Skrypty – Czit notes

In which container PID is running?

przez kszyh | 2 kwietnia 2024 - 12:06 |2 kwietnia 2024 Bez kategorii, Linux, Skrypty

Sometimes we only know the PID (e.g. from nvidia-smi). We do not know what container the PID is running in.

TARGET_PID=331711
for container in $(docker ps -q); do
    if docker top $container | awk '{print $2}' | grep -q $TARGET_PID; then
        container_name=$(docker inspect --format '{{.Name}}' $container | sed 's/^\/\(.*\)/\1/')
        echo "PID $TARGET_PID is running in container: $container (Name: $container_name)"
        exit 0
    fi
done
echo "PID $TARGET_PID is not running in any active container."

TARGET_PID=331711

for container in $(docker ps -q); do

if docker top $container | awk '{print $2}' | grep -q $TARGET_PID; then

container_name=$(docker inspect --format '{{.Name}}' $container | sed 's/^\/$.*$/\1/')

echo "PID $TARGET_PID is running in container: $container (Name: $container_name)"

exit 0

done

echo "PID $TARGET_PID is not running in any active container."

Count documents using Aggregation

przez kszyh | 21 sierpnia 2018 - 07:46 |21 sierpnia 2018 MongoDB, Skrypty

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Counts log entries, with type equal 'CREATE’ , fetch patients data from another collection, remove empty documents (if patients was not found the field is empty array), count by provided user id.

var user_id = '5ad070640c9faddd41a4b665'

db.getCollection('log').aggregate([
{ $match: { message: {$eq: 'CREATE' } }},
{
 $lookup: {
     from: 'patients',
     localField: 'meta.patient',
     foreignField: '_id',
     as: 'patient'
     }   
},
{ $match: { patient: {$not: {$size: 0}} }},
{ $match: {'meta.user': {$eq: ObjectId(user_id)}}},
    {
      $count: "created"
    }
])

var user_id = '5ad070640c9faddd41a4b665'

db.getCollection('log').aggregate([

{ $match: { message: {$eq: 'CREATE' } }},

{

$lookup: {

from: 'patients',

localField: 'meta.patient',

foreignField: '_id',

as: 'patient'

}

{ $match: { patient: {$not: {$size: 0}} }},

{ $match: {'meta.user': {$eq: ObjectId(user_id)}}},

{

$count: "created"

}

])

MongoDB – usunąć osamotnione dokumenty – błędne $ref

przez kszyh | 29 maja 2017 - 15:39 |29 maja 2017 MongoDB, Skrypty

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ModelInstance jest kolekcją dokumentów w której każdy dokumnt posiada referencję do model, np.

{
    "_id" : ObjectId("57d554df3d8b602c54005bc2"),
    "model" : {
        "$ref" : "Model",
        "$id" : ObjectId("57b1ad893d8b602844004a22"),
        "$db" : "virtrollv2"
    },
    "parameters" : []
}

{

"_id" : ObjectId("57d554df3d8b602c54005bc2"),

"model" : {

"$ref" : "Model",

"$id" : ObjectId("57b1ad893d8b602844004a22"),

"$db" : "virtrollv2"

"parameters" : []

}

Zadanie: usunąć wszystkie dokumenty które wskazują na nieistniejące modele.

db.ModelInstance.find().forEach( function(instance) {
    var cursor = db.Model.find({'_id' : instance.model.$id});
    if(!cursor.hasNext()) {
        db.ModelInstance.remove({_id : instance._id});
    }
});

db.ModelInstance.find().forEach( function(instance) {

var cursor = db.Model.find({'_id' : instance.model.$id});

if(!cursor.hasNext()) {

db.ModelInstance.remove({_id : instance._id});

}

});

Pobieranie tensora naprężeń z pliku wynikowego Abaqusa

przez kszyh | 19 grudnia 2014 - 10:49 |19 grudnia 2014 Python, Skrypty

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Skrypt pobiera tensor naprężeń z pliku wynikowego abaqusa a następnie tworzy krzywą odkształcenie/naprężenie. Skrypt działa równolegle Skrypt pobiera maksymalne wartości z ostatniego kroku obliczeń i zapisuje je do pliku

__author__ = "Krzysztof Bzowski"
__version__ = "1.0.0"


from abaqusConstants import *
from math import *
import odbAccess
import multiprocessing as mp
import os

################# CONFIGS #####################
odb11File = 'SSRVE_11'
odb12File = 'SSRVE_12'
odb22File = 'SSRVE_22'
maxPercent = 0.01
###############################################

def avgMaxFromPercentList(l, percent, revSort):
    l.sort(reverse=revSort)   
    maxElements = int(ceil(len(l) * maxPercent))
    lmax = l[:maxElements]
    avg =  sum(lmax) / float(len(lmax))
    return avg


def Analize(resultFile, direction, inOrder):
    try:
        os.remove(resultFile + '.txt')
    except OSError:
        pass
        
    try:
        os.remove(resultFile + '_MAX.txt')
    except OSError:
        pass
        
    odb = odbAccess.openOdb(resultFile+'.odb', readOnly=True)
    step=odb.steps['Step-1']

    frames = step.frames

    # Stress/Strain Curve
    for frame in frames:
        stress=frame.fieldOutputs['S'].getSubset(position=INTEGRATION_POINT).values
        strain=frame.fieldOutputs['PE'].getSubset(position=INTEGRATION_POINT).values
        volumes=frame.fieldOutputs['EVOL'].values
        
        count = len(volumes)
        summVol = 0
        summStress = 0
        summStrains = 0
        
        for i in range(0, count):
            s = stress[i].data[direction]       # S
            p = strain[i].data[direction]      # PE
            v = volumes[i].data      # VOLUME
            summVol += v
            summStress += s*v
            summStrains += p*v
            
        avgStress = summStress/summVol
        avgStrain = summStrains/summVol
        
        myFile = open(resultFile+'.txt', 'a')
        myFile.write('{0}\t{1}\n'.format(abs(avgStrain), abs(avgStress)))
        myFile.close()

    # Max stress / strain 
    lastFrame = frames[-1]
    stress=lastFrame.fieldOutputs['S'].getSubset(position=INTEGRATION_POINT).values
    strain=lastFrame.fieldOutputs['PE'].getSubset(position=INTEGRATION_POINT).values  
    count = len(stress)
    stressList = [None] * count
    strainList = [None] * count
    for i in range(0, count):
        stressList[i] = stress[i].data[direction]       # S
        strainList[i] = strain[i].data[direction]      # PE
 


    maxStress = avgMaxFromPercentList(stressList, maxPercent, inOrder)
    maxStrain = avgMaxFromPercentList(strainList, maxPercent, inOrder)
    file = open(resultFile+'_MAX.txt', 'w')
    file.write('{0}\t{1}\n'.format(maxStrain, maxStress))
    file.close()
    odb.close()
    
if __name__ == '__main__': 
    print __name__
    direction11 = 0
    direction22 = 1
    direction12 = 3
    
    p11 = mp.Process(target=Analize, args=(odb11File, direction11, False))
    p22 = mp.Process(target=Analize, args=(odb22File, direction22, False))
    p12 = mp.Process(target=Analize, args=(odb12File, direction12, True))

    p11.start()
    p22.start()
    p12.start()

    p11.join()
    p22.join()
    p12.join()

100

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102

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__author__ = "Krzysztof Bzowski"

__version__ = "1.0.0"

from abaqusConstants import *

from math import *

import odbAccess

import multiprocessing as mp

import os

################# CONFIGS #####################

odb11File = 'SSRVE_11'

odb12File = 'SSRVE_12'

odb22File = 'SSRVE_22'

maxPercent = 0.01

###############################################

def avgMaxFromPercentList(l, percent, revSort):

l.sort(reverse=revSort)

maxElements = int(ceil(len(l) * maxPercent))

lmax = l[:maxElements]

avg = sum(lmax) / float(len(lmax))

return avg

def Analize(resultFile, direction, inOrder):

try:

os.remove(resultFile + '.txt')

except OSError:

pass

try:

os.remove(resultFile + '_MAX.txt')

except OSError:

pass

odb = odbAccess.openOdb(resultFile+'.odb', readOnly=True)

step=odb.steps['Step-1']

frames = step.frames

# Stress/Strain Curve

for frame in frames:

stress=frame.fieldOutputs['S'].getSubset(position=INTEGRATION_POINT).values

strain=frame.fieldOutputs['PE'].getSubset(position=INTEGRATION_POINT).values

volumes=frame.fieldOutputs['EVOL'].values

count = len(volumes)

summVol = 0

summStress = 0

summStrains = 0

for i in range(0, count):

s = stress[i].data[direction] # S

p = strain[i].data[direction] # PE

v = volumes[i].data # VOLUME

summVol += v

summStress += s*v

summStrains += p*v

avgStress = summStress/summVol

avgStrain = summStrains/summVol

myFile = open(resultFile+'.txt', 'a')

myFile.write('{0}\t{1}\n'.format(abs(avgStrain), abs(avgStress)))

myFile.close()

# Max stress / strain

lastFrame = frames[-1]

stress=lastFrame.fieldOutputs['S'].getSubset(position=INTEGRATION_POINT).values

strain=lastFrame.fieldOutputs['PE'].getSubset(position=INTEGRATION_POINT).values

count = len(stress)

stressList = [None] * count

strainList = [None] * count

for i in range(0, count):

stressList[i] = stress[i].data[direction] # S

strainList[i] = strain[i].data[direction] # PE

maxStress = avgMaxFromPercentList(stressList, maxPercent, inOrder)

maxStrain = avgMaxFromPercentList(strainList, maxPercent, inOrder)

file = open(resultFile+'_MAX.txt', 'w')

file.write('{0}\t{1}\n'.format(maxStrain, maxStress))

file.close()

odb.close()

if __name__ == '__main__':

print __name__

direction11 = 0

direction22 = 1

direction12 = 3

p11 = mp.Process(target=Analize, args=(odb11File, direction11, False))

p22 = mp.Process(target=Analize, args=(odb22File, direction22, False))

p12 = mp.Process(target=Analize, args=(odb12File, direction12, True))

p11.start()

p22.start()

p12.start()

p11.join()

p22.join()

p12.join()

Rendering powierzchni NURBS w ParaView

przez kszyh | 7 marca 2014 - 16:16 |7 marca 2014 Lifehacking, Skrypty

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try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()

points = {
1:[0,0,2],
10:[2.103215,2.103215,2],
11:[-7.55E-08,1.728084,2]
[...]
}

cm = [
[1,2,9],
[2,3,10],
[3,4,11],
[...]
]



for key, value in points.iteritems():

    Sphere4 = Sphere()
    Sphere4.Radius = 0.15
    Sphere4.Center = value
    Sphere4.PhiResolution = 20
    Sphere4.ThetaResolution = 20
    
    RenderView1 = GetRenderView()

    DataRepresentation4 = Show()
    DataRepresentation4.EdgeColor = [0.0, 0.0, 0.5000076295109483]
    DataRepresentation4.SelectionPointFieldDataArrayName = 'Normals'
    DataRepresentation4.AmbientColor = [0.0, 0.0, 0.0]
    DataRepresentation4.CubeAxesColor = [0.0, 0.0, 0.0]
    DataRepresentation4.ScaleFactor = 0.1

    RenderView1.CameraPosition = [0.12249341845958465, 1.6783114555009098, -2.82751287919202]
    RenderView1.CameraClippingRange = [1.8715334193481947, 5.084339235287565]

    DataRepresentation4.DiffuseColor = [1.0, 0.0, 0.0]

    Render()

    
    

for value in cm:
    for i in range(1, len(value)):
        Line2 = Line()

        # toggle the 3D widget visibility.
        active_objects.source.SMProxy.InvokeEvent('UserEvent', 'ShowWidget')
        RenderView1 = GetRenderView()
        RenderView1.CameraClippingRange = [0.04313226219643915, 43.13226219643914]

        fromi = value[0]
        toi = value[i]
        frompt = points[fromi]
        topt = points[toi]
        Line2.Point1 = frompt
        Line2.Point2 = topt
        
        DataRepresentation2 = Show()
        DataRepresentation2.EdgeColor = [0.0, 0.0, 0.5000076295109483]
        DataRepresentation2.SelectionPointFieldDataArrayName = 'Texture Coordinates'
        DataRepresentation2.AmbientColor = [0.0, 0.0, 0.0]
        DataRepresentation2.CubeAxesColor = [0.0, 0.0, 0.0]
        DataRepresentation2.ScaleFactor = 0.10752979516983033


        DataRepresentation2.Representation = 'Wireframe'
        DataRepresentation2.LineWidth = 2.0

        Render()

try: paraview.simple

except: from paraview.simple import *

paraview.simple._DisableFirstRenderCameraReset()

points = {

1:[0,0,2],

10:[2.103215,2.103215,2],

11:[-7.55E-08,1.728084,2]

[...]

}

cm = [

[1,2,9],

[2,3,10],

[3,4,11],

[...]

]

for key, value in points.iteritems():

Sphere4 = Sphere()

Sphere4.Radius = 0.15

Sphere4.Center = value

Sphere4.PhiResolution = 20

Sphere4.ThetaResolution = 20

RenderView1 = GetRenderView()

DataRepresentation4 = Show()

DataRepresentation4.EdgeColor = [0.0, 0.0, 0.5000076295109483]

DataRepresentation4.SelectionPointFieldDataArrayName = 'Normals'

DataRepresentation4.AmbientColor = [0.0, 0.0, 0.0]

DataRepresentation4.CubeAxesColor = [0.0, 0.0, 0.0]

DataRepresentation4.ScaleFactor = 0.1

RenderView1.CameraPosition = [0.12249341845958465, 1.6783114555009098, -2.82751287919202]

RenderView1.CameraClippingRange = [1.8715334193481947, 5.084339235287565]

DataRepresentation4.DiffuseColor = [1.0, 0.0, 0.0]

Render()

for value in cm:

for i in range(1, len(value)):

Line2 = Line()

# toggle the 3D widget visibility.

active_objects.source.SMProxy.InvokeEvent('UserEvent', 'ShowWidget')

RenderView1 = GetRenderView()

RenderView1.CameraClippingRange = [0.04313226219643915, 43.13226219643914]

fromi = value[0]

toi = value[i]

frompt = points[fromi]

topt = points[toi]

Line2.Point1 = frompt

Line2.Point2 = topt

DataRepresentation2 = Show()

DataRepresentation2.EdgeColor = [0.0, 0.0, 0.5000076295109483]

DataRepresentation2.SelectionPointFieldDataArrayName = 'Texture Coordinates'

DataRepresentation2.AmbientColor = [0.0, 0.0, 0.0]

DataRepresentation2.CubeAxesColor = [0.0, 0.0, 0.0]

DataRepresentation2.ScaleFactor = 0.10752979516983033

DataRepresentation2.Representation = 'Wireframe'

DataRepresentation2.LineWidth = 2.0

Render()

Trywialne kolejkowanie zadań w screenie – inaczej

przez kszyh | 4 marca 2014 - 14:57 |4 marca 2014 Lifehacking, Linux, Skrypty

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#!/bin/bash
if [ $# -eq 0 ]
  then
    echo "No arguments supplied"
    exit 0
fi

inputs=()
for f in *.pts; do
   inputs+=($f)
done

echo ${inputs[@]}
arrSize=${#inputs[@]}
echo $arrSize

div=$(($1-1))

ile=$(($arrSize / $div))
for i in $(eval echo {0..$div}); do
   echo "Thread/Screen: $i"
   inp=${inputs[$i]}
   ff=`echo $inp | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`
   ff=project$ff
   screen -md -S "calc$i"
   fin=$(($div+1))
   command="for c in "
   for j in $(eval echo {$i..$arrSize..$fin}); do
      command+="$name "
      name=${inputs[$j]}
   done
   command+="; do module load deal.ii/8.2pre-gcc482 &&./Femaft \$c; done "
   echo $command
   screen -S "calc$i" -p 0 -X stuff "$command $(printf \\r) "

done

#!/bin/bash

if [ $# -eq 0 ]

then

echo "No arguments supplied"

exit 0

inputs=()

for f in *.pts; do

inputs+=($f)

done

echo ${inputs[@]}

arrSize=${#inputs[@]}

echo $arrSize

div=$(($1-1))

ile=$(($arrSize / $div))

for i in $(eval echo {0..$div}); do

echo "Thread/Screen: $i"

inp=${inputs[$i]}

ff=`echo $inp | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`

ff=project$ff

screen -md -S "calc$i"

fin=$(($div+1))

command="for c in "

for j in $(eval echo {$i..$arrSize..$fin}); do

command+="$name "

name=${inputs[$j]}

done

command+="; do module load deal.ii/8.2pre-gcc482 &&./Femaft \$c; done "

echo $command

screen -S "calc$i" -p 0 -X stuff "$command $(printf \\r) "

done

Trywialne kolejkowanie zadań w screenie

przez kszyh | 26 lutego 2014 - 13:34 |26 lutego 2014 Linux, Skrypty

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W nawiązaniu do wpisu:

#!/bin/bash
inputs=()
for f in *.pts; do
   inputs+=($f)
done

echo ${inputs[@]}
arrSize=${#inputs[@]}
echo $arrSize

div=$(($1-1))

ile=$(($arrSize / $div))
for i in $(eval echo {0..$div}); do
   echo "Thread/Screen: $i"
   inp=${inputs[$i]}
   ff=`echo $inp | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`
   ff=project$ff
   screen -md -S "calc$i"
   fin=$(($div+1))
   for j in $(eval echo {$i..$arrSize..$fin}); do
      name=${inputs[$j]}
      screen -S "calc$i" -p 0 -X stuff "module load deal.ii/8.2pre-gcc482 &&./Femaft $name$(printf \\r) "
      echo "Scheduling $name calculations...";
   done
done

#!/bin/bash

inputs=()

for f in *.pts; do

inputs+=($f)

done

echo ${inputs[@]}

arrSize=${#inputs[@]}

echo $arrSize

div=$(($1-1))

ile=$(($arrSize / $div))

for i in $(eval echo {0..$div}); do

echo "Thread/Screen: $i"

inp=${inputs[$i]}

ff=`echo $inp | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`

ff=project$ff

screen -md -S "calc$i"

fin=$(($div+1))

for j in $(eval echo {$i..$arrSize..$fin}); do

name=${inputs[$j]}

screen -S "calc$i" -p 0 -X stuff "module load deal.ii/8.2pre-gcc482 &&./Femaft $name$(printf \\r) "

echo "Scheduling $name calculations...";

done

Uruchamianie zadań w screenie w pętli

przez kszyh | 21 lutego 2014 - 09:23 |21 lutego 2014 Lifehacking, Linux, Skrypty

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Zadanie: uruchomić w screenie n instancji programu z różnymi plikami wejściowymi. Każdy plik wejściowy ma nazwę pokroju {num}_{num}.pts

#!/bin/bash
for f in *.pts; do
     ff=`echo $f | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`
     ff=project$ff
     screen -md -S $ff
     screen -S $ff -p 0 -X stuff "module load deal.ii/8.2pre-gcc482 && ./Femaft $f$(printf \\r) "
     echo "Starting $ff calculations...";
done

#!/bin/bash

for f in *.pts; do

ff=`echo $f | sed 's/_//' | sed 's/\.//' | sed 's/pts//'`

ff=project$ff

screen -md -S $ff

screen -S $ff -p 0 -X stuff "module load deal.ii/8.2pre-gcc482 && ./Femaft $f$(printf \\r) "

echo "Starting $ff calculations...";

done

Pętla po wszystkich plikach z rozszerzeniem *.pts, pobranie ich nazwy i usuniecie extra znaków, tak by zostały tylko dwie liczby, ustalenie nazwy screena na project{numer}, indywidualna nazwa – 'project’ jest potrzebna… Continue reading →

Konwersja formatu macierzy deal.ii na MarketMatrix

przez kszyh | 30 grudnia 2013 - 09:31 |21 lutego 2014 Lifehacking, Linux, Skrypty

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MATRIX_FILE="Matrix.dat"
RHS_FILE="rhs.dat"
SOLUTION_FILE="solution.dat"
perl -pi -w -e  's/\((.*?),(.*?)\).(.*)/($1+1)." ".($2+1)." ".$3/e' $MATRIX_FILE
lines=`grep -c ^ $MATRIX_FILE`
rows=`tail -n 1 $MATRIX_FILE | cut -f1 -d' '`
sed -i "1s/^/"$rows" "$rows" "$lines"\n/" $MATRIX_FILE
sed -i '1s/^/%%MatrixMarket matrix coordinate real general\n/' $MATRIX_FILE

sed -i "1s/^/"$rows"\n/" $SOLUTION_FILE
sed -i "1s/^/"$rows"\n/" $RHS_FILE

MATRIX_FILE="Matrix.dat"

RHS_FILE="rhs.dat"

SOLUTION_FILE="solution.dat"

perl -pi -w -e 's/$(.*?),(.*?)$.(.*)/($1+1)." ".($2+1)." ".$3/e' $MATRIX_FILE

lines=`grep -c ^ $MATRIX_FILE`

rows=`tail -n 1 $MATRIX_FILE | cut -f1 -d' '`

sed -i "1s/^/"$rows" "$rows" "$lines"\n/" $MATRIX_FILE

sed -i '1s/^/%%MatrixMarket matrix coordinate real general\n/' $MATRIX_FILE

sed -i "1s/^/"$rows"\n/" $SOLUTION_FILE

sed -i "1s/^/"$rows"\n/" $RHS_FILE

Film z obrazków

przez kszyh | 19 maja 2013 - 11:33 |19 maja 2013 Lifehacking, Linux, Skrypty

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ffmpeg -f image2 -r 1/0.1 -i ani.%04d.png -c:v libx264 -r 30 video.mp4 Film zakodowany kodekiem x264 wyświetlany 30 klatek na sekundę przy czym każdy obrazek będzie się wyświetlał 0.1s.

Archiwum kategorii: Skrypty

In which container PID is running?

Count documents using Aggregation

MongoDB – usunąć osamotnione dokumenty – błędne $ref

Pobieranie tensora naprężeń z pliku wynikowego Abaqusa

Rendering powierzchni NURBS w ParaView

Trywialne kolejkowanie zadań w screenie – inaczej

Trywialne kolejkowanie zadań w screenie

Uruchamianie zadań w screenie w pętli

Konwersja formatu macierzy deal.ii na MarketMatrix

Film z obrazków

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