Adding FFT Unit Tests

Change-Id: I3de741e6c66ac1e611d78962606253a3c903cbef

diff --git a/cmake/legacy_and_external.supp b/cmake/legacy_and_external.supp
index 6788ba24b8a7e2cf5150d3e65729ef021be99b76..ac043edf041454d7104d2ae3bb21d686fd43d0e6 100644 (file)
--- a/cmake/legacy_and_external.supp
+++ b/cmake/legacy_and_external.supp
@@ -104,6 +104,12 @@
    fun:_Unwind_RaiseException
    fun:__cxa_throw
 }
+{
+   posix_memalign
+   Memcheck:Leak
+   ...
+   fun:posix_memalign
+}
 
 # Intel compiler on MacOS
 {
@@ -112,3 +118,40 @@
    fun:malloc
    fun:__cilkrts_os_mutex_create
 }
+# Intel compiler with MKL
+{
+   dlerror
+   Memcheck:Leak
+   ...
+   fun:_dlerror_run
+}
+#Intel
+{
+   strlen
+   Memcheck:Addr8
+   fun:__intel_sse2_strlen
+}
+{
+   strlen2
+   Memcheck:Cond
+   fun:__intel_sse2_strlen
+}
+{
+   __kmpc_global_thread_num
+   Memcheck:Param
+   sched_setaffinity(mask)
+   ...
+   fun:__kmpc_global_thread_num
+}
+{
+   __kmpc_global_thread_num2
+   Memcheck:Cond
+   ...
+   fun:__kmpc_global_thread_num
+}
+{
+   __kmpc_global_thread_num3
+   Memcheck:Leak
+   ...
+   fun:__kmpc_global_thread_num
+}

diff --git a/src/gromacs/legacyheaders/types/commrec.h b/src/gromacs/legacyheaders/types/commrec.h
index 0d2fce9813e544359fab0a5e5574d324293378db..7d049e803f14fc81e00eab2e879a954b1f722161 100644 (file)
--- a/src/gromacs/legacyheaders/types/commrec.h
+++ b/src/gromacs/legacyheaders/types/commrec.h
@@ -45,6 +45,7 @@
 typedef void* MPI_Comm;
 typedef void* MPI_Request;
 typedef void* MPI_Group;
+#define MPI_COMM_NULL NULL
 #endif
 #endif
 

diff --git a/src/gromacs/mdlib/CMakeLists.txt b/src/gromacs/mdlib/CMakeLists.txt
index 222a53bc0fb0b3b9e24d9e7c3497221fae6163d8..a7637aa7110cef206332336d68ed3d6e05863494 100644 (file)
--- a/src/gromacs/mdlib/CMakeLists.txt
+++ b/src/gromacs/mdlib/CMakeLists.txt
@@ -3,3 +3,6 @@ if(GMX_FFT_FFTPACK)
 list(APPEND MDLIB_SOURCES ${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.c)
 endif()
 set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
+if (BUILD_TESTING)
+    add_subdirectory(tests)
+endif (BUILD_TESTING)

diff --git a/src/gromacs/mdlib/tests/CMakeLists.txt b/src/gromacs/mdlib/tests/CMakeLists.txt
new file mode 100644 (file)
index 0000000..903ed90
--- /dev/null
+++ b/src/gromacs/mdlib/tests/CMakeLists.txt
@@ -0,0 +1,2 @@
+gmx_add_unit_test(MDLibUnitTests mdlib-test
+                  fft.cpp)

diff --git a/src/gromacs/mdlib/tests/fft.cpp b/src/gromacs/mdlib/tests/fft.cpp
new file mode 100644 (file)
index 0000000..7f46120
--- /dev/null
+++ b/src/gromacs/mdlib/tests/fft.cpp
@@ -0,0 +1,281 @@
+/*
+ *
+ *                This source code is part of
+ *
+ *                 G   R   O   M   A   C   S
+ *
+ *          GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2009, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ */
+/*! \internal \file
+ * \brief
+ * Tests utilities for fft calculations.
+ *
+ * \author Roland Schulz <roland@utk.edu>
+ * \ingroup module_mdlibs
+ */
+
+#include "config.h"
+#include <vector>
+#include <complex>
+#include <gtest/gtest.h>
+#include "testutils/refdata.h"
+#include "gromacs/utility/stringutil.h"
+#include "gmx_fft.h"
+#include "gmx_parallel_3dfft.h"
+
+namespace
+{
+
+static const real inputdata[] = { //print ",\n".join([",".join(["%4s"%(random.randint(-99,99)/10.,) for i in range(25)]) for j in range(20)])
+        -3.5, 6.3, 1.2, 0.3, 1.1,-5.7, 5.8,-1.9,-6.3,-1.4, 7.4, 2.4,-9.9,-7.2, 5.4, 6.1,-1.9,-7.6, 1.4,-3.5, 0.7, 5.6,-4.2,-1.1,-4.4,
+        -6.3,-7.2, 4.6,-3.0,-0.9, 7.2, 2.5,-3.6, 6.1,-3.2,-2.1, 6.5,-0.4,-9.0, 2.3, 8.4, 4.0,-5.2,-9.0, 4.7,-3.7,-2.0,-9.5,-3.9,-3.6,
+         7.1, 0.8,-0.6, 5.2,-9.3,-4.5, 5.9, 2.2,-5.8, 5.0, 1.2,-0.1, 2.2, 0.2,-7.7, 1.9,-8.4, 4.4, 2.3,-2.9, 6.7, 2.7, 5.8,-3.6, 8.9,
+         8.9, 4.3, 9.1, 9.3,-8.7, 4.1, 9.6,-6.2, 6.6,-9.3, 8.2, 4.5, 6.2, 9.4,-8.0,-6.8,-3.3, 7.2, 1.7, 0.6,-4.9, 9.8, 1.3, 3.2,-0.2,
+         9.9, 4.4,-9.9,-7.2, 4.4, 4.7, 7.2,-0.3, 0.3,-2.1, 8.4,-2.1,-6.1, 4.1,-5.9,-2.2,-3.8, 5.2,-8.2,-7.8,-8.8, 6.7,-9.5,-4.2, 0.8,
+         8.3, 5.2,-9.0, 8.7, 9.8,-9.9,-7.8,-8.3, 9.0,-2.8,-9.2,-9.6, 8.4, 2.5, 6.0,-0.4, 1.3,-0.5, 9.1,-9.5,-0.8, 1.9,-6.2, 4.3,-3.8,
+         8.6,-1.9,-2.1,-0.4,-7.1,-3.7, 9.1,-6.4,-0.6, 2.5, 8.0,-5.2,-9.8,-4.3, 4.5, 1.7, 9.3, 9.2, 1.0, 5.3,-4.5, 6.4,-6.6, 3.1,-6.8,
+         2.1, 2.0, 7.3, 8.6, 5.0, 5.2, 0.4,-7.1, 4.5,-9.2,-9.1, 0.2,-6.3,-1.1,-9.6, 7.4,-3.7,-5.5, 2.6,-3.5,-0.7, 9.0, 9.8,-8.0, 3.6,
+         3.0,-2.2,-2.8, 0.8, 9.0, 2.8, 7.7,-0.7,-5.0,-1.8,-2.3,-0.4,-6.2,-9.1,-9.2, 0.5, 5.7,-3.9, 2.1, 0.6, 0.4, 9.1, 7.4, 7.1,-2.5,
+         7.3, 7.8,-4.3, 6.3,-0.8,-3.8,-1.5, 6.6, 2.3, 3.9,-4.6, 5.8,-7.4, 5.9, 2.8, 4.7, 3.9,-5.4, 9.1,-1.6,-1.9,-4.2,-2.6, 0.6,-5.1,
+         1.8, 5.2, 4.0,-6.2, 6.5,-9.1, 0.5, 2.1, 7.1,-8.6, 7.6,-9.7,-4.6,-5.7, 6.1,-1.8,-7.3, 9.4, 8.0,-2.6,-1.8, 5.7, 9.3,-7.9, 7.4,
+         6.3, 2.0, 9.6,-4.5,-6.2, 6.1, 2.3, 0.8, 5.9,-2.8,-3.5,-1.5, 6.0,-4.9, 3.5, 7.7,-4.2,-9.7, 2.4, 8.1, 5.9, 3.4,-7.5, 7.5, 2.6,
+         4.7, 2.7, 2.2, 2.6, 6.2, 7.5, 0.2,-6.4,-2.8,-0.5,-0.3, 0.4, 1.2, 3.5,-4.0,-0.5, 9.3,-7.2, 8.5,-5.5,-1.7,-5.3, 0.3, 3.9,-3.6,
+        -3.6, 4.7,-8.1, 1.4, 4.0, 1.3,-4.3,-8.8,-7.3, 6.3,-7.5,-9.0, 9.1, 4.5,-1.9, 1.9, 9.9,-1.7,-9.1,-5.1, 8.5,-9.3, 2.1,-5.8,-3.6,
+        -0.8,-0.9,-3.3,-2.7, 7.0,-7.2,-5.0, 7.4,-1.4, 0.0,-4.5,-9.7, 0.7,-1.0,-9.1,-5.3, 4.3, 3.4,-6.6, 9.8,-1.1, 8.9, 5.0, 2.9, 0.2,
+        -2.9, 0.8, 6.7,-0.6, 0.6, 4.1, 5.3,-1.7,-0.3, 4.2, 3.7,-8.3, 4.0, 1.3, 6.3, 0.2, 1.3,-1.1,-3.5, 2.8,-7.7, 6.2,-4.9,-9.9, 9.6,
+         3.0,-9.2,-8.0,-3.9, 7.9,-6.1, 6.0, 5.9, 9.6, 1.2, 6.2, 3.6, 2.1, 5.8, 9.2,-8.8, 8.8,-3.3,-9.2, 4.6, 1.8, 4.6, 2.9,-2.7, 4.2,
+         7.3,-0.4, 7.7,-7.0, 2.1, 0.3, 3.7, 3.3,-8.6, 9.8, 3.6, 3.1, 6.5,-2.4, 7.8, 7.5, 8.4,-2.8,-6.3,-5.1,-2.7, 9.3,-0.8,-9.2, 7.9,
+         8.9, 3.4, 0.1,-5.3,-6.8, 4.9, 4.3,-0.7,-2.2,-3.2,-7.5,-2.3, 0.0, 8.1,-9.2,-2.3,-5.7, 2.1, 2.6, 2.0, 0.3,-8.0,-2.0,-7.9, 6.6,
+         8.4, 4.0,-6.2,-6.9,-7.2, 7.7,-5.0, 5.3, 1.9,-5.3,-7.5, 8.8, 8.3, 9.0, 8.1, 3.2, 1.2,-5.4,-0.2, 2.1,-5.2, 9.5, 5.9, 5.6,-7.8,
+};
+
+
+class BaseFFTTest : public ::testing::Test
+{
+    public:
+        BaseFFTTest() : checker_(data_.rootChecker())
+        {
+        }
+        ~BaseFFTTest()
+        {
+            gmx_fft_cleanup();
+        }
+        gmx::test::TestReferenceData data_;
+        gmx::test::TestReferenceChecker checker_;
+        std::vector<real> in_, out_;
+};
+
+class FFTTest : public BaseFFTTest
+{
+    public:
+        FFTTest() : fft_(NULL)
+        {
+        }
+        ~FFTTest()
+        {
+            if (fft_)
+            {
+                gmx_fft_destroy(fft_);
+            }
+        }
+        gmx_fft_t fft_;
+};
+
+class ManyFFTTest : public BaseFFTTest
+{
+    public:
+        ManyFFTTest() : fft_(NULL)
+        {
+        }
+        ~ManyFFTTest()
+        {
+            if (fft_)
+            {
+                gmx_many_fft_destroy(fft_);
+            }
+        }
+        gmx_fft_t fft_;
+};
+
+
+//TODO: Add tests for aligned/not-aligned input/output memory
+
+class FFTTest1D : public FFTTest, public ::testing::WithParamInterface<int>
+{
+
+};
+
+class FFFTest3D : public BaseFFTTest
+{
+    public:
+        FFFTest3D() : fft_(NULL)
+        {
+        }
+        ~FFFTest3D()
+        {
+            if (fft_)
+            {
+                gmx_parallel_3dfft_destroy(fft_);
+            }
+        }
+        gmx_parallel_3dfft_t fft_;
+};
+
+
+TEST_P(FFTTest1D, Complex)
+{
+    const int nx = GetParam();
+    ASSERT_LE(nx*2,static_cast<int>(sizeof(inputdata)/sizeof(real)));
+
+    in_ = std::vector<real>(inputdata,inputdata+nx*2);
+    out_ = std::vector<real>(nx*2);
+    real* in  = &in_[0];
+    real* out = &out_[0];
+
+    gmx_fft_init_1d(&fft_,nx,0);
+
+    gmx_fft_1d(fft_,GMX_FFT_FORWARD, in, out);
+    checker_.checkSequenceArray(nx*2, out, "forward");
+    gmx_fft_1d(fft_,GMX_FFT_BACKWARD, in, out);
+    checker_.checkSequenceArray(nx*2, out, "backward");
+}
+
+TEST_P(FFTTest1D, Real)
+{
+    const int rx = GetParam();
+    const int cx = (rx/2+1);
+    ASSERT_LE(cx*2,static_cast<int>(sizeof(inputdata)/sizeof(real)));
+
+    in_ = std::vector<real>(inputdata,inputdata+cx*2);
+    out_ = std::vector<real>(cx*2);
+    real* in = &in_[0];
+    real* out = &out_[0];
+
+    gmx_fft_init_1d_real(&fft_,rx,0);
+
+    gmx_fft_1d_real(fft_,GMX_FFT_REAL_TO_COMPLEX,in,out);
+    checker_.checkSequenceArray(cx*2, out, "forward");
+    gmx_fft_1d_real(fft_,GMX_FFT_COMPLEX_TO_REAL,in,out);
+    checker_.checkSequenceArray(rx, out, "backward");
+}
+
+INSTANTIATE_TEST_CASE_P(7_8_25_36_60,
+        FFTTest1D, ::testing::Values(7,8,25,36,60));
+
+
+TEST_F(ManyFFTTest, Complex1DLength48Multi5Test)
+{
+    const int nx = 48;
+    const int N = 5;
+
+    in_ = std::vector<real>(inputdata,inputdata+nx*2*N);
+    out_ = std::vector<real>(nx*2*N);
+    real* in = &in_[0];
+    real* out = &out_[0];
+
+    gmx_fft_init_many_1d(&fft_,nx,N,0);
+
+    gmx_fft_many_1d(fft_,GMX_FFT_FORWARD, in, out);
+    checker_.checkSequenceArray(nx*2*N, out, "forward");
+    gmx_fft_many_1d(fft_,GMX_FFT_BACKWARD, in, out);
+    checker_.checkSequenceArray(nx*2*N, out, "backward");
+}
+
+TEST_F(ManyFFTTest, Real1DLength48Multi5Test)
+{
+    const int rx = 48;
+    const int cx = (rx/2+1);
+    const int N = 5;
+
+    in_ = std::vector<real>(inputdata,inputdata+cx*2*N);
+    out_ = std::vector<real>(cx*2*N);
+    real* in = &in_[0];
+    real* out = &out_[0];
+
+    gmx_fft_init_many_1d_real(&fft_,rx,N,0);
+
+    gmx_fft_many_1d_real(fft_,GMX_FFT_REAL_TO_COMPLEX,in,out);
+    checker_.checkSequenceArray(cx*2*N, out, "forward");
+    gmx_fft_many_1d_real(fft_,GMX_FFT_COMPLEX_TO_REAL,in,out);
+    checker_.checkSequenceArray(rx*N, out, "backward");
+}
+
+TEST_F(FFTTest, Real2DLength18_15Test)
+{
+    const int rx = 18;
+    const int cx = (rx/2+1);
+    const int ny = 15;
+
+    in_ = std::vector<real>(inputdata,inputdata+cx*2*ny);
+    out_ = std::vector<real>(cx*2*ny);
+    real* in = &in_[0];
+    real* out = &out_[0];
+
+    gmx_fft_init_2d_real(&fft_,rx,ny,0);
+
+    gmx_fft_2d_real(fft_,GMX_FFT_REAL_TO_COMPLEX,in,out);
+    checker_.checkSequenceArray(cx*2*ny, out, "forward");
+//    known to be wrong for gmx_fft_mkl. And not used.
+//    gmx_fft_2d_real(_fft,GMX_FFT_COMPLEX_TO_REAL,in,out);
+//    _checker.checkSequenceArray(rx*ny, out, "backward");
+}
+
+//TODO: test with threads and more than 1 MPI ranks
+TEST_F(FFFTest3D, Real5_6_9)
+{
+    int ndata[] = {5, 6, 9};
+    MPI_Comm comm[] = {MPI_COMM_NULL, MPI_COMM_NULL};
+    real* rdata;
+    t_complex* cdata;
+    ivec local_ndata, offset,rsize,csize,complex_order;
+
+    gmx_parallel_3dfft_init(&fft_, ndata, &rdata, &cdata,
+            comm, NULL, NULL, TRUE, 1);
+
+    gmx_parallel_3dfft_real_limits(fft_, local_ndata, offset, rsize);
+    gmx_parallel_3dfft_complex_limits(fft_, complex_order,
+            local_ndata, offset, csize);
+    checker_.checkVector(rsize,"rsize");
+    checker_.checkVector(csize,"csize");
+    int size = csize[0]*csize[1]*csize[2];
+
+    memcpy(rdata,inputdata,size*sizeof(t_complex));
+    gmx_parallel_3dfft_execute(fft_, GMX_FFT_REAL_TO_COMPLEX, rdata, cdata,
+            0, NULL);
+    //TODO use std::complex and add checkComplex for it
+    checker_.checkSequenceArray(size*2,
+            reinterpret_cast<real*>(cdata), "forward");
+
+    memcpy(cdata,inputdata,size*sizeof(t_complex));
+    gmx_parallel_3dfft_execute(fft_, GMX_FFT_COMPLEX_TO_REAL, rdata, cdata,
+            0, NULL);
+    for(int i=0;i<ndata[0]*ndata[1];i++) //check sequence but skip unused data
+    {
+        checker_.checkSequenceArray(ndata[2], rdata+i*rsize[2],
+                gmx::formatString("backward %d",i).c_str());
+    }
+}
+
+} // namespace

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml b/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml
new file mode 100644 (file)
index 0000000..b2cdbf2
--- /dev/null
+++ b/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="forward">
+    <Int Name="Length">14</Int>
+    <Real>-4.200000</Real>
+    <Real>-7.199999</Real>
+    <Real>-12.615427</Real>
+    <Real>-2.080840</Real>
+    <Real>1.683286</Real>
+    <Real>4.656070</Real>
+    <Real>18.848852</Real>
+    <Real>-10.344789</Real>
+    <Real>0.649853</Real>
+    <Real>32.731766</Real>
+    <Real>-20.751381</Real>
+    <Real>12.846081</Real>
+    <Real>-8.115183</Real>
+    <Real>13.491714</Real>
+  </Sequence>
+  <Sequence Name="backward">
+    <Int Name="Length">14</Int>
+    <Real>-4.200000</Real>
+    <Real>-7.199999</Real>
+    <Real>-8.115183</Real>
+    <Real>13.491714</Real>
+    <Real>-20.751381</Real>
+    <Real>12.846081</Real>
+    <Real>0.649853</Real>
+    <Real>32.731766</Real>
+    <Real>18.848852</Real>
+    <Real>-10.344789</Real>
+    <Real>1.683286</Real>
+    <Real>4.656070</Real>
+    <Real>-12.615427</Real>
+    <Real>-2.080840</Real>
+  </Sequence>
+</ReferenceData>

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml b/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml
new file mode 100644 (file)
index 0000000..e1a9a9b
--- /dev/null
+++ b/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml
@@ -0,0 +1,42 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Sequence Name="forward">
+    <Int Name="Length">16</Int>
+    <Real>1.200003</Real>
+    <Real>-1.100000</Real>
+    <Real>-7.508683</Real>
+    <Real>4.973149</Real>
+    <Real>-2.500001</Real>
+    <Real>20.400000</Real>
+    <Real>-1.174874</Real>
+    <Real>18.629290</Real>
+    <Real>-38.400002</Real>
+    <Real>-14.900000</Real>
+    <Real>16.108685</Real>
+    <Real>-11.573149</Real>
+    <Real>0.499999</Real>
+    <Real>15.199999</Real>
+    <Real>3.774874</Real>
+    <Real>18.770712</Real>
+  </Sequence>
+  <Sequence Name="backward">
+    <Int Name="Length">16</Int>
+    <Real>1.200003</Real>
+    <Real>-1.100000</Real>
+    <Real>3.774874</Real>
+    <Real>18.770712</Real>
+    <Real>0.499999</Real>
+    <Real>15.199999</Real>
+    <Real>16.108685</Real>
+    <Real>-11.573149</Real>
+    <Real>-38.400002</Real>
+    <Real>-14.900000</Real>
+    <Real>-1.174874</Real>
+    <Real>18.629290</Real>
+    <Real>-2.500001</Real>
+    <Real>20.400000</Real>
+    <Real>-7.508683</Real>
+    <Real>4.973149</Real>
+  </Sequence>
+</ReferenceData>

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml b/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml
new file mode 100644 (file)
index 0000000..9e12e17
--- /dev/null
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