Merge branch 'main' into package

AMR-Hackathon-2021 · Oct 13, 2021 · 65b4b71 · 65b4b71
2 parents 288f65c + b6f9dac
commit 65b4b71
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Showing 14 changed files with 1,017 additions and 285 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,95 +1,58 @@
 cmake_minimum_required(VERSION 3.19)
-project(SCE)
+project(cuda_kmers)
 set(CMAKE_CXX_STANDARD 14)
 cmake_policy(SET CMP0104 OLD) # Can't get CUDA_ARCHITECTURES to work with NEW
 
 # Variable definitions
 set(TARGET_NAME cuda_kmers)
 add_compile_definitions(PYTHON_EXT)
 
-IF(CMAKE_COMPILER_IS_GNUCC)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
-ENDIF(CMAKE_COMPILER_IS_GNUCC)
-
 set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
 set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0")
 # Set these to profile
 # set(CMAKE_CXX_FLAGS_RELEASE "-O2 -g")
 # set(CMAKE_CUDA_FLAGS_RELEASE "-O2 -DUSE_CUDA_PROFILER")
 
-if(UNIX AND NOT APPLE)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS")
-    set(CMAKE_LD_FLAGS "${CMAKE_LDFLAGS} -Wl,--as-needed")
-endif()
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -ffast-math -funroll-loops -m64")
-
 # Set paths for non standard lib/ and include/ locations
 if(DEFINED ENV{CONDA_PREFIX})
     include_directories($ENV{CONDA_PREFIX}/include)
     link_directories($ENV{CONDA_PREFIX}/lib)
     link_directories($ENV{CONDA_PREFIX}/lib/intel64)
-else()
-  find_package(OpenMP)
 endif()
 
 # Add libraries
-find_package(Eigen3 3.3 REQUIRED NO_MODULE)
 find_package(ZLIB)
 find_package(pybind11 REQUIRED)
 
 # Check for CUDA and compiles GPU library
-include(CheckLanguage)
-check_language(CUDA)
-if(CMAKE_CUDA_COMPILER)
-    message(STATUS "CUDA found, compiling both GPU and CPU code")
-
-    enable_language(CUDA)
-    set(CUDA_OPTS "-Wreorder -Xcompiler -fPIC -Xcompiler -Wall -Xcompiler -fopenmp -Xptxas -dlcm=ca --cudart static --relocatable-device-code=false")
-    string(APPEND CUDA_OPTS " -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_86,code=sm_86")
-    if(CMAKE_BUILD_TYPE MATCHES Debug)
-        string(APPEND CUDA_OPTS " -G")
-    else()
-        string(APPEND CUDA_OPTS " --use_fast_math")
-    endif()
-    # Set this to profile
-    # string(APPEND CUDA_OPTS " -pg --generate-line-info")
-    set(CMAKE_CUDA_FLAGS "${CUDA_OPTS}")
 
-    add_compile_definitions(GPU_AVAILABLE)
-    add_library("${TARGET_NAME}_CUDA" OBJECT src/wtsne_gpu.cu)
-    target_include_directories("${TARGET_NAME}_CUDA" PRIVATE "${pybind11_INCLUDE_DIRS}")
-    set_property(TARGET "${TARGET_NAME}_CUDA"
-                 PROPERTY POSITION_INDEPENDENT_CODE ON
-                 CUDA_SEPARABLE_COMPILATION OFF
-                 CUDA_RESOLVE_DEVICE_SYMBOLS ON   # try and ensure device link with nvcc
-                 CUDA_VISIBILITY_PRESET "hidden")
+enable_language(CUDA)
+set(CUDA_OPTS "-Wreorder -Xcompiler -fPIC -Xcompiler -Wall -Xcompiler -fopenmp -Xptxas -dlcm=ca --cudart static --relocatable-device-code=false")
+string(APPEND CUDA_OPTS " -gencode arch=compute_70,code=sm_70 -gencode arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80 -gencode arch=compute_86,code=sm_86")
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+    string(APPEND CUDA_OPTS " -G")
 else()
-    message(STATUS "CUDA not found, compiling CPU code only")
+    string(APPEND CUDA_OPTS " --use_fast_math")
 endif()
-
-# Compile CPU library
-add_library("${TARGET_NAME}" MODULE src/python_bindings.cpp)
+# Set this to profile
+# string(APPEND CUDA_OPTS " -pg --generate-line-info")
+set(CMAKE_CUDA_FLAGS "${CUDA_OPTS}")
+
+add_library("${TARGET_NAME}" MODULE src/python_bindings.cu)
+target_include_directories("${TARGET_NAME}" PRIVATE "${pybind11_INCLUDE_DIRS}")
+set_property(TARGET "${TARGET_NAME}"
+             PROPERTY POSITION_INDEPENDENT_CODE ON
+             CUDA_SEPARABLE_COMPILATION OFF
+             CUDA_RESOLVE_DEVICE_SYMBOLS ON   # try and ensure device link with nvcc
+             CUDA_VISIBILITY_PRESET "hidden")
 set_target_properties("${TARGET_NAME}" PROPERTIES
-    CXX_VISIBILITY_PRESET "hidden"
-    PREFIX "${PYTHON_MODULE_PREFIX}"
-    SUFFIX "${PYTHON_MODULE_EXTENSION}"
-)
-if(UNIX AND (NOT APPLE OR NOT CMAKE_COMPILER_IS_GNUCC))
-    set_target_properties("${TARGET_NAME}" PROPERTIES
-                          INTERPROCEDURAL_OPTIMIZATION ON)
-endif()
-
-if(CMAKE_CUDA_COMPILER)
-    target_link_libraries("${TARGET_NAME}" PRIVATE "${TARGET_NAME}_CUDA")
-    set_property(TARGET "${TARGET_NAME}" PROPERTY CUDA_RESOLVE_DEVICE_SYMBOLS ON)
-endif()
+             CXX_VISIBILITY_PRESET "hidden"
+             PREFIX "${PYTHON_MODULE_PREFIX}"
+             SUFFIX "${PYTHON_MODULE_EXTENSION}")
 
 target_link_libraries("${TARGET_NAME}" PRIVATE pybind11::module)
 if(DEFINED ENV{CONDA_PREFIX} AND (NOT APPLE OR CMAKE_COMPILER_IS_GNUCC))
   target_link_libraries("${TARGET_NAME}" PRIVATE gomp z)
 else()
   target_link_libraries("${TARGET_NAME}" PRIVATE ZLIB::ZLIB)
-  if(OpenMP_CXX_FOUND)
-      target_link_libraries("${TARGET_NAME}" PRIVATE OpenMP::OpenMP_CXX)
-  endif()
 endif()
diff --git a/gpu_kmer_counter.yml b/gpu_kmer_counter.yml
@@ -0,0 +1,44 @@
+name: gpu_kmer_counter
+channels:
+  - anaconda
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - ca-certificates=2020.10.14
+  - certifi=2020.6.20
+  - cudatoolkit=11.0.221
+  - dbus=1.13.18
+  - expat=2.2.10
+  - fontconfig=2.13.0
+  - freetype=2.10.4
+  - glib=2.56.2
+  - gst-plugins-base=1.14.0
+  - gstreamer=1.14.0
+  - icu=58.2
+  - jpeg=9b
+  - ld_impl_linux-64=2.33.1
+  - libedit=3.1.20191231
+  - libffi=3.3
+  - libgcc-ng=9.1.0
+  - libpng=1.6.37
+  - libstdcxx-ng=9.1.0
+  - libuuid=1.0.3
+  - libxcb=1.14
+  - libxml2=2.9.10
+  - ncurses=6.2
+  - openssl=1.1.1h
+  - pcre=8.44
+  - pip=20.2.4
+  - pyqt=5.9.2
+  - python=3.8.5
+  - qt=5.9.7
+  - readline=8.0
+  - setuptools=50.3.0
+  - sip=4.19.24
+  - sqlite=3.33.0
+  - tk=8.6.10
+  - wheel=0.35.1
+  - xz=5.2.5
+  - zlib=1.2.11
+prefix: /home/noahaus/miniconda3/envs/gpu_kmer_counter
diff --git a/gpu_kmer_counter/__cli__.py b/gpu_kmer_counter/__cli__.py
@@ -0,0 +1,38 @@
+import argparse
+import psutil 
+
+def cli():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i','--input',dest='input',help='Provide the path to the input directory with FAST[AQ] files.')
+    parser.add_argument('-o','--output',dest='out', default="out",help='The name used for the output results.')
+    parser.add_argument('-k','--k-size',dest='ksize',default=25,help='The k-mer length. Should be a positive integer.')
+    parser.add_argument('-K','--k-guess',dest='kguess',default=5*10^6,help='The number of approximate k-mers in the input files.')
+    parser.add_argument('-m','--avail-memory',dest='mem',default=psutil.virtual_memory().available/(1024.0 ** 3),help='The available memory to use the tool. Should be in GB')
+    parser.add_argument('-f','--false-positive-rate',dest='fpr',default=0.0,help='Set the allowable false positive rate.')
+
+    args = parser.parse_args()
+
+    def extract_cli():
+        seq_dir = args.input
+        k = args.ksize
+        k_guess = args.kguess
+        mem = args.mem
+        fpr = args.fpr
+
+        if not isinstance(k, int) or not isinstance(fpr,float):
+            sys.exit(0)
+        else:
+            print(
+"""
+Testing to see if values can be extracted: 
+{}
+{}
+{}
+{}
+{}
+""".format(seq_dir,k,k_guess,mem,fpr))
+
+
+
+if __name__ == '__cli__':
+    cli()
diff --git a/gpu_kmer_counter/__main__.py b/gpu_kmer_counter/__main__.py
@@ -1,6 +1,118 @@
+# Code for user interface 
+# Author: Noah Legall
+# Team: John Lees, Louise Cerdeira, Sam Horsfield, Noah Legall
 
-def main():
-    print("kmers")
+from PyQt5 import QtWidgets
+from PyQt5.QtWidgets import QWidget, QPushButton, QApplication, QGridLayout, QLabel, QFrame, QFileDialog
+from PyQt5.QtWidgets import *
+from PyQt5.QtCore import *
+from PyQt5.QtGui import *
+import sys
+
+# initializes the window
+def window():
+    # compulsory lines
+    app = QApplication(sys.argv)
+    win = QMainWindow()
+
+    # set window dimensions and window title
+    # x coord, y coord, width, height
+    win.setGeometry(400,400,500,300)
+    win.setWindowTitle("kmer-counter")
+
+    # actually show the window
+    win.show()
+
+    # wait for the user to click 'x' to close the window
+    sys.exit(app.exec_())
+
+class PyQtLayout(QWidget):
+
+    def __init__(self):
+        super().__init__()
+        self.UI()
+        self.setFixedHeight(300)
+        self.setFixedWidth(700)
+
+    def UI(self):
+        # Text labels for dialog boxes.
+        label1 = QLabel("input directory:")
+        label2 = QLabel("k-mer length (bps):")
+        labelGuess = QLabel("guess # of k-mers")
+        label3 = QLabel("memory available (MB):")
+        label4 = QLabel("false positivity rate (0-1):")
+
+        self.line1 = QtWidgets.QLineEdit()
+        self.line1.setFixedWidth(400)
+        self.line2 = QtWidgets.QLineEdit()
+        self.line2.setFixedWidth(150)
+        self.line3 = QtWidgets.QLineEdit()
+        self.line3.setFixedWidth(150)
+        self.line4 = QtWidgets.QLineEdit()
+        self.line4.setFixedWidth(150)  
+        self.lineGuess = QtWidgets.QLineEdit()
+        self.lineGuess.setFixedWidth(150)
 
-if __name__ == "__main__":
-    main()
+        launch = QPushButton() 
+        launch.setText("Submit")
+        launch.clicked.connect(self.extract)
+        browseLaunch = QPushButton() 
+        browseLaunch.setText("...")
+        browseLaunch.clicked.connect(self.browse)     
+
+        grid = QGridLayout()
+        grid.addWidget(label1, 0, 0)
+        grid.addWidget(label2, 1, 0)
+        grid.addWidget(label3, 2, 0)
+        grid.addWidget(label4, 3, 0)
+        grid.addWidget(labelGuess,4,0)
+        grid.addWidget(self.line1, 0, 1)
+        grid.addWidget(self.line2, 1, 1)
+        grid.addWidget(self.line3, 2, 1)
+        grid.addWidget(self.line4, 3, 1)
+        grid.addWidget(self.lineGuess,4,1)
+        grid.addWidget(launch, 5, 0)
+        grid.addWidget(browseLaunch,0,3)
+
+        self.setLayout(grid)
+        self.setGeometry(300, 300, 500, 200)
+        self.setWindowTitle('kmer-counter')
+        self.show()
+
+    def browse(self):
+        response = QFileDialog.getExistingDirectory(
+            self, 
+            caption='Select Folder'
+        )
+        print(response)
+        self.line1.setText(response)
+        return response
+
+    def extract(self):
+        seq_dir = self.line1.text()
+        k = int(self.line2.text())
+        k_guess = int(self.lineGuess.text())
+        mem = int(self.line3.text())
+        fpr = float(self.line4.text())
+
+        if not isinstance(k, int) or not isinstance(fpr,float):
+            sys.exit(0)
+        else:
+            print(
+"""
+Testing to see if values can be extracted: 
+{}
+{}
+{}
+{}
+{}
+""".format(seq_dir,k,k_guess,mem,fpr))
+
+
+def main():
+    app = QApplication(sys.argv)
+    ex = PyQtLayout()
+    sys.exit(app.exec_())
+
+if __name__ == '__main__':
+    main()