Problem with custom installation

j3gu commented 11 months ago

Checks before submitting the issue

[x] I installed the latest Dictys version successfully
[x] I downloaded the whole folder for the tutorial
[] I ran the tutorial cells and notebooks (if more than one) in the correct order and only once
[ ] The preceeding cells and notebooks finished successfully (i.e. the reported error is the first encountered)

I only have the option of installing Dictys with PIP on the clusters. With current version v1.0.0, I encountered errors on running wellington_footprints.py, which is "TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. I compared this script with the one download through Conda, and suspected that the version on PIP was not the most updated one. Could you please take a look? Thanks.

Here is a list of the installed packages in the virtual environment. Name Version Build Channel _libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
accelerate 0.21.0 pypi_0 pypi aiohttp 3.8.5 pypi_0 pypi aiosignal 1.3.1 pypi_0 pypi appdirs 1.4.4 pypi_0 pypi async-timeout 4.0.3 pypi_0 pypi attrs 23.1.0 pypi_0 pypi audioread 3.0.0 pypi_0 pypi bitsandbytes 0.41.1 pypi_0 pypi blas 1.0 mkl
bottleneck 1.3.5 py39h7deecbd_0
brotlipy 0.7.0 py39h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
ca-certificates 2023.08.22 h06a4308_0
certifi 2023.7.22 py39h06a4308_0
cffi 1.15.1 py39h74dc2b5_0
charset-normalizer 2.1.1 pypi_0 pypi cryptography 41.0.3 py39h130f0dd_0
cuda-cudart 11.7.99 0 nvidia cuda-cupti 11.7.101 0 nvidia cuda-libraries 11.7.1 0 nvidia cuda-nvrtc 11.7.99 0 nvidia cuda-nvtx 11.7.91 0 nvidia cuda-runtime 11.7.1 0 nvidia datasets 2.14.4 pypi_0 pypi decorator 5.1.1 pypi_0 pypi dill 0.3.7 pypi_0 pypi ffmpeg 4.2.2 h20bf706_0
filelock 3.8.2 pypi_0 pypi freetype 2.12.1 h4a9f257_0
frozenlist 1.4.0 pypi_0 pypi fsspec 2023.6.0 pypi_0 pypi giflib 5.2.1 h5eee18b_3
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py39heeb90bb_0
gnutls 3.6.15 he1e5248_0
huggingface-hub 0.16.4 pypi_0 pypi idna 3.4 py39h06a4308_0
intel-openmp 2021.4.0 h06a4308_3561
jinja2 3.1.2 py39h06a4308_0
jpeg 9e h5eee18b_1
lame 3.100 h7b6447c_0
lazy-loader 0.3 pypi_0 pypi lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libcublas 11.10.3.66 0 nvidia libcufft 10.7.2.124 h4fbf590_0 nvidia libcufile 1.7.1.12 0 nvidia libcurand 10.3.3.129 0 nvidia libcusolver 11.4.0.1 0 nvidia libcusparse 11.7.4.91 0 nvidia libdeflate 1.17 h5eee18b_0
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libidn2 2.3.4 h5eee18b_0
libnpp 11.7.4.75 0 nvidia libnvjpeg 11.8.0.2 0 nvidia libopus 1.3.1 h7b6447c_0
libpng 1.6.39 h5eee18b_0
librosa 0.10.1 pypi_0 pypi libstdcxx-ng 11.2.0 h1234567_1
libtasn1 4.19.0 h5eee18b_0
libtiff 4.5.1 h6a678d5_0
libunistring 0.9.10 h27cfd23_0
libvpx 1.7.0 h439df22_0
libwebp 1.2.4 h11a3e52_1
libwebp-base 1.2.4 h5eee18b_1
llvmlite 0.40.1 pypi_0 pypi lz4-c 1.9.4 h6a678d5_0
mako 1.2.4 pypi_0 pypi markupsafe 2.1.1 py39h7f8727e_0
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpmath 1.3.0 py39h06a4308_0
msgpack 1.0.5 pypi_0 pypi multidict 6.0.4 pypi_0 pypi multiprocess 0.70.15 pypi_0 pypi ncurses 6.4 h6a678d5_0
nettle 3.7.3 hbbd107a_1
networkx 3.1 py39h06a4308_0
numba 0.57.1 pypi_0 pypi numexpr 2.8.4 py39he184ba9_0
numpy 1.24.3 py39h14f4228_0
numpy-base 1.24.3 py39h31eccc5_0
openh264 2.1.1 h4ff587b_0
openssl 1.1.1w h7f8727e_0
packaging 23.1 py39h06a4308_0
pandas 1.5.2 py39h417a72b_0
pillow 9.3.0 pypi_0 pypi pip 23.2.1 py39h06a4308_0
platformdirs 3.10.0 pypi_0 pypi pooch 1.7.0 pypi_0 pypi psutil 5.9.5 pypi_0 pypi pyarrow 12.0.1 pypi_0 pypi pycparser 2.21 pyhd3eb1b0_0
pycuda 2022.2.2 pypi_0 pypi pyopenssl 23.2.0 py39h06a4308_0
pysocks 1.7.1 py39h06a4308_0
python 3.9.12 h12debd9_1
python-dateutil 2.8.2 pyhd3eb1b0_0
pytools 2023.1.1 pypi_0 pypi pytorch 2.0.0 py3.9_cuda11.7_cudnn8.5.0_0 pytorch pytorch-cuda 11.7 h778d358_5 pytorch pytorch-mutex 1.0 cuda pytorch pytz 2022.7 py39h06a4308_0
readline 8.2 h5eee18b_0
regex 2022.10.31 pypi_0 pypi requests 2.28.1 pypi_0 pypi safetensors 0.3.2 pypi_0 pypi scikit-learn 1.3.0 pypi_0 pypi scipy 1.11.2 pypi_0 pypi setuptools 68.0.0 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
soundfile 0.12.1 pypi_0 pypi soxr 0.3.6 pypi_0 pypi sqlite 3.41.2 h5eee18b_0
sympy 1.11.1 py39h06a4308_0
threadpoolctl 3.2.0 pypi_0 pypi tk 8.6.12 h1ccaba5_0
tokenizers 0.13.3 pypi_0 pypi torch 1.11.0+cu115 pypi_0 pypi torchaudio 0.11.0+cu115 pypi_0 pypi torchtriton 2.0.0 py39 pytorch torchvision 0.12.0+cu115 pypi_0 pypi tqdm 4.64.1 pypi_0 pypi transformers 4.31.0 pypi_0 pypi typing-extensions 4.4.0 pypi_0 pypi typing_extensions 4.7.1 py39h06a4308_0
tzdata 2023c h04d1e81_0
urllib3 1.26.13 pypi_0 pypi wheel 0.38.4 py39h06a4308_0
x264 1!157.20191217 h7b6447c_0
xxhash 3.3.0 pypi_0 pypi xz 5.4.2 h5eee18b_0
yarl 1.9.2 pypi_0 pypi zlib 1.2.13 h5eee18b_0
zstd 1.5.5 hc292b87_0

lingfeiwang commented 11 months ago

Hi j3gu,

From your list of installed packages, you seem to have access to conda installation method. Have you tried that?

Also could you post the full error message?

j3gu commented 11 months ago

Yes, I have tried the Conda installation method. I did not have problem running the scripts except for the GPU computation. To run PyTorch, I have to use a pre-installed conda environment, which needs administrator access.

Here is the full error message:

Traceback (most recent call last): File "/home/jinggu/.local/bin/wellington_footprints.py", line 106, in print >> wigout, "track type=wiggle_0" TypeError: unsupported operand type(s) for >>: 'builtin_function_or_method' and '_io.TextIOWrapper'. Did you mean " print(, file=)"?

lingfeiwang commented 11 months ago

This file "/home/jinggu/.local/bin/wellington_footprints.py" appears to be your own file. This does not appear to be a Dictys problem. Please first try the tutorial and let us know if you encountered any error there.

pinellolab / dictys

Problem with custom installation #39