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.
library(dplyr) | |
library(httr) | |
library(rvest) | |
library(xml2) | |
library(stringr) | |
library(DT) | |
library(htmltools) | |
domains_to_remove <- c( |
library(biomaRt) | |
species_tx2gene_map = c( | |
"btaurus", | |
"mauratus", | |
"mmulatta", | |
"ggallus", | |
"sscrofa", | |
"mmusculus", | |
"dreiro") | |
"rnorvegicus", |
barplot <- function(df, showCategory=15){ | |
df <- df[with(df, order(ratio, padj, decreasing = c(TRUE, FALSE))),] | |
df <- head(df, n=showCategory) | |
breaks <- round( c(0, 1/4, 2/4, 3/4, 1) * max(df[['ratio']]) , 2) | |
p_plot <- ggplot(df, aes_string(x="term", y="ratio", fill="padj")) + | |
geom_col() + | |
scale_y_continuous(expand=c(0, 0), breaks=breaks, limits=c(0, max(df[["ratio"]]+0.05))) + | |
scale_x_discrete(name='GO term') + | |
scale_fill_continuous(low="#00dbde", high="#FFF94C") + | |
theme(text=ggplot2::element_text(size=9)) + |
1088 Email Press | |
The 5th Publisher | |
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Abhinav | |
Academe Research Journals | |
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Academia Scholarly Journals (ASJ) | |
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@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 |
#!/usr/bin/env python | |
# coding: utf-8 | |
# In[1]: | |
from collections import defaultdict, OrderedDict | |
import warnings | |
import gffutils | |
import pybedtools |
#!/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 |
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() |
#!/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 |