clone --depth=1 https://github.com/ar4/deepwave.git) and modify the compilation command (in setup.py) to remove the '-march=native' bits and then install this local version (pip install .). If you would instead prefer to switch to GCC 10, then I think you can specify which compiler to use with environment variables (CXX=<path to GCC 10 C++ compiler> pip install deepwave). I hope that works. Let me know how it goes.

-Alan

@yongmayer
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yongmayer commented Jan 17, 2022 •
edited
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Hi Alan,

That's great! After I installed and switched to gcc-10, it successfully installed deepwave-0.0.9.
I also agree that making it python native sounds very attractive.
On a slightly different note, I noticed from another thread regarding the 8th order implementation. However, the installation for that version is not successful. FYI, the following error message:

Thank you very much,
Yong

(seis) yma@lambda [~]$ pip install git+https://github.com/ar4/deepwave.git@8th-order
Collecting git+https://github.com/ar4/deepwave.git@8th-order
  Cloning https://github.com/ar4/deepwave.git (to revision 8th-order) to /tmp/pip-req-build-3vx65ncm
  Running command git clone -q https://github.com/ar4/deepwave.git /tmp/pip-req-build-3vx65ncm
  Running command git checkout -b 8th-order --track origin/8th-order
  Switched to a new branch '8th-order'
  Branch '8th-order' set up to track remote branch '8th-order' from 'origin'.
  Resolved https://github.com/ar4/deepwave.git to commit 30d99d7434494747ee59dbe565bfb47b6f78b42b
Requirement already satisfied: numpy in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave==0.0.8) (1.21.2)
Requirement already satisfied: scipy in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave==0.0.8) (1.7.3)
Requirement already satisfied: torch>=1.7.1 in ./anaconda3/envs/seis/lib/python3.9/site-packages (from deepwave==0.0.8) (1.10.1)
Requirement already satisfied: typing_extensions in ./anaconda3/envs/seis/lib/python3.9/site-packages (from torch>=1.7.1->deepwave==0.0.8) (3.10.0.2)
Building wheels for collected packages: deepwave
  Building wheel for deepwave (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-612y98av
       cwd: /tmp/pip-req-build-3vx65ncm/
  Complete output (72 lines):
  Warning: 'classifiers' should be a list, got type 'tuple'
  running bdist_wheel
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:381: UserWarning: Attempted to use ninja as the BuildExtension backend but we could not find ninja.. Falling back to using the slow distutils backend.
    warnings.warn(msg.format('we could not find ninja.'))
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/wavelets.py -> build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/__init__.py -> build/lib.linux-x86_64-3.9/deepwave
  copying deepwave/utils.py -> build/lib.linux-x86_64-3.9/deepwave
  creating build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/scalar.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/scalar_born.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  copying deepwave/scalar/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
  creating build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/pad.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/model.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/propagator.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/extract.py -> build/lib.linux-x86_64-3.9/deepwave/base
  copying deepwave/base/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/base
  running build_ext
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:782: UserWarning: The detected CUDA version (11.1) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
    warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
  building 'scalar1d_cpu_iso_8_float' extension
  creating build/temp.linux-x86_64-3.9
  creating build/temp.linux-x86_64-3.9/deepwave
  creating build/temp.linux-x86_64-3.9/deepwave/scalar
  gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar_cpu.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar_cpu.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar_wrapper.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar_wrapper.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
  <command-line>: error: expected ‘>’ before numeric constant
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:34:32: note: in expansion of macro ‘DIM’
     34 |                 template <bool DIM = false>
        |                                ^~~
  In file included from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeFunctions.h:6,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/TensorIndexing.h:11,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/ATen.h:20,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/types.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader_options.h:4,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/base.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/stateful.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/all.h:8,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/extension.h:4,
                   from deepwave/scalar/scalar_wrapper.cpp:1:
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: In member function ‘at::meta::structured_all_dim::precompute_out<true> at::meta::structured_all_dim::precompute_out<<anonymous> >::set_dim(int64_t)’:
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:38:43: error: static assertion failed: dim already set
     38 |                         static_assert(DIM == false, "dim already set");
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: At global scope:
  <command-line>: error: expected ‘>’ before numeric constant
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:51:32: note: in expansion of macro ‘DIM’
     51 |                 template <bool DIM = false>
        |                                ^~~
  In file included from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeFunctions.h:6,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/TensorIndexing.h:11,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/ATen.h:20,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/types.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader_options.h:4,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/base.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/stateful.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data.h:3,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/all.h:8,
                   from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/extension.h:4,
                   from deepwave/scalar/scalar_wrapper.cpp:1:
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: In member function ‘at::meta::structured_any_dim::precompute_out<true> at::meta::structured_any_dim::precompute_out<<anonymous> >::set_dim(int64_t)’:
  /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:55:43: error: static assertion failed: dim already set
     55 |                         static_assert(DIM == false, "dim already set");
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for deepwave
  Running setup.py clean for deepwave
Failed to build deepwave
Installing collected packages: deepwave
    Running setup.py install for deepwave ... error
    ERROR: Command errored out with exit status 1:
     command: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-pkuwdw4n/install-record.txt --single-version-externally-managed --compile --install-headers /home/yxm906/anaconda3/envs/seis/include/python3.9/deepwave
         cwd: /tmp/pip-req-build-3vx65ncm/
    Complete output (72 lines):
    Warning: 'classifiers' should be a list, got type 'tuple'
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/wavelets.py -> build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/__init__.py -> build/lib.linux-x86_64-3.9/deepwave
    copying deepwave/utils.py -> build/lib.linux-x86_64-3.9/deepwave
    creating build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/scalar.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/scalar_born.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    copying deepwave/scalar/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/scalar
    creating build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/pad.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/model.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/propagator.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/extract.py -> build/lib.linux-x86_64-3.9/deepwave/base
    copying deepwave/base/__init__.py -> build/lib.linux-x86_64-3.9/deepwave/base
    running build_ext
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:381: UserWarning: Attempted to use ninja as the BuildExtension backend but we could not find ninja.. Falling back to using the slow distutils backend.
      warnings.warn(msg.format('we could not find ninja.'))
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/utils/cpp_extension.py:782: UserWarning: The detected CUDA version (11.1) has a minor version mismatch with the version that was used to compile PyTorch (11.3). Most likely this shouldn't be a problem.
      warnings.warn(CUDA_MISMATCH_WARN.format(cuda_str_version, torch.version.cuda))
    building 'scalar1d_cpu_iso_8_float' extension
    creating build/temp.linux-x86_64-3.9
    creating build/temp.linux-x86_64-3.9/deepwave
    creating build/temp.linux-x86_64-3.9/deepwave/scalar
    gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
    gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar_cpu.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar_cpu.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
    gcc -pthread -B /home/yxm906/anaconda3/envs/seis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -I/home/yxm906/anaconda3/envs/seis/include -fPIC -O2 -isystem /home/yxm906/anaconda3/envs/seis/include -fPIC -DDIM=1 -DTYPE=float -Ideepwave/scalar -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/TH -I/home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/THC -I/home/yxm906/anaconda3/envs/seis/include/python3.9 -c deepwave/scalar/scalar_wrapper.cpp -o build/temp.linux-x86_64-3.9/deepwave/scalar/scalar_wrapper.o -Ofast -march=native -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=scalar1d_cpu_iso_8_float -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
    <command-line>: error: expected ‘>’ before numeric constant
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:34:32: note: in expansion of macro ‘DIM’
       34 |                 template <bool DIM = false>
          |                                ^~~
    In file included from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeFunctions.h:6,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/TensorIndexing.h:11,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/ATen.h:20,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/types.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader_options.h:4,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/base.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/stateful.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/all.h:8,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/extension.h:4,
                     from deepwave/scalar/scalar_wrapper.cpp:1:
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: In member function ‘at::meta::structured_all_dim::precompute_out<true> at::meta::structured_all_dim::precompute_out<<anonymous> >::set_dim(int64_t)’:
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:38:43: error: static assertion failed: dim already set
       38 |                         static_assert(DIM == false, "dim already set");
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: At global scope:
    <command-line>: error: expected ‘>’ before numeric constant
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:51:32: note: in expansion of macro ‘DIM’
       51 |                 template <bool DIM = false>
          |                                ^~~
    In file included from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeFunctions.h:6,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/TensorIndexing.h:11,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/ATen.h:20,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/types.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader_options.h:4,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/base.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader/stateful.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data/dataloader.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/data.h:3,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/csrc/api/include/torch/all.h:8,
                     from /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/torch/extension.h:4,
                     from deepwave/scalar/scalar_wrapper.cpp:1:
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h: In member function ‘at::meta::structured_any_dim::precompute_out<true> at::meta::structured_any_dim::precompute_out<<anonymous> >::set_dim(int64_t)’:
    /home/yxm906/anaconda3/envs/seis/lib/python3.9/site-packages/torch/include/ATen/NativeMetaFunctions.h:55:43: error: static assertion failed: dim already set
       55 |                         static_assert(DIM == false, "dim already set");
    error: command '/usr/bin/gcc' failed with exit code 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/yxm906/anaconda3/envs/seis/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-3vx65ncm/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-pkuwdw4n/install-record.txt --single-version-externally-managed --compile --install-headers /home/yxm906/anaconda3/envs/seis/include/python3.9/deepwave Check the logs for full command output.

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ar4 commented Jan 17, 2022

That's great, and I'm glad that the fix was so easy.

I think the 8th order version should work now (I had to rename some macros to avoid a conflict as recent PyTorch versions have also started using the same names). I haven't integrated the ability to switch to the 8th order version in the master branch as the results didn't look much less dispersive to me (maybe even higher order of accuracy is needed), but hopefully it is still useful.

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That was quick! Thank you, Alan!

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ar4 commented Jun 5, 2022

Hi Yong,

The ability to select the 8th order propagator (as well as 2nd, 4th, or 6th), as well as a better PML and other improvements, is now included in the master branch. Unfortunately the performance of the pure TorchScript version that I hoped to use was inadequate, so it is still necessary to compile C++/CUDA code. I am trying a slightly different approach to that now, though, which might be less problematic for users (but I expect it will still be the main source of issues). The current implementation of the new PML makes this release a bit slower than the previous one, but I hope to reduce the difference in the next release.

-Alan

@ar4 ar4 closed this as completed Jun 5, 2022
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