SteveBronder’s gists

SteveBronder / doc_change.hpp

Created March 27, 2020 23:01

	/**
	* \ingroup opencl
	* \defgroup opencl_kernel_generator OpenCL Kernel Generator
	*
	* The OpenCL kernel generator is used to combine multiple matrix operations into a
	* single OpenCL kernel. This is much simpler than writing multi-operation kernels by
	* hand.
	*
	* Because global GPU memory loads and stores are relativly slow compared to
	* calculations in a kernel, using one kernel for multiple operations is faster than using one kernel

SteveBronder / stan_gpu_flags

Created March 18, 2020 18:25

	USER_OPTIM_FLAGS= -pipe -fPIC -O3 -mtune=native -march=native
	# I couldn't tell whether the opencl headers we use existed in `StanHeaders` on cran
	# So I do a
	# git clone --recursive https://github.com/stan-dev/rstan
	# and then include the OpenCL headers
	USER_OPENCL_FLAGS= -I"/path_to_rstan/rstan/StanHeaders/inst/include/mathlib/lib/opencl_2.1.0"
	# You can get these with clinfo -l
	USER_OPENCL_FLAGS+= -DSTAN_OPENCL=1 -DOPENCL_DEVICE_ID=1 -DOPENCL_PLATFORM_ID=2 -lOpenCL
	# Some extra bits we need
	USER_OPENCL_FLAGS+= -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120 -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes

SteveBronder / debug.stan

Created March 12, 2020 18:21

	data {
	int<lower = 1> nSubjects;
	int nIIV;
	}

	parameters {
	cholesky_factor_corr[nIIV] L;
	matrix[nIIV, nSubjects] etaStd;
	}

SteveBronder / ben_test.cpp

Last active March 6, 2020 04:34

	#include <stan/math/prim/core.hpp>
	#include <stan/math.hpp>
	#include <gtest/gtest.h>
	#include <algorithm>
	#include <sstream>
	#include <tuple>
	#include <vector>

	std::ostream* msgs = nullptr;

SteveBronder / move_vs_copy_bench.csv

Created March 3, 2020 16:43

bench	time	cpu	iters	type	test
add_copy_bench/2_mean	187 ns	187 ns	35	mean	copy
add_copy_bench/2_median	186 ns	186 ns	35	median	copy
add_copy_bench/2_stddev	3.10 ns	3.09 ns	35	stddev	copy
add_copy_bench/4_mean	335 ns	334 ns	35	mean	copy
add_copy_bench/4_median	333 ns	333 ns	35	median	copy
add_copy_bench/4_stddev	3.46 ns	3.46 ns	35	stddev	copy
add_copy_bench/8_mean	1159 ns	1159 ns	35	mean	copy
add_copy_bench/8_median	1156 ns	1156 ns	35	median	copy
add_copy_bench/8_stddev	9.47 ns	9.47 ns	35	stddev	copy

SteveBronder / bad_single_index.hpp

Last active February 28, 2020 04:36


	// Code generated by stanc acfb4612
	#include <stan/model/model_header.hpp>
	namespace example_model_namespace {

	template <typename T, typename S>
	std::vector<T> resize_to_match__(std::vector<T> &dst,
	const std::vector<S> &src) {
	dst.resize(src.size());
	return dst;

SteveBronder / bad_assign_operator.hpp

Created February 25, 2020 22:58


	// Code generated by stanc acfb4612
	#include <stan/model/model_header.hpp>
	namespace blah_model_namespace {

	template <typename T, typename S>
	std::vector<T> resize_to_match__(std::vector<T> &dst,
	const std::vector<S> &src) {
	dst.resize(src.size());
	return dst;

SteveBronder / benford_signif_patch.R

Last active January 24, 2020 21:34

	test_x = runif(10000, min = 0, 1000)
	test_x = test_x * 1e+10

	orig_signif = function(x, digits = 1) {
	xx = abs(x);
	return(trunc((10^((floor(log10(x)) * -1) + digits - 1)) * x))
	}

	new_signif = function(x, digits = 1) {
	xx = abs(x);

SteveBronder / ex_brm.stan

Last active January 13, 2020 07:27

	// generated with brms 2.10.3
	functions {
	}
	data {
	int<lower=1> N; // number of observations
	vector[N] Y; // response variable
	// data needed for ARMA correlations
	int<lower=0> Kar; // AR order
	int<lower=0> Kma; // MA order
	// number of lags per observation

SteveBronder / transform_data_nogpu.hpp

Created January 10, 2020 16:46

	// Code generated by Stan version 2.21.0

	#include <stan/model/model_header.hpp>

	namespace test_mod1_model_namespace {

	using std::istream;
	using std::string;
	using std::stringstream;
	using std::vector;

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