OXPHOS

Install Mysql:

export PATH=$PATH:/usr/local/mysql/bin

Run Mysql:

mysql -uroot -ppassword

CREATE DATABASE dbname;

OXPHOS

Xml files are small (~100kB per file), but the ingest, transform and dump-to-database is extremely slow.

Two improvements can be done with the code:

Bottleneck 1:

Because the error, using psycopg2 to connect to PostgreSQL across nodes are not easy. Originally, updating entries in psql database is done by extracting dataframe information as plain strings and save to dictionary:

 def update_patient_info(info, key):

OXPHOS

Setup Spark manually - gap filling of Insight Spark Intro

1. log on to control machine, usually ssh dd-control

2. spin up clusters.

~/aws-ops-insight/terraform$ terraform apply

OXPHOS

#!/bin/bash
# Test Cholesky decomposition with different Eigen versions

function fclean {
    make clean
    rm -rf ../third_party/Eigen3
    rm -rf ../third_party/include/eigen
}

function frun {

OXPHOS

class LinalgBackendBase
{
public:
	/**
	* Wrapper method that computes mean of SGVectors and SGMatrices.
	*
	* @see linalg::mean
	*/
	#define BACKEND_GENERIC_COMPLEX_MEAN(Type, Container) \
	virtual typename std::enable_if<std::is_same<Type, complex128_t>::type, complex128_t>::type \

OXPHOS

/*
 * Copyright (c) 2016, Shogun-Toolbox e.V. <shogun-team@shogun-toolbox.org>
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 *  1. Redistributions of source code must retain the above copyright notice,
 *     this list of conditions and the following disclaimer.
 *

OXPHOS

		template<class Archive>
		void cereal_save(Archive& ar) const
		{
			switch (m_datatype.e_containertype) {
			case TYPE_SGVECTOR
			case TYPE_INT_32:
				ar(*(reinterpret_cast<int32_t*>(storage))); break;
			case TYPE_FLOAT_64:
				ar(*(reinterpret_cast<float64_t*>(storage))); break;
			case TYPE_SGVECTOR_INT_32:

OXPHOS

template<class Archive>
void CSGObject::cereal_save(Archive& ar) const
{
	int y = 0;
	for (auto it = self->map.begin(); it != self->map.end(); ++it, ++y)
	{
		std::cerr << "num. " << y << std::endl;
		ar(it->second);
	}
}

OXPHOS

#define CEREAL_SAVE_FUNCTION_NAME cereal_save
#define CEREAL_LOAD_FUNCTION_NAME cereal_load
template<class Archive>
void CSGObject::cereal_save(Archive& ar) const
{

	for (auto it = self->map.begin(); it != self->map.end(); ++it)
	    ar(it->second);     // archive Any object
	    
}

OXPHOS

Mac148934:test2 zora$ g++ -c -std=c++11 base.cpp
Mac148934:test2 zora$ g++ -c -std=c++11 test.cpp
Mac148934:test2 zora$ g++ -std=c++11 base.o test.o -o test

Undefined symbols for architecture x86_64:
  "void base::serialize<cereal::JSONOutputArchive>(cereal::JSONOutputArchive&) const", referenced from:
      decltype(fp0.serialize(fp)) cereal::access::member_serialize<cereal::JSONOutputArchive, derived>(cereal::JSONOutputArchive&, derived&) in test.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)