Merge pull request #173 from GOMC-WSU/development

Version 2.60

CHANGELOG.md

@@ -1,6 +1,12 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.60] - 6/16/2020
++ Changed the way we calculate pair interactions. The new approach allows us to optimize GPU by reducing the amount of cudaMemcpy needed.
++ Added C++11 support to our code base and removed any `using namespace std;` statements.
++ GPU memory management class to watch the allocation and deallocation of GPU memories.
++ Bug fixes related to lambda functionalities on GPU
+
 ## [2.51] - 4/30/2020
 + Fixed a bug with EwaldCached
 + Fixed a warning due to ignoring return value of fscanf

CMake/FileLists.cmake

@@ -187,13 +187,15 @@ set(cudaHeaders
     src/GPU/CalculateEnergyCUDAKernel.cuh
     src/GPU/CalculateForceCUDAKernel.cuh
     src/GPU/CalculateEwaldCUDAKernel.cuh
-    src/GPU/VariablesCUDA.cuh)
+    src/GPU/VariablesCUDA.cuh
+    src/GPU/CUDAMemoryManager.cuh)
 
 set(cudaSources
     src/GPU/CalculateEnergyCUDAKernel.cu
     src/GPU/CalculateForceCUDAKernel.cu
     src/GPU/CalculateEwaldCUDAKernel.cu
-    src/GPU/ConstantDefinitionsCUDAKernel.cu)
+    src/GPU/ConstantDefinitionsCUDAKernel.cu
+    src/GPU/CUDAMemoryManager.cu)
 
 source_group("Header Files" FILES ${headers})
 source_group("Lib Headers" FILES ${libHeaders})

CMake/GOMCCUDASetup.cmake

@@ -1,16 +1,7 @@
 # Find CUDA is enabled, set it up
 
 set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-DGOMC_CUDA)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-Wno-deprecated-gpu-targets)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-Xcompiler -std=c++98)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-Xcompiler -D__CORRECT_ISO_CPP11_MATH_H_PROTO)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_30,code=sm_30)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_35,code=sm_35)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_50,code=sm_50)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_70,code=sm_70)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_70,code=compute_70)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_75,code=sm_75)
-set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_75,code=compute_75)
+set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -std=c++11")
 include_directories(src/GPU)
 #set(CUDA_VERBOSE_BUILD ON)
 set(CUDA_SEPARABLE_COMPILATION ON)

CMakeLists.txt

@@ -6,6 +6,7 @@ include_directories(lib)
 include_directories(src)
 include_directories(src/cbmc)
 include_directories(src/moves)
+include_directories(src/GPU)
 
 #fix new policy of cmake about FindOpenMP.cmake (will have to check later if they fixed this issue)
 if(POLICY CMP0012)
@@ -79,8 +80,10 @@ elseif(MSVC)
     set(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "${CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT} /MT /Zi /O2 /Ob1 /D NDEBUG")
 endif()
 
-#EnsemblePreprocessor defines NVT = 1, GEMC = 2, GCMC = 3, NPT = 4
+# add c++11 flag
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 
+#EnsemblePreprocessor defines NVT = 1, GEMC = 2, GCMC = 3, NPT = 4
 #NPT (Isothermal-Isobaric) Ensemble
 set(NPT_flags "-DENSEMBLE=4")
 set(NPT_name "GOMC_CPU_NPT")

README.md

@@ -1,6 +1,6 @@
 # GOMC - GPU Optimized Monte Carlo
 
-Current Release: 2.51 (4/30/2020)
+Current Release: 2.60 (6/16/2020)
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/GOMC_WSU/Lobby?utm_source=share-link&utm_medium=link&utm_campaign=share-link)
 [![Build Status](https://travis-ci.org/GOMC-WSU/GOMC.svg?branch=master)](https://travis-ci.org/GOMC-WSU/GOMC)

lib/BasicTypes.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/BitLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/GeomLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/Lambda.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/NumLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/StrLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/StrStrmLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/VectorLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

metamake.sh

@@ -55,4 +55,4 @@ ICPC_PATH="$(which icpc)"
 export CC=${ICC_PATH}
 export CXX=${ICPC_PATH}
 cmake ..
-make
+make -j8

src/BlockOutput.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -56,12 +56,12 @@ void BlockAverage::DoWrite(const ulong step, uint precision)
 {
   if (tot >= 1) {
     if (outBlock0->is_open()) {
-      if(abs(block[0]) > 1e99) {
-        (*outBlock0) << right << std::scientific  << std::setprecision(precision - 1) <<
+      if(std::abs(block[0]) > 1e99) {
+        (*outBlock0) << std::right << std::scientific  << std::setprecision(precision - 1) <<
                      std::setw(OUTPUTWIDTH);
         (*outBlock0) << block[0];
       } else {
-        (*outBlock0) << right << std::scientific  << std::setprecision(precision) <<
+        (*outBlock0) << std::right << std::scientific  << std::setprecision(precision) <<
                      std::setw(OUTPUTWIDTH);
         (*outBlock0) << block[0];
       }
@@ -70,12 +70,12 @@ void BlockAverage::DoWrite(const ulong step, uint precision)
   }
   if (tot >= 2) {
     if (outBlock1->is_open()) {
-      if(abs(block[0]) > 1e99) {
-        (*outBlock1) << right << std::scientific  << std::setprecision(precision - 1) <<
+      if(std::abs(block[0]) > 1e99) {
+        (*outBlock1) << std::right << std::scientific  << std::setprecision(precision - 1) <<
                      std::setw(OUTPUTWIDTH);
         (*outBlock1) << block[1];
       } else {
-        (*outBlock1) << right << std::scientific  << std::setprecision(precision) <<
+        (*outBlock1) << std::right << std::scientific  << std::setprecision(precision) <<
                      std::setw(OUTPUTWIDTH);
         (*outBlock1) << block[1];
       }
@@ -132,8 +132,8 @@ void BlockAverages::Sample(const ulong step)
 void BlockAverages::DoOutput(const ulong step)
 {
   ulong nextStep = step + 1;
-  outBlock0 << left << std::scientific << std::setw(OUTPUTWIDTH) << nextStep;
-  outBlock1 << left << std::scientific << std::setw(OUTPUTWIDTH) << nextStep;
+  outBlock0 << std::left << std::scientific << std::setw(OUTPUTWIDTH) << nextStep;
+  outBlock1 << std::left << std::scientific << std::setw(OUTPUTWIDTH) << nextStep;
   for (uint v = 0; v < totalBlocks; ++v) {
     if(v < out::TOTAL_SINGLE)
       blocks[v].Write(nextStep, firstPrint, 8);
@@ -147,9 +147,9 @@ void BlockAverages::DoOutput(const ulong step)
 
 void BlockAverages::InitWatchSingle(config_setup::TrackedVars const& tracked)
 {
-  outBlock0 << left << std::scientific << std::setw(OUTPUTWIDTH) << "#STEPS";
+  outBlock0 << std::left << std::scientific << std::setw(OUTPUTWIDTH) << "#STEPS";
   if(outBlock1.is_open())
-    outBlock1 << left << std::scientific << std::setw(OUTPUTWIDTH) << "#STEPS";
+    outBlock1 << std::left << std::scientific << std::setw(OUTPUTWIDTH) << "#STEPS";
   //Note: The order of Init should be same as order of SetRef
   blocks[out::ENERGY_TOTAL_IDX].Init(&outBlock0, &outBlock1, tracked.energy.block, invSteps, out::ENERGY_TOTAL, BOXES_WITH_U_NB);
   blocks[out::ENERGY_INTER_IDX].Init(&outBlock0, &outBlock1, tracked.energy.block, invSteps, out::ENERGY_INTER, BOXES_WITH_U_NB);
@@ -251,14 +251,14 @@ void BlockAverage::printTitle(std::string output, uint boxes)
 {
   if(tot >= 1) {
     if((*outBlock0).is_open()) {
-      (*outBlock0) << left << std::scientific << std::setw(OUTPUTWIDTH) << output;
+      (*outBlock0) << std::left << std::scientific << std::setw(OUTPUTWIDTH) << output;
     } else {
       std::cerr << "Unable to write to Block_0 output file!" << std::endl;
     }
   }
   if(tot >= 2) {
     if((*outBlock1).is_open()) {
-      (*outBlock1) << left << std::scientific << std::setw(OUTPUTWIDTH) << output;
+      (*outBlock1) << std::left << std::scientific << std::setw(OUTPUTWIDTH) << output;
     } else {
       std::cerr << "Unable to write to Block_1 output file!" << std::endl;
     }

src/BlockOutput.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/BoxDimensions.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/BoxDimensions.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/BoxDimensionsNonOrth.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -79,7 +79,7 @@ void BoxDimensionsNonOrth::Init(config_setup::RestartSettings const& restart,
     XYZ bxc = Cross(cellBasis[b].Get(1), cellBasis[b].Get(2));
     XYZ cxa = Cross(cellBasis[b].Get(2), cellBasis[b].Get(0));
     //Calculate volume = A.(B x C)
-    volume[b] = abs(Dot(cellBasis[b].Get(0), bxc));
+    volume[b] = std::abs(Dot(cellBasis[b].Get(0), bxc));
     volInv[b] = 1.0 / volume[b];
     //normalizing unitcell
     for(uint i = 0; i < 3; i++) {

src/BoxDimensionsNonOrth.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CBMC.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CBMC.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/COM.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CPUSide.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CPUSide.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.51
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.60
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.