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saketkc / Beall_list.txt
Last active Oct 8, 2020
CSV versions of UGC approved journal list from http://www.ugc.ac.in/ugc_notices.aspx?id=1604 Raw
View Beall_list.txt
1088 Email Press
The 5th Publisher
ABC Journals
A M Publishers
Abhinav
Academe Research Journals
Academia Publishing
Academia Research
Academia Scholarly Journals (ASJ)
Academic and Business Research Institute
View nvidia_driver_mismatch_without_rebooting.md

NVML: Driver/library version mismatch

Need to unload the the Nvidia driver kernel module (kmod) and then load it again as the current version is wrong.

Which drivers are loaded?

View gist:9135b397ce306b6c6177ac6681259d32
@HD VN:1.6 SO:coordinate
@SQ SN:chr1 LN:248956422
@SQ SN:chr10 LN:133797422
@SQ SN:chr11 LN:135086622
@SQ SN:chr12 LN:133275309
@SQ SN:chr13 LN:114364328
@SQ SN:chr14 LN:107043718
@SQ SN:chr15 LN:101991189
@SQ SN:chr16 LN:90338345
@SQ SN:chr17 LN:83257441
View hg38.py
#!/usr/bin/env python
# coding: utf-8
# In[1]:
from collections import defaultdict, OrderedDict
import warnings
import gffutils
import pybedtools
View init_rapids_ai_colab_step2_minimal.sh
#!/bin/bash
set -eox pipefail
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai
pip install git+https://github.com/dask/dask.git
pip install git+https://github.com/dask/distributed.git
conda install -y cuml cugraph louvain scanpy cudf cupy umap-learn scikit-learn numba>=0.48* leidenalg r-seurat r-reticulate
View update_modules.py
import re
import sys
import os
sys.path = ['', '/env/python', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/site-packages', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages', '/usr/local/lib/python3.6/dist-packages/IPython/extensions', '/root/.ipython']
print('***********************************************************************')
print('Let us check on those pyarrow and cffi versions...')
print('***********************************************************************')
print()
View one_liner_globals_revised.sh
#!/bin/bash
set -eox pipefail
#python -c "import sys, os; dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages'); sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]; sys.path.append('/usr/local/lib/python3.6/site-packages/'); exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
python -c "import sys, os; ['', '/env/python', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/site-packages', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages', '/usr/local/lib/python3.6/site-packages/']; exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
nvcc --version
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai
View one_liner_globals.sh
#!/bin/bash
set -eox pipefail
python -c "import sys, os; dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages'); sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]; sys.path.append('/usr/local/lib/python3.6/site-packages/'); exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()); print(sys.path)"
nvcc --version
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels nvidia
conda config --add channels rapidsai
conda install -y dask-cuda dask-cudf cuml cugraph numba=0.48* scipy ucx-py ucx-proc=*=gpu scikit-learn louvain cupy=7 scanpy umap-learn pip
View init_rapids_ai_colab_step2_revised.sh
#!/bin/bash
set -eox pipefail
#echo "#!/usr/bin/env python
#import sys, os
#print(sys.path)
#dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages')
#print(dist_package_index)
#sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:]
#sys.path.append('/usr/local/lib/python3.6/site-packages/')
#print(sys.path)
View init_rapids_ai_colab.sh
#!/bin/bash
set -eox pipefail
git clone https://github.com/rapidsai/rapidsai-csp-utils.git
bash rapidsai-csp-utils/colab/rapids-colab.sh stable