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// thp_madvfree_check: does this x86-64 kernel lose data written to MADV_FREE'd transparent huge pages?
//
// Linux commit f7491d7c81db ("x86/mm: Fix user-space data loss with MADV_FREE and THP", CVE-2026-97945):
// pmd_modify() drops the hardware dirty bit of a PMD-mapped huge page. A huge page that was lazily freed
// (MADV_FREE) and then written again is therefore discarded by reclaim, and later reads return zeros.
// mprotect() and NUMA-balancing hinting faults both go through pmd_modify().
//
//   thp_madvfree_check <MiB> <trigger> <thp> <madv> [pressure_file ...]
//     trigger: mprotect = mprotect(PROT_READ) then mprotect(PROT_READ|PROT_WRITE) after the rewrite
//              numa     = only read the buffer for $NUMA_SECONDS (default 90), leaving it to NUMA hinting

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#!/bin/bash
#SBATCH -t 24:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --array 1-97

cd /home/mcdonadt/agp_demux_barcode_assessment-8.4.21
source activate qiime2-2020.11
export TMPDIR=/panfs/dtmcdonald/
python processor.py demux.details $SLURM_ARRAY_TASK_ID

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import qiime2
import pandas as pd
import glob
from collections import defaultdict
import sys
import time, os

details = [l.strip() for l in open(sys.argv[1])]
f = details[int(sys.argv[2]) - 1]

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#!/bin/bash
set -e
set -x

envname=q2deblur_mvp_test
executiondir=mvp
redeploy=$1

source deactivate

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# python 2
# conda install biom-format -c bioconda
# conda install matplotlib  # pysurvey setup.py is incomplete
# pip install -e "hg+https://bitbucket.org/yonatanf/pysurvey#egg=pysurvey"
# note: the pysurvey build in pypi does not work. unsure why. 

import click

# this little gem is because pysurvey depends on an older version of scipy
# and attempts to import nanmedian from scipy.stats. This is a dirty hack.

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import numpy as np
import bp
import biom
import skbio
import sys
import joblib
import h5py

class biom_counts_wrapper(object):
    def __init__(self, table_f):

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