Comments (27)
jakirkham
commented on July 18, 2024
Could you please include the result of conda env export for the environment in question?
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JarnoRFB
commented on July 18, 2024
The output of $ conda env export is:
name: test
channels:
- defaults
dependencies:
- boost=1.61.0=py36_0
- caffe=1.0.0rc5=np112py36_0
- cycler=0.10.0=py36_0
- dbus=1.10.20=0
- decorator=4.1.2=py36_0
- expat=2.1.0=0
- fontconfig=2.12.1=3
- freetype=2.5.5=2
- gflags=2.2.0=1
- glib=2.50.2=1
- glog=0.3.5=0
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=0
- h5py=2.7.0=np112py36_0
- hdf5=1.8.17=2
- icu=54.1=0
- ipython=6.1.0=py36_0
- ipython_genutils=0.2.0=py36_0
- jbig=2.1=0
- jedi=0.10.2=py36_2
- jpeg=8d=2
- leveldb=1.20=0
- libffi=3.2.1=1
- libgcc=5.2.0=0
- libgfortran=3.0.0=1
- libiconv=1.14=0
- libpng=1.6.27=0
- libprotobuf=3.2.0=0
- libtiff=4.0.6=2
- libxcb=1.12=1
- libxml2=2.9.4=0
- lmdb=0.9.21=0
- matplotlib=2.0.2=np112py36_0
- mkl=2017.0.3=0
- networkx=1.11=py36_0
- numpy=1.12.1=py36_0
- opencv=3.1.0=np112py36_1
- openssl=1.0.2l=0
- pandas=0.20.3=py36_0
- path.py=10.3.1=py36_0
- pcre=8.39=1
- pexpect=4.2.1=py36_0
- pickleshare=0.7.4=py36_0
- pillow=3.4.2=py36_0
- pip=9.0.1=py36_1
- prompt_toolkit=1.0.15=py36_0
- protobuf=3.2.0=py36_0
- ptyprocess=0.5.2=py36_0
- pygments=2.2.0=py36_0
- pyparsing=2.2.0=py36_0
- pyqt=5.6.0=py36_2
- python=3.6.2=0
- python-dateutil=2.6.1=py36_0
- python-gflags=3.1.1=py36_0
- python-leveldb=0.194=py36_1
- pytz=2017.2=py36_0
- pywavelets=0.5.2=np112py36_0
- pyyaml=3.12=py36_0
- qt=5.6.2=2
- readline=6.2=2
- scikit-image=0.13.0=np112py36_0
- scipy=0.19.1=np112py36_0
- setuptools=27.2.0=py36_0
- simplegeneric=0.8.1=py36_1
- sip=4.18=py36_0
- six=1.10.0=py36_0
- snappy=1.1.6=0
- sqlite=3.13.0=0
- tk=8.5.18=0
- traitlets=4.3.2=py36_0
- wcwidth=0.1.7=py36_0
- wheel=0.29.0=py36_0
- xz=5.2.3=0
- yaml=0.1.6=0
- zlib=1.2.11=0
- pip:
- ipython-genutils==0.2.0
- prompt-toolkit==1.0.15
prefix: /work/miniconda/envs/test
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djsutherland
commented on July 18, 2024
Note that this recipe is only built for python 2.7, so you're actually using caffe from the default repositories.
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JarnoRFB
commented on July 18, 2024
So the version from this feedstock is only for Python 2.7?
When I try to install it inside a Python 2 environment I get even more errors though...
For
$ conda create -n caffe_test python=2.7
$ source activate caffe_test
$ conda install -c conda-forge caffe
$ convert_imageset
I get convert_imageset: error while loading shared libraries: libprotobuf.so.14: cannot open shared object file: No such file or directory
And similarly
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/__init__.py", line 1, in <module>
from .pycaffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, RMSPropSolver, AdaDeltaSolver, AdamSolver, NCCL, Timer
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/pycaffe.py", line 13, in <module>
from ._caffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, \
ImportError: libprotobuf.so.14: cannot open shared object file: No such file or directoryThe fix from #31 $ conda install protobuf=3.2 did not improve the situation.
The output of $ conda env export is
name: caffe_test
channels:
- conda-forge
- defaults
dependencies:
- backports.shutil_get_terminal_size=1.0.0=py27_1
- backports_abc=0.5=py27_0
- blas=1.1=openblas
- boost=1.64.0=py27_4
- boost-cpp=1.64.0=1
- bzip2=1.0.6=1
- caffe=1.0.0rc4=py27_blas_openblas_203
- cairo=1.14.6=4
- cycler=0.10.0=py27_0
- decorator=4.1.2=py27_0
- enum34=1.1.6=py27_1
- ffmpeg=3.2.4=1
- fontconfig=2.12.1=4
- freetype=2.7=1
- functools32=3.2.3.2=py27_1
- gettext=0.19.7=1
- gflags=2.2.0=1
- giflib=5.1.4=0
- glib=2.51.4=0
- glog=0.3.5=0
- h5py=2.7.1=py27_1
- harfbuzz=1.3.4=2
- hdf5=1.8.18=0
- icu=58.1=1
- ipython=5.4.1=py27_0
- ipython_genutils=0.2.0=py27_0
- jasper=1.900.1=4
- jpeg=9b=0
- leveldb=1.18=0
- libffi=3.2.1=3
- libiconv=1.14=4
- libpng=1.6.28=0
- libtiff=4.0.6=7
- libwebp=0.5.2=7
- libxml2=2.9.4=4
- lmdb=0.9.18=1
- matplotlib=2.0.0=np112py27_2
- networkx=1.11=py27_0
- numpy=1.12.1=py27_blas_openblas_200
- olefile=0.44=py27_0
- openblas=0.2.19=2
- opencv=3.2.0=np112py27_blas_openblas_203
- pandas=0.20.3=py27_1
- pango=1.40.3=3
- pathlib2=2.3.0=py27_0
- pcre=8.39=0
- pexpect=4.2.1=py27_0
- pickleshare=0.7.4=py27_0
- pillow=4.2.1=py27_0
- pixman=0.34.0=0
- prompt_toolkit=1.0.15=py27_0
- protobuf=3.3.2=py27_0
- ptyprocess=0.5.2=py27_0
- pygments=2.2.0=py27_0
- pyparsing=2.2.0=py27_0
- pyqt=4.11.4=py27_2
- python-dateutil=2.6.1=py27_0
- python-gflags=2.0=py27_1
- python-leveldb=0.193=py27_0
- pytz=2017.2=py27_0
- pyyaml=3.12=py27_1
- qt=4.8.7=7
- scandir=1.5=py27_1
- scikit-image=0.12.3=np112py27_0
- scipy=0.19.1=py27_blas_openblas_202
- simplegeneric=0.8.1=py27_0
- singledispatch=3.4.0.3=py27_0
- sip=4.18=py27_1
- six=1.10.0=py27_1
- snappy=1.1.6=1
- ssl_match_hostname=3.5.0.1=py27_1
- subprocess32=3.2.7=py27_0
- tornado=4.5.2=py27_0
- traitlets=4.3.2=py27_0
- wcwidth=0.1.7=py27_0
- x264=20131217=3
- xz=5.2.3=0
- yaml=0.1.6=0
- certifi=2016.2.28=py27_0
- libgfortran=3.0.0=1
- openssl=1.0.2l=0
- pip=9.0.1=py27_1
- python=2.7.13=0
- readline=6.2=2
- setuptools=36.4.0=py27_0
- sqlite=3.13.0=0
- tk=8.5.18=0
- wheel=0.29.0=py27_0
- zlib=1.2.11=0
- pip:
- backports-abc==0.5
- backports.shutil-get-terminal-size==1.0.0
- backports.ssl-match-hostname==3.5.0.1
- ipython-genutils==0.2.0
- prompt-toolkit==1.0.15
prefix: /work/miniconda/envs/caffe_test
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djsutherland
commented on July 18, 2024
Those are because this recipe doesn't pin protobuf (a bug). Try conda install -c conda-forge protobuf=3.2 to work around.
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JarnoRFB
commented on July 18, 2024
Unfortunately, that did not help either.
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djsutherland
commented on July 18, 2024
Oh, wait, it's looking for .14? That's protobuf 3.4 I think, but I'm confused by that.
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JarnoRFB
commented on July 18, 2024
Alright so after doing
$ conda install -c conda-forge protobuf=3.4 convert_imageset works, but now $ python -c "import caffe" gives me
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/__init__.py", line 1, in <module>
from .pycaffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, RMSPropSolver, AdaDeltaSolver, AdamSolver, NCCL, Timer
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/pycaffe.py", line 13, in <module>
from ._caffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, \
ImportError: numpy.core.multiarray failed to import
Only after $ conda install -c conda-forge numpy=1.13 this works as well, which is strange since conda should install the right numpy version in the first place.
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djsutherland
commented on July 18, 2024
That problem is because you have numpy installed from defaults, using MKL, and it's not compatible with the openblas-based numpy in conda-forge. You might have problems with scipy and similar too. See conda-forge/conda-forge.github.io#434
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JarnoRFB
commented on July 18, 2024
But how can I avoid this? Even if I set conda-forge to be highest priority by doing conda config --add channels conda-forge I get exactly the same behavior. And shouldn't conda be able to figure out this things on its own, so the end user does not have to think about getting the right dependencies together. I have only known conda from this end user perspective so I am a bit confused.
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jakirkham
commented on July 18, 2024
Please try conda install blas=*=openblas.
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JarnoRFB
commented on July 18, 2024
The output of $ conda install blas=*=openblas is
# All requested packages already installed.
# packages in environment at /work/miniconda/envs/caffe_test:
#
blas 1.1 openblas conda-forge
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jakirkham
commented on July 18, 2024
Can you please share the most recent result of conda env export and conda list (sadly the environment export doesn't show channels any more
from caffe-feedstock.
JarnoRFB
commented on July 18, 2024
$ conda env export gives now
channels:
- conda-forge
- defaults
dependencies:
- asn1crypto=0.22.0=py27_0
- backports.shutil_get_terminal_size=1.0.0=py27_1
- backports_abc=0.5=py27_0
- bkcharts=0.2=py27_0
- blas=1.1=openblas
- bokeh=0.12.6=py27_0
- boost=1.64.0=py27_4
- boost-cpp=1.64.0=1
- bzip2=1.0.6=1
- ca-certificates=2017.7.27.1=0
- caffe=1.0.0rc4=py27_blas_openblas_203
- cairo=1.14.6=4
- certifi=2017.7.27.1=py27_0
- cffi=1.10.0=py27_0
- chardet=3.0.4=py27_0
- click=6.7=py27_0
- cloudpickle=0.4.0=py27_0
- cryptography=2.0.3=py27_0
- cycler=0.10.0=py27_0
- dask=0.15.2=py27_0
- dask-core=0.15.2=py27_0
- decorator=4.1.2=py27_0
- distributed=1.18.3=py27_0
- enum34=1.1.6=py27_1
- ffmpeg=3.2.4=1
- fontconfig=2.12.1=4
- freetype=2.7=1
- functools32=3.2.3.2=py27_1
- futures=3.0.5=py27_0
- gettext=0.19.7=1
- gflags=2.2.0=1
- giflib=5.1.4=0
- glib=2.51.4=0
- glog=0.3.5=0
- h5py=2.7.1=py27_1
- harfbuzz=1.3.4=2
- hdf5=1.8.18=0
- heapdict=1.0.0=py27_0
- icu=58.1=1
- idna=2.5=py27_0
- imageio=2.2.0=py27_0
- ipaddress=1.0.18=py27_0
- ipython=5.4.1=py27_0
- ipython_genutils=0.2.0=py27_0
- jasper=1.900.1=4
- jinja2=2.9.6=py27_0
- jpeg=9b=0
- leveldb=1.18=0
- libffi=3.2.1=3
- libiconv=1.14=4
- libpng=1.6.28=0
- libtiff=4.0.6=7
- libwebp=0.5.2=7
- libxml2=2.9.4=4
- lmdb=0.9.18=1
- locket=0.2.0=py27_1
- markupsafe=1.0=py27_0
- matplotlib=2.0.0=np112py27_2
- msgpack-python=0.4.8=py27_0
- ncurses=5.9=10
- networkx=1.11=py27_0
- numpy=1.12.1=py27_blas_openblas_200
- olefile=0.44=py27_0
- openblas=0.2.19=2
- opencv=3.2.0=np112py27_blas_openblas_203
- openssl=1.0.2l=0
- pandas=0.20.3=py27_1
- pango=1.40.3=3
- partd=0.3.8=py27_0
- pathlib2=2.3.0=py27_0
- pcre=8.39=0
- pexpect=4.2.1=py27_0
- pickleshare=0.7.4=py27_0
- pillow=4.2.1=py27_0
- pip=9.0.1=py27_0
- pixman=0.34.0=0
- prompt_toolkit=1.0.15=py27_0
- protobuf=3.4.0=py27_0
- psutil=5.2.2=py27_0
- ptyprocess=0.5.2=py27_0
- pycparser=2.18=py27_0
- pygments=2.2.0=py27_0
- pyopenssl=17.2.0=py27_0
- pyparsing=2.2.0=py27_0
- pyqt=4.11.4=py27_2
- pysocks=1.6.7=py27_0
- python=2.7.13=1
- python-dateutil=2.6.1=py27_0
- python-gflags=2.0=py27_1
- python-leveldb=0.193=py27_0
- pytz=2017.2=py27_0
- pywavelets=0.5.2=np112py27_0
- pyyaml=3.12=py27_1
- qt=4.8.7=7
- readline=6.2=0
- requests=2.18.4=py27_1
- scandir=1.5=py27_1
- scikit-image=0.13.0=py27_1
- scipy=0.19.1=py27_blas_openblas_202
- setuptools=36.3.0=py27_0
- simplegeneric=0.8.1=py27_0
- singledispatch=3.4.0.3=py27_0
- sip=4.18=py27_1
- six=1.10.0=py27_1
- snappy=1.1.6=1
- sortedcontainers=1.5.7=py27_0
- sqlite=3.13.0=1
- ssl_match_hostname=3.5.0.1=py27_1
- subprocess32=3.2.7=py27_0
- tblib=1.3.2=py27_0
- tk=8.5.19=2
- toolz=0.8.2=py27_0
- tornado=4.5.2=py27_0
- traitlets=4.3.2=py27_0
- urllib3=1.22=py27_0
- wcwidth=0.1.7=py27_0
- wheel=0.29.0=py27_0
- x264=20131217=3
- xz=5.2.3=0
- yaml=0.1.6=0
- zict=0.1.2=py27_0
- zlib=1.2.8=3
- libgfortran=3.0.0=1
- pip:
- backports-abc==0.5
- backports.shutil-get-terminal-size==1.0.0
- backports.ssl-match-hostname==3.5.0.1
- ipython-genutils==0.2.0
- prompt-toolkit==1.0.15
and $ conda env list gives
# packages in environment at /work/miniconda/envs/caffe_test:
#
asn1crypto 0.22.0 py27_0 conda-forge
backports.shutil_get_terminal_size 1.0.0 py27_1 conda-forge
backports_abc 0.5 py27_0 conda-forge
bkcharts 0.2 py27_0 conda-forge
blas 1.1 openblas conda-forge
bokeh 0.12.6 py27_0 conda-forge
boost 1.64.0 py27_4 conda-forge
boost-cpp 1.64.0 1 conda-forge
bzip2 1.0.6 1 conda-forge
ca-certificates 2017.7.27.1 0 conda-forge
caffe 1.0.0rc4 py27_blas_openblas_203 [blas_openblas] conda-forge
cairo 1.14.6 4 conda-forge
certifi 2017.7.27.1 py27_0 conda-forge
cffi 1.10.0 py27_0 conda-forge
chardet 3.0.4 py27_0 conda-forge
click 6.7 py27_0 conda-forge
cloudpickle 0.4.0 py27_0 conda-forge
cryptography 2.0.3 py27_0 conda-forge
cycler 0.10.0 py27_0 conda-forge
dask 0.15.2 py27_0 conda-forge
dask-core 0.15.2 py27_0 conda-forge
decorator 4.1.2 py27_0 conda-forge
distributed 1.18.3 py27_0 conda-forge
enum34 1.1.6 py27_1 conda-forge
ffmpeg 3.2.4 1 conda-forge
fontconfig 2.12.1 4 conda-forge
freetype 2.7 1 conda-forge
functools32 3.2.3.2 py27_1 conda-forge
futures 3.0.5 py27_0 conda-forge
gettext 0.19.7 1 conda-forge
gflags 2.2.0 1 conda-forge
giflib 5.1.4 0 conda-forge
glib 2.51.4 0 conda-forge
glog 0.3.5 0 conda-forge
h5py 2.7.1 py27_1 conda-forge
harfbuzz 1.3.4 2 conda-forge
hdf5 1.8.18 0 conda-forge
heapdict 1.0.0 py27_0 conda-forge
icu 58.1 1 conda-forge
idna 2.5 py27_0 conda-forge
imageio 2.2.0 py27_0 conda-forge
ipaddress 1.0.18 py27_0 conda-forge
ipython 5.4.1 py27_0 conda-forge
ipython_genutils 0.2.0 py27_0 conda-forge
jasper 1.900.1 4 conda-forge
jinja2 2.9.6 py27_0 conda-forge
jpeg 9b 0 conda-forge
leveldb 1.18 0 conda-forge
libffi 3.2.1 3 conda-forge
libgfortran 3.0.0 1
libiconv 1.14 4 conda-forge
libpng 1.6.28 0 conda-forge
libtiff 4.0.6 7 conda-forge
libwebp 0.5.2 7 conda-forge
libxml2 2.9.4 4 conda-forge
lmdb 0.9.18 1 conda-forge
locket 0.2.0 py27_1 conda-forge
markupsafe 1.0 py27_0 conda-forge
matplotlib 2.0.0 np112py27_2 conda-forge
msgpack-python 0.4.8 py27_0 conda-forge
ncurses 5.9 10 conda-forge
networkx 1.11 py27_0 conda-forge
numpy 1.12.1 py27_blas_openblas_200 [blas_openblas] conda-forge
olefile 0.44 py27_0 conda-forge
openblas 0.2.19 2 conda-forge
opencv 3.2.0 np112py27_blas_openblas_203 [blas_openblas] conda-forge
openssl 1.0.2l 0 conda-forge
pandas 0.20.3 py27_1 conda-forge
pango 1.40.3 3 conda-forge
partd 0.3.8 py27_0 conda-forge
pathlib2 2.3.0 py27_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.2.1 py27_0 conda-forge
pickleshare 0.7.4 py27_0 conda-forge
pillow 4.2.1 py27_0 conda-forge
pip 9.0.1 py27_0 conda-forge
pixman 0.34.0 0 conda-forge
prompt_toolkit 1.0.15 py27_0 conda-forge
protobuf 3.4.0 py27_0 conda-forge
psutil 5.2.2 py27_0 conda-forge
ptyprocess 0.5.2 py27_0 conda-forge
pycparser 2.18 py27_0 conda-forge
pygments 2.2.0 py27_0 conda-forge
pyopenssl 17.2.0 py27_0 conda-forge
pyparsing 2.2.0 py27_0 conda-forge
pyqt 4.11.4 py27_2 conda-forge
pysocks 1.6.7 py27_0 conda-forge
python 2.7.13 1 conda-forge
python-dateutil 2.6.1 py27_0 conda-forge
python-gflags 2.0 py27_1 conda-forge
python-leveldb 0.193 py27_0 conda-forge
pytz 2017.2 py27_0 conda-forge
pywavelets 0.5.2 np112py27_0 conda-forge
pyyaml 3.12 py27_1 conda-forge
qt 4.8.7 7 conda-forge
readline 6.2 0 conda-forge
requests 2.18.4 py27_1 conda-forge
scandir 1.5 py27_1 conda-forge
scikit-image 0.13.0 py27_1 conda-forge
scipy 0.19.1 py27_blas_openblas_202 [blas_openblas] conda-forge
setuptools 36.3.0 py27_0 conda-forge
simplegeneric 0.8.1 py27_0 conda-forge
singledispatch 3.4.0.3 py27_0 conda-forge
sip 4.18 py27_1 conda-forge
six 1.10.0 py27_1 conda-forge
snappy 1.1.6 1 conda-forge
sortedcontainers 1.5.7 py27_0 conda-forge
sqlite 3.13.0 1 conda-forge
ssl_match_hostname 3.5.0.1 py27_1 conda-forge
subprocess32 3.2.7 py27_0 conda-forge
tblib 1.3.2 py27_0 conda-forge
tk 8.5.19 2 conda-forge
toolz 0.8.2 py27_0 conda-forge
tornado 4.5.2 py27_0 conda-forge
traitlets 4.3.2 py27_0 conda-forge
urllib3 1.22 py27_0 conda-forge
wcwidth 0.1.7 py27_0 conda-forge
wheel 0.29.0 py27_0 conda-forge
x264 20131217 3 conda-forge
xz 5.2.3 0 conda-forge
yaml 0.1.6 0 conda-forge
zict 0.1.2 py27_0 conda-forge
zlib 1.2.8 3 conda-forge
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jakirkham
commented on July 18, 2024
Sorry remind me what the error message is that you are getting now? Still this one or something else?
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JarnoRFB
commented on July 18, 2024
Exactly, it's
RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/__init__.py", line 1, in <module>
from .pycaffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, RMSPropSolver, AdaDeltaSolver, AdamSolver, NCCL, Timer
File "/work/miniconda/envs/caffe_test/lib/python2.7/site-packages/caffe/pycaffe.py", line 13, in <module>
from ._caffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, \
ImportError: numpy.core.multiarray failed to import
but only after doing conda install -c conda-forge protobuf=3.4.
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jakirkham
commented on July 18, 2024
What if you just run python -c "import numpy.core.multiarray"?
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JarnoRFB
commented on July 18, 2024
That works without error...
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jakirkham
commented on July 18, 2024
What about python -c "from numpy.core.multiarray import dot"? Also may want to run echo $? right after these commands to verify there is not a silent error.
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JarnoRFB
commented on July 18, 2024
The result from python -c "from numpy.core.multiarray import dot" | echo $? is just 0.
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jakirkham
commented on July 18, 2024
We are rebuilding with the latest protobuf. Once it is out, could you please recheck if this is still an issue?
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JarnoRFB
commented on July 18, 2024
Sure, when will it be out?
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jakirkham
commented on July 18, 2024
Should be out now.
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JarnoRFB
commented on July 18, 2024
Seems to work fine for environments with python 2.7! Was this intended to work with python 3 as well, because this still gives errors
convert_imageset: error while loading shared libraries: libprotobuf.so.12: cannot open shared object file: No such file or directory
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djsutherland
commented on July 18, 2024
No, conda-forge still doesn't build caffe for python 3, so that's a problem with the caffe from defaults.
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JarnoRFB
commented on July 18, 2024
Alright, then I would consider this issue fixed. Thanks very much for your help and keep up the good work!
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jakirkham
commented on July 18, 2024
Thanks for testing. :)
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Related Issues (16)
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