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JDACS4C-IMPROVE / DrugCell

A visible neural network model for drug response prediction
MIT License
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Error in setup #35

Open wilke opened 11 months ago

wilke commented 11 months ago

After following your install instructions i get an error at:

python3 -m pip install -r requirements.txt

Output:

Collecting intel-openmp==2021.4.0 (from -r requirements.txt (line 7))
  Downloading intel_openmp-2021.4.0-py2.py3-none-manylinux1_x86_64.whl (9.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 113.7 MB/s eta 0:00:00
Collecting mkl==2021.4.0 (from -r requirements.txt (line 8))
  Downloading mkl-2021.4.0-py2.py3-none-manylinux1_x86_64.whl (280.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 280.9/280.9 MB 12.8 MB/s eta 0:00:00
ERROR: Could not find a version that satisfies the requirement mkl-service==2.4.0 (from versions: none)
ERROR: No matching distribution found for mkl-service==2.4.0
RylieWeaver commented 11 months ago

I'm getting something slightly more. Not sure where it's getting a couple of the things that these dependency errors are coming from. For example I don't see tensorflow anywhere in DrugCell's requirements.txt, nor candle_lib's requirements.txt.

Collecting numpy<1.23.0,>=1.22.3 Downloading numpy-1.22.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.9 MB) |████████████████████████████████| 16.9 MB 86.7 MB/s Collecting intel-cmplr-lic-rt==2023.2.0 Downloading intel_cmplr_lic_rt-2023.2.0-py2.py3-none-manylinux1_x86_64.whl (19 kB) Collecting intel-opencl-rt==2023.2.0 Downloading intel_opencl_rt-2023.2.0-py2.py3-none-manylinux1_x86_64.whl (233.5 MB) |████████████████████████████████| 233.5 MB 380 kB/s Collecting intel-cmplr-lib-rt==2023.2.0 Downloading intel_cmplr_lib_rt-2023.2.0-py2.py3-none-manylinux1_x86_64.whl (44.9 MB) |████████████████████████████████| 44.9 MB 88.8 MB/s ERROR: tensorflow 2.12.0 has requirement protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<5.0.0dev,>=3.20.3, but you'll have protobuf 3.20.0 which is incompatible. ERROR: nemo 4.2.1 has requirement cryptography==37.0.4, but you'll have cryptography 38.0.4 which is incompatible. ERROR: dpcpp-cpp-rt 2023.2.0 has requirement intel-openmp==2023.2.0, but you'll have intel-openmp 2021.4.0 which is incompatible. ERROR: mkl-random 1.2.2 has requirement numpy<1.25.0,>=1.24.3, but you'll have numpy 1.22.4 which is incompatible.

rohandavidg commented 11 months ago

i edited the requirements.txt and i seem to have it running on lambda0

Collecting pip Downloading pip-23.2.1-py3-none-any.whl (2.1 MB) |████████████████████████████████| 2.1 MB 30.6 MB/s Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 21.2.2 Uninstalling pip-21.2.2: Successfully uninstalled pip-21.2.2 Successfully installed pip-23.2.1 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

rohandavidg commented 11 months ago

Forgot to add here is the command i ran on lambda0 within the Singularity/src repo on lambda0 ./bootstrap.sh -n Drugcell_test -d ../definitions/DrugCell.def

RylieWeaver commented 11 months ago

This works for me when I try the singularity container. However, not when trying with an environment. It seems like installing python will automatically install mkl-random. Hence why starting an environment with some regular python causes issues, but not with the singularity container's specific version.

wilke commented 11 months ago

I was trying to setup the repo in a standard conda environment. If this is failing I suggest updating the README with some links and short instructions on how to setup and develop within a container??

rohandavidg commented 11 months ago

updated the README in the latest pull request. i followed the readme in Pacman_MCA