質問編集履歴
2
誤字の修正と実行情報の追加
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test
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@@ -23,7 +23,8 @@
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＜円周率計算プログラムの情報＞
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実行コマンド：
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-
$mpirun --hostfile host64 -n 14 python3 pi_chudnovsky.py 1
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$mpirun --hostfile host64 -n 14 python3 pi_chudnovsky.py 13 : --hostfile host32 -n 2 python3 pi_chudnovsky.py 13
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↑ちなみに、13のところを12以下にするとエラーなく実行できます。
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pi_chudnovsky.pyについて：
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https://github.com/kemusiro/openmpi-sample/からダウンロード
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ソースコード及びエラーを本文に記載、プログラム名等の微修正
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test
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@@ -6,6 +6,7 @@
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にて、 いわゆるハローワールドが動作するところまでは確認できました。
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次に円周率を計算しようと思ったのですが、どうもcomm.sendとcomm.recvにおけるnp.array(dtype=object)のやりとりに起因してエラーが発生しているようです。
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クラスタの構造は２分木転送方式であり、broadcastやreduceは使っていません。
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ちなみに、hostlistに64bitPCのみ、32bitPCのみを指定した場合は円周率がうまく計算できるので、
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32bitノードと64bitノードがデータをやりとりする時に問題が起こっている可能性が高いと思います。
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@@ -16,3 +17,206 @@
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ご教示いただけますと幸いです。
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よろしくお願いいたします。
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＜円周率計算プログラムの情報＞
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実行コマンド：
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$mpirun --hostfile host64 -n 14 python3 pi_chudnovsky.py 12 : --hostfile host32 -n 2 python3 pi_chudnovsky.py 12
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pi_chudnovsky.pyについて：
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https://github.com/kemusiro/openmpi-sample/からダウンロード
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ライセンス
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MIT License
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Copyright (c) 2021 Kenichi Miyata
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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コード本文
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```python 3.x
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from mpi4py import MPI
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import gmpy2 as mp
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from gmpy2 import mpz
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import numpy as np
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import mmap
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import sys
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import os
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# 円周率を並列に計算する。
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65
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def calc_PQT_root(n):
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66
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# まず自分の割り当て分を計算する。
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alloc = int(n / size)
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PQT2 = calc_PQT_local(rank * alloc, (rank + 1) * alloc)
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+
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# 各ノードの計算結果をマージする。
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level = int(mp.ceil(mp.log2(size)))
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k = 1
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for _ in range(level):
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if (rank & k) == k:
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PQT1 = comm.recv(source=rank-k, tag=0)
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PQT2 = np.array([PQT1[0] * PQT2[0],
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PQT1[1] * PQT2[1],
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PQT1[2] * PQT2[1] + PQT1[0] * PQT2[2]])
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k *= 2
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else:
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comm.send(PQT2, dest=rank+k, tag=0)
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break
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return PQT2
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+
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# ノード内でP(n1, n2), Q(n1, n2), T(n1, n2)を計算する。
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86
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def calc_PQT_local(n1, n2):
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if n1 + 1 == n2:
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P = mpz((-1) * (2 * n2 - 1) * (6 * n2 - 5) * (6 * n2 - 1))
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return np.array([P, C3over24 * n2 ** 3, (A + B * n2) * P])
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else:
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m = int((n1 + n2) / 2)
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PQT1 = calc_PQT_local(n1, m)
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PQT2 = calc_PQT_local(m, n2)
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return np.array([PQT1[0] * PQT2[0],
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PQT1[1] * PQT2[1],
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PQT1[2] * PQT2[1] + PQT1[0] * PQT2[2]])
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# 円周率が何桁まで一致するかを判定する。
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def check_pi(outfile, pifile):
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with open(pifile, 'rb') as f0, \
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open(outfile, 'rb') as f1:
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# 2つのファイルをメモリにマップして比較する。
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with mmap.mmap(f0.fileno(), 0, flags=mmap.MAP_PRIVATE) as mm0, \
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mmap.mmap(f1.fileno(), 0, flags=mmap.MAP_PRIVATE) as mm1:
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index = mpz(0)
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length = 1024 * 1024 # 一度にチェックする桁数
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found = False
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while not found:
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ans = mm0.read(length)
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calc = mm1.read(length)
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if ans != calc:
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maxlen = min(len(ans), len(calc))
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for i in range(maxlen):
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if ans[i] != calc[i]:
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n = index + i - 2
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found = True
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break
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else:
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n = index + maxlen - 3
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break
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else:
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index += length
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return n
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if __name__ == '__main__':
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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size = comm.Get_size()
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if len(sys.argv) < 2:
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if rank == size - 1:
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print('python3 pi_chudnovsky.py <power> [pifile]')
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sys.exit(0)
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if not sys.argv[1].isdecimal():
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if rank == size - 1:
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print('not decimal value: {}'.format(sys.argv[1]))
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print('python3 pi_chudnovsky.py power [pifile]')
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sys.exit(0)
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power = int(sys.argv[1])
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+
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if len(sys.argv) == 2:
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pifile = '/share/common/pi-10oku.txt'
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else:
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pifile = sys.argv[2]
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if not os.path.exists(pifile):
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if rank == size - 1:
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print('{} does not exist'.format(pifile))
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print('python3 pi_chudnovsky.py <power> [pifile]')
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sys.exit(0)
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outfile = 'pi.txt'
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152
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+
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153
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+
A = mpz(13591409)
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+
B = mpz(545140134)
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+
C = mpz(640320)
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156
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+
C3over24 = mpz(C**3 / 24)
|
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157
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+
|
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158
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+
n = 2 ** power
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159
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+
digits = n * 14
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160
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+
# gmpy2の浮動小数の精度として、求められる円周率の桁数を設定する。
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mp.get_context().precision = int(digits * mp.log2(10))
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162
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+
|
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163
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+
if rank == size - 1:
|
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164
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+
print('calculating...')
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165
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+
start = MPI.Wtime()
|
|
166
|
+
PQT = calc_PQT_root(n)
|
|
167
|
+
if rank == size - 1:
|
|
168
|
+
temp1 = C * mp.sqrt(C) * PQT[1]
|
|
169
|
+
temp2 = 12 * (PQT[2] + A * PQT[1])
|
|
170
|
+
pi = temp1 / temp2
|
|
171
|
+
end = MPI.Wtime()
|
|
172
|
+
with open(outfile, 'w') as f:
|
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+
f.write(str(pi))
|
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+
print('checking...')
|
|
175
|
+
n = check_pi(outfile, pifile)
|
|
176
|
+
print('time = {:.2f} sec.'.format(end - start))
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|
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|
+
print(f'match = {n}')
|
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+
```
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179
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+
|
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180
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+
出力：
|
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181
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+
… 途中省略 …
|
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+
calculating...
|
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183
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+
[debian10:08494] *** Process received signal ***
|
|
184
|
+
[debian10:08494] Signal: Segmentation fault (11)
|
|
185
|
+
[debian10:08494] Signal code: (128)
|
|
186
|
+
[debian10:08494] Failing at address: (nil)
|
|
187
|
+
[debian10:08494] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x14140)[0x7fc4662bc140]
|
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188
|
+
[debian10:08494] [ 1] /usr/local/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_put+0x17)[0x7fc45f6f6a87]
|
|
189
|
+
[debian10:08494] [ 2] /usr/local/lib/openmpi/mca_btl_tcp.so(+0x9087)[0x7fc4640b5087]
|
|
190
|
+
[debian10:08494] [ 3] /usr/local/lib/libopen-pal.so.40(opal_libevent2022_event_base_loop+0x697)[0x7fc4657c6247]
|
|
191
|
+
[debian10:08494] [ 4] /usr/local/lib/libopen-pal.so.40(+0x37256)[0x7fc46577f256]
|
|
192
|
+
[debian10:08494] [ 5] /usr/local/lib/libopen-pal.so.40(opal_progress+0x84)[0x7fc46577f3a4]
|
|
193
|
+
[debian10:08494] [ 6] /usr/local/lib/libopen-pal.so.40(ompi_sync_wait_mt+0xb5)[0x7fc4657859b5]
|
|
194
|
+
[debian10:08494] [ 7] /usr/local/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x1292)[0x7fc45f6e6b82]
|
|
195
|
+
[debian10:08494] [ 8] /usr/local/lib/libmpi.so.40(PMPI_Send+0x11b)[0x7fc46599372b]
|
|
196
|
+
[debian10:08494] [ 9] /usr/lib/python3/dist-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so(+0xe45b8)[0x7fc465b155b8]
|
|
197
|
+
[debian10:08494] [10] python3[0x53f350]
|
|
198
|
+
[debian10:08494] [11] python3(_PyObject_MakeTpCall+0x39b)[0x51d89b]
|
|
199
|
+
[debian10:08494] [12] python3(_PyEval_EvalFrameDefault+0x5f7f)[0x517a0f]
|
|
200
|
+
[debian10:08494] [13] python3(_PyFunction_Vectorcall+0x1a3)[0x528b63]
|
|
201
|
+
[debian10:08494] [14] python3(_PyEval_EvalFrameDefault+0x525)[0x511fb5]
|
|
202
|
+
[debian10:08494] [15] python3[0x5106ed]
|
|
203
|
+
[debian10:08494] [16] python3(_PyEval_EvalCodeWithName+0x47)[0x510497]
|
|
204
|
+
[debian10:08494] [17] python3(PyEval_EvalCode+0x23)[0x5f5be3]
|
|
205
|
+
[debian10:08494] [18] python3[0x619de7]
|
|
206
|
+
[debian10:08494] [19] python3[0x615610]
|
|
207
|
+
[debian10:08494] [20] python3[0x619d79]
|
|
208
|
+
[debian10:08494] [21] python3(PyRun_SimpleFileExFlags+0x196)[0x619816]
|
|
209
|
+
[debian10:08494] [22] python3(Py_RunMain+0x2b3)[0x60d4e3]
|
|
210
|
+
[debian10:08494] [23] python3(Py_BytesMain+0x29)[0x5ea6e9]
|
|
211
|
+
[debian10:08494] [24] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea)[0x7fc465f6cd0a]
|
|
212
|
+
[debian10:08494] [25] python3(_start+0x2a)[0x5ea5ea]
|
|
213
|
+
[debian10:08494] *** End of error message ***
|
|
214
|
+
--------------------------------------------------------------------------
|
|
215
|
+
Primary job terminated normally, but 1 process returned
|
|
216
|
+
a non-zero exit code. Per user-direction, the job has been aborted.
|
|
217
|
+
--------------------------------------------------------------------------
|
|
218
|
+
--------------------------------------------------------------------------
|
|
219
|
+
mpirun noticed that process rank 7 with PID 8494 on node 192.168.10.128 exited on signal 11 (Segmentation fault).
|
|
220
|
+
--------------------------------------------------------------------------
|
|
221
|
+
|
|
222
|
+
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