Intro
====
Yesterday I posted [this question](http://codereview.stackexchange.com/q/107621/84610). Since then, I've updated my code to incorporate [these](http://codereview.stackexchange.com/a/107726/84610) suggestions. I've also removed the dependence on C++11. Finally, I've made the following changes that get me closer to my overall goal:
* Rather than iterate over different values for `dt` within my script, I have `dt` specified on the command line. Specifically, an integer is specified on the command line that corresponds to (1 +) an index in `dt_array`. This allows me to process different values of `dt` in parallel using the Sun Grid Engine.
* Rather than use a single value for `I_syn_bar`, I now iterate over 100 values of `I_syn_bar`.
If you read through the current state of my script below, you'll see that I'm writing to disk 100 text files per `dt`. When I set `n_x` to 2 instead of 100, the script is very fast: 6 s on my machine. But when I set `n_x` to 100, and submit the script as a job to the SGE, it takes ~1 hour to complete (more than 6 s * 50). Hence, there seems to be some penalty being imposed on me for the heavy file I/O I'm using (in addition to the general SGE overhead).
**My goal now is to change the code so that I'm writing the data for all 100 values of `I_syn_bar`, but in fewer files.** I have a 2D matrix for each value of `I_syn_bar`. In order to write data for multiple values of `I_syn_bar` to the same text file, I need a 3D object of some kind (and a strategy for writing this object to file). Another constraint I have is that I need these files to be able to be read into Python.
Code
===
#include <math.h>
#include <vector>
#include <string>
#include <fstream>
#include <iostream>
#include <iterator>
#include <Eigen/Dense>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <stdlib.h>
#include <sstream>
using Eigen::MatrixXd;
using Eigen::ArrayXd;
bool save_mat(const MatrixXd& pdata, const std::stringstream& file_path)
{
std::ofstream os(file_path.str().c_str());
if (!os.is_open())
{
std::cout << "Failure!" << std::endl;
return false;
}
os.precision(11);
const int n_rows = pdata.rows();
const int n_cols = pdata.cols();
for (int i = 0; i < n_rows; i++)
{
for (int j = 0; j < n_cols; j++)
{
os << pdata(i, j);
if (j + 1 == n_cols)
{
os << std::endl;
}
else
{
os << ",";
}
}
}
os.close();
return true;
}
std::string get_save_file()
{
std::string dan_dir;
struct stat statbuf;
if (stat("/home/daniel", &statbuf) == 0 && S_ISDIR(statbuf.st_mode))
{
dan_dir = "/home/daniel/Science";
}
else if (stat("/home/dan", &statbuf) == 0 && S_ISDIR(statbuf.st_mode))
{
dan_dir = "/home/dan/Science";
}
else if (stat("/home/despo", &statbuf) == 0 && S_ISDIR(statbuf.st_mode))
{
dan_dir = "/home/despo/dbliss";
}
std::string save_file = "/dopa_net/results/hansel/test/test_hansel";
save_file = dan_dir + save_file;
return save_file;
}
double f(const double t, const double tau_1, const double tau_2)
{
return tau_2 / (tau_1 - tau_2) * (exp(-t / tau_1) - exp(-t / tau_2));
}
ArrayXd set_initial_V(const double tau, const double g_L, const double I_0,
const double theta, const double V_L, const int N,
const double c)
{
const double T = -tau * log(1 - g_L / I_0 * (theta - V_L));
ArrayXd V(N);
for (int i = 0; i < N; i++)
{
V(i) = V_L + I_0 / g_L * (1 - exp(-c * (i - 1) / N * T / tau));
}
return V;
}
int main(int argc, char *argv[])
{
// Declare variables set inside loops below.
double t;
double I_syn_bar;
int i;
std::stringstream complete_save_file;
// Declare and initialize constant parameters.
const int n_x = 100;
const int x_min = 0; // uA / cm^2.
const int x_max = 1; // uA / cm^2.
const double x_step = (x_max - x_min) / (n_x - 1); // uA / cm^2.
const double tau_1 = 3.0; // ms.
const double tau_2 = 1.0; // ms.
const int N = 128;
const double dt_array[3] = {0.25, 0.1, 0.01}; // ms.
const char* task_id = argv[argc - 1];
const int task_id_int = task_id[0] - '0';
const double dt = dt_array[task_id_int - 1];
const double tau = 10; // ms.
const double g_L = 0.1; // mS / cm^2.
const double I_0 = 2.3; // uA / cm^2.
const double theta = -40; // mV.
const double V_L = -60; // mV.
const double c = 0.5;
const double C = 1; // uF / cm^2.
const int sim_t = 10000; // ms.
const int n_t = sim_t / dt;
const std::string save_file = get_save_file();
// Save V for each I_syn_bar, for the dt specified on the command line.
for (double I_syn_bar = x_min; I_syn_bar < x_max; I_syn_bar += x_step)
{
MatrixXd V(N, n_t);
V.col(0) = set_initial_V(tau, g_L, I_0, theta, V_L, N, c);
double I_syn = 0; // uA / cm^2.
ArrayXd t_spike_array = ArrayXd::Zero(N);
i = 1;
for (double t = dt; t < sim_t; t += dt)
{
ArrayXd prev_V = V.col(i - 1).array();
ArrayXd current_V = prev_V + dt * (-g_L * (prev_V - V_L) + I_syn +
I_0) / C;
V.col(i) = current_V;
I_syn = 0;
for (int j = 0; j < N; j++)
{
if (current_V(j) > theta)
{
t_spike_array(j) = t;
V(j, i) = V_L;
}
I_syn += I_syn_bar / N * f(t - t_spike_array(j), tau_1, tau_2);
}
i++;
}
complete_save_file << save_file << dt << "_" << I_syn_bar << ".txt";
save_mat(V, complete_save_file);
complete_save_file.str("");
complete_save_file.clear();
}
return 0;
}
Timing Information
=====
---------------------------------------------
| n_x | command-line arg | SGE? | Time |
---------------------------------------------
| 2 | 1 | no | 6 s |
---------------------------------------------
| 2 | 1 | yes | 30 s |
---------------------------------------------
| 100 | 1 | no | 10 m 16 s |
---------------------------------------------
| 100 | 1 | yes | 53 m 5 s |
---------------------------------------------