From fbfee74d89fa011f3f9ea1abe276d2fea99a351a Mon Sep 17 00:00:00 2001
From: "Reza Rafati Bonab (pma753)" <reza.rafati@usask.ca>
Date: Fri, 6 Sep 2024 14:16:54 -0600
Subject: [PATCH] Add code Files
---
Makefile | 30 ++++++++
SW-Actor.cpp | 185 ++++++++++++++++++++++++++++++++++++++++++++++++++
config.hpp | 22 ++++++
job.sh | 24 +++++++
makePairs.cpp | 16 +++++
makePairs.hpp | 5 ++
readFasta.cpp | 33 +++++++++
readFasta.hpp | 7 ++
8 files changed, 322 insertions(+)
create mode 100644 Makefile
create mode 100644 SW-Actor.cpp
create mode 100644 config.hpp
create mode 100644 job.sh
create mode 100644 makePairs.cpp
create mode 100644 makePairs.hpp
create mode 100644 readFasta.cpp
create mode 100644 readFasta.hpp
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..5d8f32c
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,30 @@
+# Compiler
+CXX = g++
+
+# Compiler flags
+CXXFLAGS = -std=c++17 -O3 -I/globalhome/pma753/HPC/root/install/include
+
+# Linker flags
+LDFLAGS = -L/globalhome/pma753/HPC/root/install/lib64
+
+# Libraries
+LIBS = -lcaf_core -lcaf_io
+
+# Source files
+SRCS = SW-Actor.cpp readFasta.cpp makePairs.cpp
+
+# Target executable
+TARGET = swActor
+
+# Set library path
+export LD_LIBRARY_PATH := /globalhome/pma753/HPC/root/install/lib64:$(LD_LIBRARY_PATH)
+
+# Build rule
+all: $(TARGET)
+
+$(TARGET): $(SRCS)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TARGET) $(SRCS) $(LIBS)
+
+# Clean rule
+clean:
+ rm -f $(TARGET)
diff --git a/SW-Actor.cpp b/SW-Actor.cpp
new file mode 100644
index 0000000..6fd8794
--- /dev/null
+++ b/SW-Actor.cpp
@@ -0,0 +1,185 @@
+/*
+A program that reads Multiple sequences from a fasta file and calls the
+Smith-Waterman algorithm to align any possible pair of them Using Actor Model.
+The aligned sequences and the alignment score are then printed to the output
+file.
+ */
+// include the necessary libraries
+#include "config.hpp"
+
+using namespace std;
+using namespace caf;
+
+// The Manager Actor
+behavior workerActor(event_based_actor *self)
+{
+ // recive the messages
+ return {[=](actor manager, int position)
+ {
+ // Set the scores
+ int matchScore = 2;
+ int mismatchScore = -1;
+ int gapScore = -2;
+
+ // Get the length of the sequences
+ int index1 = workList1[position];
+ int index2 = workList2[position];
+ string seq1 = sequences[index1];
+ string seq2 = sequences[index2];
+ int m = seq1.length();
+ int n = seq2.length();
+
+ // Create a matrix to store the scores
+ vector<vector<int>> scoreMatrix(m + 1, vector<int>(n + 1, 0));
+
+ // Fill the matrix and find the max score
+ int maxScore = 0;
+ int indexFirst, indexSecond;
+
+ // loop through the matrix row by row
+ for (int i = 1; i <= m; ++i)
+ {
+ for (int j = 1; j <= n; ++j)
+ {
+ // find 3 scores for adjacent cells according to the SW algorithm
+ int diagonal = scoreMatrix[i - 1][j - 1] + (seq1[i - 1] == seq2[j - 1] ? matchScore : mismatchScore);
+ int left = scoreMatrix[i - 1][j] + gapScore;
+ int above = scoreMatrix[i][j - 1] + gapScore;
+ // take the maximum of the three scores and 0
+ scoreMatrix[i][j] = max({0, diagonal, left, above});
+
+ // update the max score and the corresponding indices
+ if (scoreMatrix[i][j] > maxScore)
+ {
+ maxScore = scoreMatrix[i][j];
+ indexFirst = i;
+ indexSecond = j;
+ }
+ }
+ }
+
+ // Traceback and find the aligned sequences
+ string alignedSeq1, alignedSeq2;
+ int i = indexFirst;
+ int j = indexSecond;
+
+ // start from the cell with the max score and loop until a cell with score 0 is reached
+ while (i > 0 || j > 0)
+ {
+ // get the current score and the scores of the adjacent cells
+ int score = scoreMatrix[i][j];
+ // check termination condition
+ if (score == 0)
+ {
+ break;
+ }
+ // check different strategies for updating the aligned sequences
+ // match/mismatch case
+ int diagonal = scoreMatrix[i - 1][j - 1];
+ if (score == diagonal + (seq1[i - 1] == seq2[j - 1] ? matchScore : mismatchScore))
+ {
+ alignedSeq1 = seq1[i - 1] + alignedSeq1;
+ alignedSeq2 = seq2[j - 1] + alignedSeq2;
+ --i;
+ --j;
+ continue;
+ }
+ // gap for first sequence cases
+ int above = scoreMatrix[i - 1][j];
+ if (score == above + gapScore)
+ {
+ alignedSeq1 = seq1[i - 1] + alignedSeq1;
+ alignedSeq2 = '-' + alignedSeq2;
+ --i;
+ continue;
+ }
+ // gap for second sequence cases
+ int left = scoreMatrix[i][j - 1];
+ if (score == left + gapScore)
+ {
+ alignedSeq1 = '-' + alignedSeq1;
+ alignedSeq2 = seq2[j - 1] + alignedSeq2;
+ --j;
+ continue;
+ }
+ }
+
+ // write the aligned sequences and the score to the output file
+ self->println("Pair: {}, {} with score: {}, \nAligned seq1: {}, \nAligned seq2: {}\n",
+ workList1[position], workList2[position], maxScore, alignedSeq1, alignedSeq2);
+
+ // send message to the manager to request new work
+ anon_mail(self, position, maxScore).send(manager);
+ }};
+}
+
+// Define the state of the Manager Actor
+struct state_full_actor
+{
+ int position = 0;
+ int counter = 0;
+};
+// The Manager Actor
+behavior managerActor(stateful_actor<state_full_actor> *self)
+{
+ // recive the messages
+ return {
+ [=](int actorNumber)
+ {
+ // Spawn the worker Actors and send them the position in the workList
+ for (int i = 0; i < actorNumber; ++i)
+ {
+ actor worker = self->spawn(workerActor);
+ anon_mail(self, i).send(worker);
+ }
+ self->state().position = actorNumber - 1;
+ },
+ [=](actor sender, int position, int score)
+ {
+ // update the position and the counter
+ self->state().position++;
+ self->state().counter++;
+
+ // check if there is more work to do
+ if (self->state().position < workList1.size())
+ {
+ // send the next work to the worker
+ anon_mail(self, self->state().position).send(sender);
+ }
+
+ if (self->state().counter == workList1.size())
+ {
+ // Stop the timer
+ auto stop = std::chrono::high_resolution_clock::now();
+ auto duration = std::chrono::duration_cast<std::chrono::seconds>(stop - start);
+ self->println("Time taken by function: {} seconds\n", duration.count());
+ self->quit();
+ }
+ },
+ };
+}
+
+// Main now takes a config object as an additional argument
+void caf_main(actor_system &system)
+{
+ // Read sequences from the input file
+ sequences = readFasta("/globalhome/pma753/HPC/Two-Level-Test/Data/BRCA1.fasta");
+
+ // Create a list of all possible pairs of sequences
+ vector<vector<int>> paires = makePairs(sequences.size());
+ workList1 = paires[0];
+ workList2 = paires[1];
+ // Start the timer
+ start = std::chrono::high_resolution_clock::now();
+
+ // Span the Manager Actor
+ actor manager = system.spawn(managerActor);
+
+ // Send a message to the manager with actorNumber to start the process
+ int actorNumber = 40;
+ anon_mail(actorNumber).send(manager);
+
+ // The rest of the process is being don inside the managerActor
+}
+
+CAF_MAIN()
\ No newline at end of file
diff --git a/config.hpp b/config.hpp
new file mode 100644
index 0000000..7270a7f
--- /dev/null
+++ b/config.hpp
@@ -0,0 +1,22 @@
+#ifndef CONFIG_HPP
+#define CONFIG_HPP
+
+#include "caf/all.hpp"
+#include <vector>
+#include <string>
+#include <chrono>
+#include <utility>
+#include <algorithm>
+
+// include the necessary headers
+#include "readFasta.hpp"
+#include "makePairs.hpp"
+
+// Declare the global variables
+std::vector<std::string> sequences;
+std::vector<std::pair<int, int>> pairs;
+std::vector<int> workList1;
+std::vector<int> workList2;
+auto start = std::chrono::high_resolution_clock::now();
+
+#endif // CONFIG_HPP
\ No newline at end of file
diff --git a/job.sh b/job.sh
new file mode 100644
index 0000000..58ab13b
--- /dev/null
+++ b/job.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+#SBATCH --account=hpc_p_spiteri
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=40
+#SBATCH --mem=185GB
+#SBATCH --time=01:00:00
+#SBATCH --constraint=skylake
+
+
+# Navigate to the directory containing your MPI program
+cd $SLURM_SUBMIT_DIR
+
+# Set LD_LIBRARY_PATH if needed
+export LD_LIBRARY_PATH=/globalhome/pma753/HPC/root/install/lib64:$LD_LIBRARY_PATH
+
+make clean
+make
+
+echo "40 cpus 40 actors"
+echo "BRCA1.fasta"
+
+# Run your program
+time ./swActor --caf.scheduler.max-threads=40 > outputjob.txt
+
\ No newline at end of file
diff --git a/makePairs.cpp b/makePairs.cpp
new file mode 100644
index 0000000..299a546
--- /dev/null
+++ b/makePairs.cpp
@@ -0,0 +1,16 @@
+#include "makePairs.hpp"
+
+std::vector<std::vector<int>> makePairs(int seqSize)
+{
+ std::vector<std::vector<int>> pairs(2);
+ // Create a list of all possible pairs of sequences
+ for (int i = 0; i < seqSize; ++i)
+ {
+ for (int j = i + 1; j < seqSize; ++j)
+ {
+ pairs[0].push_back(i);
+ pairs[1].push_back(j);
+ }
+ }
+ return pairs;
+}
diff --git a/makePairs.hpp b/makePairs.hpp
new file mode 100644
index 0000000..260105e
--- /dev/null
+++ b/makePairs.hpp
@@ -0,0 +1,5 @@
+#include <iostream>
+#include <vector>
+
+// Define the makePairs function
+std::vector<std::vector<int>> makePairs(int seqSize);
diff --git a/readFasta.cpp b/readFasta.cpp
new file mode 100644
index 0000000..31bf56d
--- /dev/null
+++ b/readFasta.cpp
@@ -0,0 +1,33 @@
+#include "readFasta.hpp"
+
+// A function to read multiple sequences from a fasta file
+std::vector<std::string> readFasta(std::string filename)
+{
+ // a vector to store the sequences
+ std::vector<std::string> sequences;
+
+ // Read Multiple sequences from the input file
+ std::ifstream inputFile(filename);
+ std::string line;
+ std::string seq;
+ while (std::getline(inputFile, line))
+ {
+ line.erase(line.find_last_not_of(" \t\r\n") + 1);
+ if (line[0] == '>')
+ {
+ if (!seq.empty())
+ {
+ sequences.push_back(seq);
+ seq.clear();
+ }
+ }
+ else
+ {
+ seq += line;
+ }
+ }
+ sequences.push_back(seq);
+ inputFile.close();
+
+ return sequences;
+}
diff --git a/readFasta.hpp b/readFasta.hpp
new file mode 100644
index 0000000..9c1f98b
--- /dev/null
+++ b/readFasta.hpp
@@ -0,0 +1,7 @@
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <vector>
+
+// A function to read multiple sequences from a fasta file
+std::vector<std::string> readFasta(std::string filename);
--
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