Building from Docker on clean machine fails #49
Comments
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@fboemer Hi Fabian, could you please look into this issue with copying the file. The dockuser is given sudo access (in contrib/docker/run_as_ubuntu_user.sh) but this command: |
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This might solve the problem with sudo access: https://github.com/IntelAI/he-transformer/blob/be835adf0aa0953f0eafab734080add58249b241/contrib/docker/run_as_ubuntu_user.sh#L88 |
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@adam-dziedzic @fboemer Hello, I am getting the same error as above while trying to install he-transformer with docker. I have uncommented the line https://github.com/IntelAI/he-transformer/blob/be835adf0aa0953f0eafab734080add58249b241/contrib/docker/run_as_ubuntu_user.sh#L90 and moreover added "RUN useradd -m docker && echo "docker:docker" | chpasswd && adduser docker sudo" in the dockerfile. Unfortunately, I still get the same error about permission. I was wondering if there is any solution to this issue. Thank you! |
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Check my answer here: #51 |
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@adam-dziedzic Thank you so much for your fast reply! So I have installed ABY and I already had g++ version 9.5 and installed boost library. After installing all the libraries I have mentioned, I ran again "make check_all OS_ID=ubuntu1804", should this work? Thanks however, I didn't really get the point of how to install he-transformer using ABY. Do I just run again the command to make check_all? Thanks a lot for your help! |
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After that, I installed all the targets in the makefile separately until I could do |
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@adam-dziedzic do you mind contacting me at gp3917@ic.ac.uk so that I don't spam here? I was wondering if you have a VM with he-transformer already installed where I could test my code since literally I cant install it. Thanks |
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Hi, I experience the same permission denied problem. Is this issue resolved? |
In trying to build this project using the docker images, with the following commands:
make check_gss OS_ID=ubuntu1804 RM_CONTAINER=false
and
make check_gss OS_ID=ubuntu1804
on a clean matching with ubuntu 20 OS and docker version 19.03.12
I run into the error pasted below. I tried using the details in #45 to resolve this issue but have not been able to install the docker image to our clean machine.
`Installing collected packages: ngraph-tensorflow-bridge
Successfully installed ngraph-tensorflow-bridge-0.22.0rc3
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1
type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (
1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3/lib/
python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1
) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (
type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
ARTIFACTS location: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cm
ake/artifacts
Loading virtual environment from: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngra
ph_tf/build_cmake/venv-tf-py3
Loading virtual environment from: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngra
ph_tf/build_cmake/venv-tf-py3
PIP location
Target Arch: native
Building TensorFlow from source
PYTHON_BIN_PATH: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake
/venv-tf-py3/bin/python
SOURCE DIR: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/tens
orflow
ARTIFACTS DIR: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/a
rtifacts/tensorflow
TF Wheel: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/artifa
cts/tensorflow/tensorflow-1.14.0-cp36-cp36m-linux_x86_64.whl
PYTHON_BIN_PATH: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake
/venv-tf-py3/bin/python
SOURCE DIR: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/tens
orflow
ARTIFACTS DIR: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/a
rtifacts/tensorflow
Cannot remove: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/a
rtifacts/tensorflow/libtensorflow_cc.so.1
Copying bazel-bin/tensorflow/libtensorflow_cc.so.1 to /home/dockuser/he-transformer-test/BUILD-GCC/ext_ng
raph_tf/src/ext_ngraph_tf/build_cmake/artifacts/tensorflow
Loading virtual environment from: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngra
ph_tf/build_cmake/venv-tf-py3
LIB: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3
/lib/python3.6/site-packages/tensorflow
CXX_ABI: 1
Using local nGraph source in directory /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph/src/ext_n
graph
Source location: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph/src/ext_ngraph
Running COMMAND: cmake -DNGRAPH_INSTALL_PREFIX=/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf
/src/ext_ngraph_tf/build_cmake/artifacts -DNGRAPH_USE_CXX_ABI=1 -DNGRAPH_DEX_ONLY=TRUE -DNGRAPH_DEBUG_ENA
BLE=NO -DNGRAPH_UNIT_TEST_ENABLE=NO -DNGRAPH_TARGET_ARCH=native -DNGRAPH_TUNE_ARCH=native -DNGRAPH_TBB_EN
ABLE=FALSE -DNGRAPH_DISTRIBUTED_ENABLE=OFF -DNGRAPH_TOOLS_ENABLE=YES -DNGRAPH_GPU_ENABLE=NO -DNGRAPH_PLAI
DML_ENABLE=NO -DNGRAPH_INTELGPU_ENABLE=NO /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph/src/ext
_ngraph
Running COMMAND: make -j20
Running COMMAND: make install
TF_SRC_DIR: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/ten
sorflow
Loading virtual environment from: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngra
ph_tf/build_cmake/venv-tf-py3
Source location: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf
OUTPUT WHL FILE: ngraph_tensorflow_bridge-0.22.0rc3-py2.py3-none-manylinux1_x86_64.whl
OUTPUT WHL DST: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/
artifacts/ngraph_tensorflow_bridge-0.22.0rc3-py2.py3-none-manylinux1_x86_64.whl
SUCCESSFULLY generated wheel: ngraph_tensorflow_bridge-0.22.0rc3-py2.py3-none-manylinux1_x86_64.whl
PWD: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake
Running COMMAND: cp -r /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build
_cmake/tensorflow/tensorflow/python /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ng
raph_tf/build_cmake/artifacts/tensorflow
Loading virtual environment from: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngra
ph_tf/build_cmake/venv-tf-py3
Version information
TensorFlow version: 1.14.0
C Compiler version used in building TensorFlow: 7.5.0
nGraph bridge version: b'0.22.0-rc3'
nGraph version used for this build: b'0.28.0-rc.1+d2cd873'
TensorFlow version used for this build: v1.14.0-0-g87989f6959
CXX11_ABI flag used for this build: 1
nGraph bridge built with Grappler: True
nGraph bridge built with Variables and Optimizers Enablement: False
nGraph bridge built with Distributed Build: 0
Build successful
cd /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf && /usr/local/lib/python3
.6/dist-packages/cmake/data/bin/cmake -E touch /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf
/src/ext_ngraph_tf-stamp/ext_ngraph_tf-build
[100%] Performing install step for 'ext_ngraph_tf'
cd /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf && ln -fs /home/dockuser/
he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/venv-tf-py3 /home/dockuser/he-t
ransformer-test/BUILD-GCC/external
cd /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf && /usr/local/lib/python3
.6/dist-packages/cmake/data/bin/cmake -E touch /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf
/src/ext_ngraph_tf-stamp/ext_ngraph_tf-install
[100%] Completed 'ext_ngraph_tf'
/usr/local/lib/python3.6/dist-packages/cmake/data/bin/cmake -E make_directory /home/dockuser/he-transform
er-test/BUILD-GCC/CMakeFiles
/usr/local/lib/python3.6/dist-packages/cmake/data/bin/cmake -E touch /home/dockuser/he-transformer-test/B
UILD-GCC/CMakeFiles/ext_ngraph_tf-complete
/usr/local/lib/python3.6/dist-packages/cmake/data/bin/cmake -E touch /home/dockuser/he-transformer-test/B
UILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf-stamp/ext_ngraph_tf-done
make[2]: Leaving directory '/home/dockuser/he-transformer-test/BUILD-GCC'
[100%] Built target ext_ngraph_tf
make[1]: Leaving directory '/home/dockuser/he-transformer-test/BUILD-GCC'
/usr/local/lib/python3.6/dist-packages/cmake/data/bin/cmake -E cmake_progress_start /home/dockuser/he-tra
nsformer-test/BUILD-GCC/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/home/dockuser/he-transformer-test/BUILD-GCC'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/home/dockuser/he-transformer-test/BUILD-GCC'
Install the project...
/usr/local/lib/python3.6/dist-packages/cmake/data/bin/cmake -P cmake_install.cmake
-- Install configuration: "RelWithDebInfo"
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libdnnl.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libngraph_test_util.a
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libngraph.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libmklml_intel.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libcpu_backend.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libiomp5.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libngraph_bridge.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libnop_backend.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libinterpreter_backend.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libngraph_bridge_device.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libgcpu_backend.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/include/ngraph_backend_manager.h
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/include/ngraph_log.h
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/include/ngraph/version.hpp
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libz.so.1.2.11
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libz.so.1
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libz.so
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/zlibstatic.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/minigzip.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/minigzip.dir/test
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/CheckTypeSize
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/example.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/example.dir/test
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/minigzip64.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/minigzip64.dir/test
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/3.18.2
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/3.18.2/CompilerIdC
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/3.18.2/CompilerIdC/tm
p
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/CMakeTmp
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/zlib.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/example64.dir
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/CMakeFiles/example64.dir/test
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libz.a
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libhe_seal_backend.so
-- Set runtime path of "/home/dockuser/he-transformer-test/BUILD-GCC/external/lib/libhe_seal_backend.so"
to "$ORIGIN"
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/v
env-tf-py3/lib/python3.6/site-packages/ngraph_bridge/libhe_seal_backend.so
-- Set runtime path of "/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/buil
d_cmake/venv-tf-py3/lib/python3.6/site-packages/ngraph_bridge/libhe_seal_backend.so" to "$ORIGIN"
-- Installing: /home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/build_cmake/a
rtifacts/lib/libhe_seal_backend.so
-- Set runtime path of "/home/dockuser/he-transformer-test/BUILD-GCC/ext_ngraph_tf/src/ext_ngraph_tf/buil
d_cmake/artifacts/lib/libhe_seal_backend.so" to "$ORIGIN"
-- Installing: /usr/local/lib/libhe_seal_backend.so
CMake Error at src/cmake_install.cmake:153 (file):
file INSTALL cannot copy file
"/home/dockuser/he-transformer-test/BUILD-GCC/src/libhe_seal_backend.so" to
"/usr/local/lib/libhe_seal_backend.so": Success.
Call Stack (most recent call first):
cmake_install.cmake:83 (include)
Makefile:104: recipe for target 'install' failed
$USER@equus:~/Documents/he-transformer/contrib/docker$ ls
$USER@equus:~/Documents/he-transformer/contrib/docker$ `
make: *** [install] Error 1
make: *** [Makefile:157: build_gcc] Error 2
build_docker_image.sh Dockerfile.he_transformer.fedora28 Makefile
build-he-transformer-and-test.sh Dockerfile.he_transformer.ubuntu1604 ngraph-tf.cmake
CMakeLists.txt Dockerfile.he_transformer.ubuntu1804 README.md
docker_cleanup.sh fix_numpy_for_tf.patch run_as_centos_user.sh
Dockerfile make-dimage.sh run_as_fedora_user.sh
Dockerfile.he_transformer.centos74 make_docker_image.sh run_as_ubuntu_user.sh
The text was updated successfully, but these errors were encountered: