Buggy python submission (verdict: Runtime Error):
import sys

from collections import deque
# q = deque(); q.append(x); q.appendleft(x); q.pop() -> x; q.popleft() -> x
from collections import defaultdict
# d = defaultdict(lambda: []); d[key] -> []
import heapq
# hq = []; heapq.heappush(hq, x); heapq.heappop(hq) -> x; heapq.heappushpop(hq, x) -> x
import bisect
# i = bisect.bisect_left([1,2,3,4], 1.5); i = bisect.bisect_right([4,3,2,1], 1.5)

import numpy as np
#from scipy.misc import comb

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

"""
マスは1つの色を持つ -> c[i][j]
マスは3グループのいずれかに属する -> (i+j)%3
グループは1つの色 gc を持つ、ただし他のグループと同じ色を持てない gc1 != gc2 != gc3
マス違和感 = D[マスの色][グループの色]
グループ違和感 = グループ内のマスの、マス違和感の合計 = DG[グループ色]
全体違和感 = 3グループの、グループ違和感の合計
答え = 全体違和感
"""
def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    iwakanG = [[0] * C for _ in range(3)]  # グループ違和感[グループID][グループ色] = グループID/色ごとのマス違和感の計
    for i in range(N):
        for j in range(N):
            groupID = (i + j) % 3  # グループID
            cM = c[i][j] - 1  # マス色
            for cG in range(C):
                iwakanM = D[cM][cG]   # マス違和感
                iwakanG[groupID][cG] += iwakanM  # グループ違和感にマス違和感を加算
    iwakan = 1e+9
    for gc1 in range(C):
        for gc2 in range(C):
            for gc3 in range(C):
                if gc1 == gc2 or gc2 == gc3 or gc3 == gc1:
                    continue
                n = iwakanG[0][gc1] + iwakanG[1][gc2] + iwakanG[2][gc3]
                if iwakan > n:
                    iwakan = n  # 全体違和感の最小化
    print(iwakan)

main()


Fixed submission:
# ContestName
# URL
import sys
#import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    E = [[0] * C for _ in range(3)]
    for i in range(N):
        for j in range(N):
            before = c[i][j]
            e = (i+j) % 3
            for after in range(1, C+1):
                E[e][after-1] += D[before-1][after-1]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0][c1] + E[1][c2] + E[2][c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()

Buggy python submission (verdict: Time Limit Exceeded):
# ContestName
# URL
import sys
import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = np.array(ii2nnn(C))
    c = np.array(ii2nnn(N))
    E = np.array([[0] * C for _ in range(3)])
    for i in range(N):
        for j in range(N):
            before = c[i,j]
            e = (i+j) % 3
            E[e,:] += D[before-1,:]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0,c1] + E[1,c2] + E[2,c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()


Fixed submission:
# ContestName
# URL
import sys
#import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    E = [[0] * C for _ in range(3)]
    for i in range(N):
        for j in range(N):
            before = c[i][j]
            e = (i+j) % 3
            for after in range(1, C+1):
                E[e][after-1] += D[before-1][after-1]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0][c1] + E[1][c2] + E[2][c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()

Buggy python submission (verdict: Time Limit Exceeded):
# ContestName
# URL
import sys
import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = np.array(ii2nnn(C))
    c = np.array(ii2nnn(N))
    E = np.array([[0] * C for _ in range(3)])
    for i in range(N):
        for j in range(N):
            before = c[i][j]
            e = (i+j) % 3
            for after in range(1, C+1):
                E[e][after-1] += D[before-1][after-1]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0][c1] + E[1][c2] + E[2][c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()


Fixed submission:
# ContestName
# URL
import sys
#import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    E = [[0] * C for _ in range(3)]
    for i in range(N):
        for j in range(N):
            before = c[i][j]
            e = (i+j) % 3
            for after in range(1, C+1):
                E[e][after-1] += D[before-1][after-1]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0][c1] + E[1][c2] + E[2][c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()

Buggy python submission (verdict: Time Limit Exceeded):
# ContestName
# URL
import sys
#import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    def main2(afters):
        #print('step %d' % cl)
        n = 0
        for i in range(N):
            for j in range(N):
                before = c[i][j]
                after = afters[(i + j) % 3]
                if before  == after:
                    continue
                iwakan = D[before-1][after-1]
                n += iwakan
        return n
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = main2((c1+1, c2+1, c3+1))
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()


Fixed submission:
# ContestName
# URL
import sys
#import numpy as np

s2nn = lambda s: [int(c) for c in s.split(' ')]
ss2nn = lambda ss: [int(s) for s in ss]
ss2nnn = lambda ss: [s2nn(s) for s in ss]
i2s = lambda: sys.stdin.readline().rstrip()
i2n = lambda: int(i2s())
i2nn = lambda: s2nn(i2s())
ii2ss = lambda n: [sys.stdin.readline().rstrip() for _ in range(n)]
ii2nn = lambda n: ss2nn(ii2ss(n))
ii2nnn = lambda n: ss2nnn(ii2ss(n))

def main():
    N, C = i2nn()
    D = ii2nnn(C)
    c = ii2nnn(N)
    E = [[0] * C for _ in range(3)]
    for i in range(N):
        for j in range(N):
            before = c[i][j]
            e = (i+j) % 3
            for after in range(1, C+1):
                E[e][after-1] += D[before-1][after-1]
    iwakan = N * N * 1000
    for c1 in range(C):
        for c2 in range(C):
            for c3 in range(C):
                if c1 == c2 or c2 == c3 or c3 == c1:
                    continue
                n = E[0][c1] + E[1][c2] + E[2][c3]
                if n < iwakan:
                    iwakan = n
    print(iwakan)

main()