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- function maybe_make_diffmap () {
- local stem="$1"
- local name="$2"
- local epsilon="$3"
- local points="$4"
- local k="$5"
- local normalize="$6"
- local start_time="$7"
- # Not sure how CPUWeight and CPUQuota work, given that this reaches
- # 100% usage on my system, but at least the system doesn't hang anymore.
- local to="$name(k=$k,eps=$epsilon,points=$points,$normalize,start-time=${start_time}).diffmap"
- if [ ! -f "$to" ]
- then
- echo "computing: $to"
- # TODO: How does CPUQuota work? 1%, 400%, ???
- # TODO: make this non-systemd-specific, avoid sudo
- if sudo -E env PATH=$PATH systemd-run --scope -p MemoryAccounting=yes -p CPUAccounting=true -p MemorySwapMax=20M -p MemoryMax=6G -p CPUWeight=10 --uid=$USER --gid=$USER timeout 40s python3 construct-diffusion-map.py "$stem" "$to.tmp" "--points=$points" -k "$k" "--eps=$epsilon" "$normalize" --start-time "${start_time}";
- then
- mv "$to.tmp" "$to" && echo "done!"
- else
- echo "$? oops, timeout or OOM?"
- exit 1
- fi
- else
- echo "already exists: $to, not recomputing"
- fi
- }
- # # Opgelet: kan traag zijn!!
- # #
- # # 0.01 en 0.001 duren erg lang voor BOFC
- # # Voor BOFC geen 100 nodig.
- # for eps in 40 10 1 0.1;
- # do
- # for points in 1000 2000 5000; # 7000; 7000 too expensive, always fails due to timeout
- # do
- # for k in 64 512 "$points";
- # do
- # #if [ "$k" -eq "7000" ]; then
- # # k=2000 # 7000 is too expensive to finish in a reasonable amount of time
- # #fi
- # # if [ "$k" -eq "5000" ]; then
- # # k=2000 # 7000 is too expensive to finish in a reasonable amount of time (with some exceptions)
- # # fi
- # for normalize in --normalize --no-normalize;
- # do
- # maybe_make_diffmap results_9010/PDL_9010 BOFC "$eps" "$points" "$k" "$normalize" 25
- # done
- # done
- # done
- # done
- # #Grrr
- #maybe_make_diffmap results_9010/PDL_9010 BOFC "0.01" "5000" 64 --no-normalize 10
- #python3 plot-diffusion-map.py --fit 300000 --ith-stem results_9010/PDL_9010 --interactive 'BOFC(k=64,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "transformed scatterplot"
- #python3 plot-diffusion-map.py 'BOFC(k=64,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "correlation plots"
- #maybe_make_diffmap results_9010/PDL_9010 BOFC "0.01" "5000" 64 --no-normalize 22
- #python3 plot-diffusion-map.py --fit 300000 --ith-stem results_9010/PDL_9010 --interactive 'BOFC(k=64,eps=0.01,points=5000,--no-normalize,start-time=22).diffmap' BOFC "transformed scatterplot"
- #python3 plot-diffusion-map.py --fit 300000 --ith-stem results_9010/PDL_9010 --interactive BOFC\(k=64,eps=0.01,p
- maybe_make_diffmap results_9010/PDL_9010 BOFC "0.01" "5000" 32 --no-normalize 10
- #python3 plot-diffusion-map.py --fit 300000 --ith-stem results_9010/PDL_9010 --interactive 'BOFC(k=64,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "transformed scatterplot"
- python3 plot-diffusion-map.py 'BOFC(k=32,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "transformed scatterplot"
- python3 plot-diffusion-map.py 'BOFC(k=32,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "eigenvalues"
- # Maximal number of points: 45079875
- # Success: 2
- #sudo -E env PATH=$PATH systemd-run --scope -p MemoryAccounting=yes -p CPUAccounting=true -p MemorySwapMax=20M -p MemoryMax=4.8G -p CPUWeight=10 --uid=$USER --gid=$USER python3 plot-diffusion-map.py --ith-stem results_9010/PDL_9010 --fit 2000000 'BOFC(k=32,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "transformed scatterplot"
- python3 plot-diffusion-map.py --axes 'BOFC(k=32,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC "correlation plots"
- #python3 plot-diffusion-map.py 'BOFC(k=32,eps=0.01,points=5000,--no-normalize,start-time=10).diffmap' BOFC --ith-stem results_9010/PDL_9010 --fit 5000 "transformed scatterplot"
- # Courtemanche. To avoid file name length limits on some systems,
- # Courtemanche2D is abbreviated to CM.
- maybe_make_diffmap myokit12/myokit_2 'CM-nospiral' 400 6000 6000 --normalize 22 # ?? all eigenvalues are approx -0.0025
- maybe_make_diffmap myokit_CMspiral3/myokit_5 'CM-spiral' 400 6000 6000 --normalize 27 # ???
- python3 plot-diffusion-map.py 'CM-nospiral(k=6000,eps=400,points=6000,--normalize,start-time=22).diffmap' CM-nospiral "transformed scatterplot"
- python3 plot-diffusion-map.py 'CM-spiral(k=6000,eps=400,points=6000,--normalize,start-time=27).diffmap' CM-spiral "transformed scatterplot"
- python3 plot-diffusion-map.py 'CM-nospiral(k=6000,eps=400,points=6000,--normalize,start-time=22).diffmap' CM-nospiral "correlation plots"
- python3 plot-diffusion-map.py 'CM-nospiral(k=6000,eps=400,points=6000,--normalize,start-time=22).diffmap' CM-nospiral "eigenvalues"
- python3 plot-diffusion-map.py 'CM-spiral(k=6000,eps=400,points=6000,--normalize,start-time=27).diffmap' CM-spiral "eigenvalues"
- # Transformed phaseplot
- #sudo -E env PATH=$PATH systemd-run --scope -p MemoryAccounting=yes -p CPUAccounting=true -p MemorySwapMax=20M -p MemoryMax=2.4G -p CPUWeight=10 --uid=$USER --gid=$USER python3 plot-diffusion-map.py --ith-stem myokit12/myokit_2 --fit 10000 'Courtemanche2D-nospiral(k=6000,eps=400,points=6000,--normalize,start-time=22).diffmap' Courtemanche2D-nospiral "transformed scatterplot"
- #python3 plot-diffusion-map.py 'Courtemanche2D-nospiral(k=6000,eps=400,points=6000,--normalize,start-time=22).diffmap' Courtemanche2D-nospiral "correlation plots"
- # AP model
- # 0.04 werkt
- # 0.03 werkt (wel trager)
- e=0.02
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 100 100 --no-normalize 2
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 200 200 --no-normalize 2
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 1000 1000 --no-normalize 2
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 3000 3000 --no-normalize 2
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 5000 5000 --no-normalize 2
- maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 6000 6000 --no-normalize 2
- #maybe_make_diffmap phase_1000/phase_1000 'AP' "$e" 7000 7000 --no-normalize 2
- # Plots for AP model
- python3 plot-diffusion-map.py "AP(k=6000,eps=$e,points=6000,--no-normalize,start-time=2).diffmap" AP --ith-stem phase_1000/phase_1000 "transformed scatterplot"
- python3 plot-diffusion-map.py "AP(k=6000,eps=$e,points=6000,--no-normalize,start-time=2).diffmap" AP --ith-stem phase_1000/phase_1000 "eigenvalues"
- python3 plot-diffusion-map.py "AP(k=6000,eps=$e,points=6000,--no-normalize,start-time=2).diffmap" AP --ith-stem phase_1000/phase_1000 "correlation plots"
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