crYOLO

root@ubuntu:~# cat /etc/os-release
NAME="Ubuntu"
VERSION="21.04 (Hirsute Hippo)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 21.04"
VERSION_ID="21.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=hirsute
UBUNTU_CODENAME=hirsute
 
root@ubuntu:~# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f61-5aa00052d084)
 
root@ubuntu:~#
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
eval "$(pyenv init - --no-rehash)"
 
 
 
pyenv install anaconda3-5.3.1
pyenv global anaconda3-5.3.1
export PATH=$PYENV_ROOT/versions/anaconda3-5.3.1/bin/:$PATH
conda update conda
conda create -n cryolo-1.8.0-c11 -c conda-forge -c anaconda pyqt=5 python=3.8 numpy=1.16 libtiff wxPython=4.1.1 adwaita-icon-theme
source activate cryolo-1.8.0-c11
pip install nvidia-pyindex
pip install nvidia-tensorflow[horovod]
pip install 'cryolo[c11]'
(cryolo-1.8.0-c11) root@ubuntu:~/cryolo# cryolo_predict.py -c config_cryolo_.json -w /mnt/gmodel_phosnet_202005_N63_c17.h5 -i test*.mrc -o ./
2021-12-27 21:09:46.172254: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
WARNING:root:Limited tf.compat.v2.summary API due to missing TensorBoard installation.
Using TensorFlow backend.
2021-12-27 21:09:46.665517: I tensorflow/core/platform/cpu_feature_guard.cc:145] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX
2021-12-27 21:09:46.669201: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3792000000 Hz
2021-12-27 21:09:46.669367: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55734762d560 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-12-27 21:09:46.669414: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version
2021-12-27 21:09:46.670672: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2021-12-27 21:09:47.075740: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.075920: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55734747b6a0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:
2021-12-27 21:09:47.075969: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): NVIDIA RTX A2000, Compute Capability 8.6
2021-12-27 21:09:47.076130: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.076266: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1666] Found device 0 with properties:
name: NVIDIA RTX A2000 major: 8 minor: 6 memoryClockRate(GHz): 1.2
pciBusID: 0000:0b:00.0
2021-12-27 21:09:47.076386: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
2021-12-27 21:09:47.078845: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
2021-12-27 21:09:47.096837: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
2021-12-27 21:09:47.097060: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
2021-12-27 21:09:47.097536: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.11
2021-12-27 21:09:47.099335: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.11
2021-12-27 21:09:47.099487: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
2021-12-27 21:09:47.099594: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.099758: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.099877: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1794] Adding visible gpu devices: 0
2021-12-27 21:09:47.099946: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.11.0
2021-12-27 21:09:47.299591: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1206] Device interconnect StreamExecutor with strength 1 edge matrix:
2021-12-27 21:09:47.299688: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1212]      0
2021-12-27 21:09:47.299723: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1225] 0:   N
2021-12-27 21:09:47.299907: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.300102: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:1082] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2021-12-27 21:09:47.300240: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1351] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 3904 MB memory) -> physical GPU (device: 0, name: NVIDIA RTX A2000, pci bus id: 0000:0b:00.0, compute capability: 8.6)
/apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo-1.8.0-c11/lib/python3.8/site-packages/mrcfile/mrcinterpreter.py:209: RuntimeWarning: Map ID string not found - not an MRC file, or file is corrupt
  warnings.warn(msg, RuntimeWarning)
/apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo-1.8.0-c11/lib/python3.8/site-packages/mrcfile/mrcinterpreter.py:219: RuntimeWarning: Unrecognised machine stamp: 0x00 0x00 0x00 0x00
  warnings.warn(str(err), RuntimeWarning)
Load crYOLO model which was trained with 1.7.0b2
Read Anchor from model [3.2220039292730847, 3.2220039292730847]
Initialization of model with /apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo-1.8.0-c11/lib/python3.8/site-packages/cryolo/full_yolo_backend.h5
 
 Load weights:  /mnt/gmodel_phosnet_202005_N63_c17.h5
Filtering  /root/cryolo/test7.mrc ( Progress: 50 % )
Filtering  /root/cryolo/test8.mrc ( Progress: 100 % )
Time needed for filtering: 0.27701520919799805
Reset progress bar: ( Progress: -1 % )
2021-12-27 21:09:52.137615: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.8
2021-12-27 21:09:53.902892: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.11
497 particles are found in image batch 1  /  1  ( Progress:  100 % )
#####################################
497 particles in total has been found ( 6 seconds)
Deleted 52 particles as they were not fully immersed in the micrograph
Deleted 0 particles as they were out of specified size range
#####################################
#####################################
 
## Particle diameter distribution ##
MEAN: 224 px
SD: 16 px
25%-Quantile: 211 px
50%-Quantile: 222 px
75%-Quantile: 237 px
Wrote particle size distribution summary to ./DISTR/size_distribution_summary_20211227-211000.txt
Wrote plot of particle size distribution to ./DISTR/size_distribution_20211227-211000.png
 
## Particle confidence distribution ##
Wrote confidence distribution summary ./DISTR/confidence_distribution_summary_20211227-211000.txt
Wrote confidence distribution to ./DISTR/confidence_distribution_20211227-211000.png
 
#####################################
(cryolo-1.8.0-c11) root@ubuntu:~/cryolo#
(cryolo-1.8.0-c11) root@ubuntu:~/cryolo# conda list
# packages in environment at /apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo-1.8.0-c11:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
absl-py                   1.0.0                    pypi_0    pypi
adwaita-icon-theme        41.0                 ha770c72_1    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
ansi2html                 1.6.0                    pypi_0    pypi
astor                     0.8.1                    pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
atk-1.0                   2.36.0               h3371d22_4    conda-forge
brotlipy                  0.7.0           py38h497a2fe_1003    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
certifi                   2021.10.8        py38h578d9bd_1    conda-forge
cffi                      1.15.0           py38h3931269_0    conda-forge
charset-normalizer        2.0.9              pyhd8ed1ab_0    conda-forge
cloudpickle               2.0.0                    pypi_0    pypi
colored                   1.4.3                    pypi_0    pypi
cryolo                    1.8.0                    pypi_0    pypi
cryolobm                  1.4.1                    pypi_0    pypi
cryptography              36.0.1           py38h3e25421_0    conda-forge
cycler                    0.11.0                   pypi_0    pypi
cython                    0.29.26                  pypi_0    pypi
dbus                      1.13.6               h5008d03_3    conda-forge
expat                     2.4.2                h9c3ff4c_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gast                      0.3.3                    pypi_0    pypi
gdk-pixbuf                2.42.6               h04a7f16_0    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
glib                      2.70.2               h780b84a_0    conda-forge
glib-tools                2.70.2               h780b84a_0    conda-forge
gooeydev                  1.0.8b4                  pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
graphite2                 1.3.13            h58526e2_1001    conda-forge
grpcio                    1.43.0                   pypi_0    pypi
gst-plugins-base          1.18.5               hf529b03_2    conda-forge
gstreamer                 1.18.5               h9f60fe5_2    conda-forge
gtk2                      2.24.33              h539f30e_1    conda-forge
h5py                      2.10.0                   pypi_0    pypi
harfbuzz                  2.9.1                h83ec7ef_1    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       68.2                 h9c3ff4c_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
imageio                   2.13.5                   pypi_0    pypi
janni                     0.3.0b5                  pypi_0    pypi
jbig                      2.1               h7f98852_2003    conda-forge
joblib                    1.1.0                    pypi_0    pypi
jpeg                      9d                   h36c2ea0_0    conda-forge
keras                     2.3.1                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.3.2                    pypi_0    pypi
krb5                      1.19.2               hcc1bbae_3    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           12_linux64_openblas    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libdeflate                1.8                  h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            11.2.0              h69a702a_11    conda-forge
libgfortran5              11.2.0              h5c6108e_11    conda-forge
libglib                   2.70.2               h174f98d_0    conda-forge
libglu                    9.0.0             he1b5a44_1001    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.5                 hd57d9b9_1    conda-forge
librsvg                   2.52.5               hc3c00ef_0    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libtiff                   4.3.0                h6f004c6_2    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.1                h7f98852_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lineenhancer              1.0.9.dev2               pypi_0    pypi
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
matplotlib                3.4.3                    pypi_0    pypi
mrcfile                   1.3.0                    pypi_0    pypi
mysql-common              8.0.27               ha770c72_3    conda-forge
mysql-libs                8.0.27               hfa10184_3    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
networkx                  2.6.3                    pypi_0    pypi
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.73                 hb5efdd6_0    conda-forge
numpy                     1.18.5                   pypi_0    pypi
nvidia-cublas-cu115       11.7.4.6                 pypi_0    pypi
nvidia-cuda-cupti-cu115   11.5.114                 pypi_0    pypi
nvidia-cuda-nvcc-cu115    11.5.119                 pypi_0    pypi
nvidia-cuda-runtime-cu115 11.5.117                 pypi_0    pypi
nvidia-cudnn-cu115        8.3.1.22                 pypi_0    pypi
nvidia-cufft-cu115        10.6.0.107               pypi_0    pypi
nvidia-curand-cu115       10.2.7.107               pypi_0    pypi
nvidia-cusolver-cu115     11.3.2.107               pypi_0    pypi
nvidia-cusparse-cu115     11.7.0.107               pypi_0    pypi
nvidia-dali-cuda110       1.8.0                    pypi_0    pypi
nvidia-dali-nvtf-plugin   1.8.0+nv21.12            pypi_0    pypi
nvidia-horovod            0.22.1+nv21.12           pypi_0    pypi
nvidia-nccl-cu115         2.11.4                   pypi_0    pypi
nvidia-pyindex            1.0.9                    pypi_0    pypi
nvidia-tensorflow         1.15.5+nv21.12           pypi_0    pypi
openssl                   1.1.1l               h7f98852_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    1.1.4                    pypi_0    pypi
pango                     1.48.10              hb8ff022_1    conda-forge
pathlib2                  2.3.6            py38h578d9bd_1    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    8.4.0                    pypi_0    pypi
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
protobuf                  3.19.1                   pypi_0    pypi
psutil                    5.8.0                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygtrie                   2.4.2                    pypi_0    pypi
pyopenssl                 21.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.6                    pypi_0    pypi
pypubsub                  4.0.3                      py_0    conda-forge
pyqt                      5.12.3           py38h578d9bd_8    conda-forge
pyqt-impl                 5.12.3           py38h0ffb2e6_8    conda-forge
pyqt5-sip                 4.19.18          py38h709712a_8    conda-forge
pyqtchart                 5.12             py38h7400c14_8    conda-forge
pyqtwebengine             5.12.1           py38h7400c14_8    conda-forge
pysocks                   1.7.1            py38h578d9bd_4    conda-forge
pystardb                  0.3.1                    pypi_0    pypi
python                    3.8.12          hb7a2778_2_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.8                      2_cp38    conda-forge
pytz                      2021.3                   pypi_0    pypi
pywavelets                1.2.0                    pypi_0    pypi
pyyaml                    6.0                      pypi_0    pypi
qt                        5.12.9               hda022c4_4    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_1    conda-forge
scikit-image              0.19.1                   pypi_0    pypi
scikit-learn              0.23.2                   pypi_0    pypi
scipy                     1.7.3                    pypi_0    pypi
setuptools                60.1.0           py38h578d9bd_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
tensorboard               1.15.0                   pypi_0    pypi
tensorflow-estimator      1.15.1                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminaltables            3.1.10                   pypi_0    pypi
threadpoolctl             3.0.0                    pypi_0    pypi
tifffile                  2020.9.3                 pypi_0    pypi
tk                        8.6.11               h27826a3_1    conda-forge
tqdm                      4.62.3                   pypi_0    pypi
trackpy                   0.5.0                    pypi_0    pypi
urllib3                   1.26.7             pyhd8ed1ab_0    conda-forge
watchdog                  2.1.6                    pypi_0    pypi
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.13.3                   pypi_0    pypi
wxpython                  4.1.1            py38h1c15066_3    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.1                ha95c52a_0    conda-forge
(cryolo-1.8.0-c11) root@ubuntu:~/cryolo#

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Last-modified: 2022-03-18 (金) 20:07:24 (154d)