我正在尝试运行以下模型,但是在编译期间失败:
import numpy as np
import pymc3 as pm
def sample_data(G=1, K=2):
# mean proportion ([0,1]) for each g
p_g = np.random.beta(2, 2, size=G)
# concentration around each p_g
c_g = np.random.lognormal(mean=0.5, sigma=1, size=G)
# reparameterization for standard Beta(a,b)
a_g = c_g * p_g / np.sqrt(p_g**2 + (1.-p_g)**2)
b_g = c_g*(1.-p_g) / np.sqrt(p_g**2 + (1.-p_g)**2)
# for each p_g, sample K proportions
p_gk = np.random.beta(a_g[:, np.newaxis], b_g[:, np.newaxis], size=(G, K))
return p_gk
# Data size
G = 3
K = 5
# obtain a G x K array of proportions p_gk in [0,1]
data = sample_data(G, K)
with pm.Model() as m:
# Parameters
p_g = pm.Beta('p_g', 1., 1., shape=G)
sd_g = pm.HalfNormal('sd_g', sd=1., shape=G)
# Observed proportions
p_gk = pm.Beta('p_gk', mu=p_g, sd=sd_g, shape=(G, K), observed=data)
trace = pm.sample(2000)
这些错误:
Exception: ("Compilation failed (return status=1):
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:400:27:
error: non-constant-expression cannot be narrowed from type 'npy_intp' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
int init_totals[2] = {V3_n0, V3_n1};.
^~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:400:27:
note: insert an explicit cast to silence this issue.
int init_totals[2] = {V3_n0, V3_n1};.
^~~~~.
static_cast<int>( ).
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:400:34:
error: non-constant-expression cannot be narrowed from type 'npy_intp' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
int init_totals[2] = {V3_n0, V3_n1};.
^~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:400:34:
note: insert an explicit cast to silence this issue.
int init_totals[2] = {V3_n0, V3_n1};.
^~~~~.
static_cast<int>( ).
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:412:9:
error: non-constant-expression cannot be narrowed from type 'ssize_t' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
V3_stride0, V3_stride1, .
^~~~~~~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:412:9:
note: insert an explicit cast to silence this issue.
V3_stride0, V3_stride1, .
^~~~~~~~~~.
static_cast<int>( ).
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:412:21:
error: non-constant-expression cannot be narrowed from type 'ssize_t' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
V3_stride0, V3_stride1, .
^~~~~~~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:412:21:
note: insert an explicit cast to silence this issue.
V3_stride0, V3_stride1, .
^~~~~~~~~~.
static_cast<int>( ).
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:413:1:
error: non-constant-expression cannot be narrowed from type 'ssize_t' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
V1_stride0, V1_stride1.
^~~~~~~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:413:1:
note: insert an explicit cast to silence this issue.
V1_stride0, V1_stride1.
^~~~~~~~~~.
static_cast<int>( ).
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:413:13:
error: non-constant-expression cannot be narrowed from type 'ssize_t' (aka 'long') to 'int' in initializer list [-Wc++11-narrowing].
V1_stride0, V1_stride1.
^~~~~~~~~~.
/Users/mfansler/.theano/compiledir_Darwin-17.6.0-x86_64-i386-64bit-i386-3.6.3-64/tmpr58gulp2/mod.cpp:413:13:
note: insert an explicit cast to silence this issue.
V1_stride0, V1_stride1.
^~~~~~~~~~.
static_cast<int>( ).
6 errors generated.. ", '[Elemwise{log,no_inplace}(TensorConstant{[[0.297343..76841722]]})]')
我是PyMC3的新手。运行现有的PyMC3示例时,我看不到这些错误。我怀疑看到这些是因为我使用的是多维格式(即(G,K)
),因为我还没有看到其他人使用此格式(我可能是对Stan表示熟悉)。
通常,我很难理解如何实现具有多个维度的多级模型。
知道是什么原因导致了我所看到的错误吗?
版本号
python 3.6.3
numpy的1.14.5
Theano 1.0.2
pymc3 3.4.1
Mac OS 10.13.5
更新资料
我在HPC节点(CentOS 7)上安装了相同的软件包版本(通过conda
),并且能够运行the modified version of the model suggested by @colcarroll。但是,在OS X机器上,即使更改了模型,我仍然看到上面指出的Theano编译错误。这可能是clang
问题吗?可以指定Theano使用的编译器吗?
python大神给出的解决方案
一种解决方法是抑制编译错误:
import theano
theano.config.gcc.cxxflags = "-Wno-c++11-narrowing"
这些错误对程序正确性的影响程度尚不清楚。当我在CentOS 7上编译时,它们不会出现(即使使用-Wc++11-narrowing
明确检查它们)。在Mac OS X上具有抑制错误的采样结果与在没有CentOS的情况下具有可比性。
我还是希望看到一个可以解释根本问题的答案。
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