content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy
   * of this software and associated documentation files (the "Software"), to deal
   * in the Software without restriction, including without limitation the rights
   * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   * copies of the Software, and to permit persons to whom the Software is
   * furnished to do so, subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in
   * all copies or substantial portions of the Software.
   *
   *  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   *  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   *  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   *  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   *  THE SOFTWARE.
   */
  
  package juicebox.tools.utils.juicer.hiccups;
  
  import jcuda.Pointer;
  import jcuda.Sizeof;
  import jcuda.driver.CUdeviceptr;
  import juicebox.tools.utils.common.MatrixTools;
  
  import static jcuda.driver.JCudaDriver.*;
  
  /**
   * Created by muhammadsaadshamim on 5/8/15.
   */
  class GPUHelper {
  
      public static CUdeviceptr allocateOutput(int size, int typeSize) {
          CUdeviceptr dOutput = new CUdeviceptr();
          cuMemAlloc(dOutput, size * typeSize);
          return dOutput;
      }
  
      public static CUdeviceptr allocateInput(float[] input) {
          int typeSize = Sizeof.FLOAT;
          Pointer ptr = Pointer.to(input);
          int size = input.length;
          CUdeviceptr dInput = new CUdeviceptr();
          cuMemAlloc(dInput, size * Sizeof.FLOAT);
          cuMemcpyHtoD(dInput, ptr, size * typeSize);
          return dInput;
      }
  
      public static void freeUpMemory(CUdeviceptr[] pointers) {
          for (CUdeviceptr pointer : pointers) {
              cuMemFree(pointer);
          }
      }
  
      public static float[][] GPUArraytoCPUMatrix(float[] result, int n, int x1, int x2, int y1, int y2) {
          return MatrixTools.extractLocalMatrixRegion(
                  MatrixTools.reshapeFlatMatrix(result, n), x1, x2, y1, y2);
      }
  }
  
  