Merge branch 'release/3.4'

.travis.yml

@@ -1,8 +1,4 @@
 language: cpp
-
-notifications:
-  email: false
-  slack: ukqcd:mQLXCtz8D2cg89xT8j1a4wku
   
 cache:
   directories:
@@ -12,56 +8,34 @@ cache:
 matrix:
   include:
     - os:        osx
-      osx_image: xcode7.2
+      osx_image: xcode10.1
       compiler: clang
     - os:        osx
-      osx_image: xcode7.2
+      osx_image: xcode10.1
       compiler: gcc
-      env: VERSION=-5
+      env: VERSION=-7
     - compiler: gcc
       addons:
         apt:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-4.9
+            - g++-7
             - libgsl0-dev
             - flex
             - bison
-      env: VERSION=-4.9
+      env: VERSION=-7
-    - compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-5
-            - libgsl0-dev
-            - flex
-            - bison
-      env: VERSION=-5
     - compiler: clang
       addons:
         apt:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-4.8
+            - g++-7
             - libgsl0-dev
             - flex
             - bison
-      env: CLANG_LINK=http://llvm.org/releases/3.6.0/clang+llvm-3.6.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
+      env: CLANG_LINK=http://releases.llvm.org/7.0.1/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-14.04.tar.xz
-    - compiler: clang
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.8
-            - libgsl0-dev
-            - flex
-            - bison
-      env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
 
 before_install:
   - export LATDIR=`pwd`
@@ -72,7 +46,7 @@ before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc@${VERSION#-}; fi
   
 install:
   - export CC=$CC$VERSION
@@ -85,6 +59,7 @@ install:
   - ./install-deps.sh `pwd`/local
   - cd ..
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export LD_LIBRARY_PATH=${LATDIR}/ci-scripts/local/lib:$LD_LIBRARY_PATH; fi
+  - if [[ "$CC" == "gcc-7" ]]; then export CXXFLAGS='-Wno-int-in-bool-context'; fi
 
 script:
   - cd ci-scripts

Makefile.am

@@ -1,3 +1,5 @@
 SUBDIRS = lib utils physics examples
 
+bin_SCRIPTS=latan-config
+
 ACLOCAL_AMFLAGS = -I .buildutils/m4

Readme.md

@@ -55,6 +55,17 @@ in the `ci-scripts` directory where `<prefix>` is where you want LatAnalyze (and
 For a more customised installation, one first needs to generate the build system by running `./bootstrap.sh` in the root directory. Then the library can be built and installed through the usual GNU mantra `./configure <options> && make && make install`. Use `./configure --help` to obtain a list of possible options for `./configure`. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the `CXXFLAGS` variable to `-O3 -march=native -mtune=native`.
 
 ## History
+#### v3.4
+Additions:
+* `latan-config` utility to easily compile LatAnalyze-based programs
+* Linear and constant models to the 2-point fitter
+
+Changes:
+* HDF5 is now a compulsory dependency
+
+Fixes:
+* Variance matrix computation fix.
+
 #### v3.3
 Additions:
 * Sample plot CL utility.
@@ -78,7 +89,7 @@ Fixes:
 * Variance matrix computation fix.
 
 #### v3.2.1
-Fix:
+Fixes:
 * Wrong argument number check in `latan-resample`
 
 #### v3.2 (needs LatCore 1.1)

ci-scripts/install-latan.sh

@@ -14,6 +14,6 @@ cd ..
 mkdir -p build
 cd build
 if [[ "$OS" == "osx" ]]; then EXTRA_FLAGS='--with-gsl=/usr/local'; fi
-../configure --prefix=$PREFIX --with-minuit=$PREFIX --with-nlopt=$PREFIX --with-latcore=$PREFIX --with-hdf5=$PREFIX $EXTRA_FLAGS CXXFLAGS='-O3 -march=native -mtune=native'
+../configure --prefix=$PREFIX --with-minuit=$PREFIX --with-nlopt=$PREFIX --with-latcore=$PREFIX --with-hdf5=$PREFIX $EXTRA_FLAGS CXXFLAGS="${CXXFLAGS} -O3 -march=native -mtune=native"
 make -j4
 make install

configure.ac

@@ -2,7 +2,7 @@
 
 # Initialization
 AC_PREREQ([2.63])
-AC_INIT([LatAnalyze],[3.3],[antonin.portelli@me.com],[LatAnalyze])
+AC_INIT([LatAnalyze],[3.4],[antonin.portelli@me.com],[LatAnalyze])
 AC_CONFIG_AUX_DIR([.buildutils])
 AC_CONFIG_SRCDIR([lib/Global.cpp])
 AC_CONFIG_SRCDIR([utils/sample_read.cpp])
@@ -53,9 +53,6 @@ AC_ARG_WITH([latcore],
     [use this option for a non-standard install prefix of the LatCore library])],
     [AM_CXXFLAGS="$AM_CXXFLAGS -I$with_latcore/include"]
     [AM_LDFLAGS="$AM_LDFLAGS -L$with_latcore/lib"])
-CFLAGS="$AM_CFLAGS $CFLAGS"
-CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 
 # Get compilers informations
 AX_COMPILER_VENDOR
@@ -78,6 +75,10 @@ AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
 			[version of g++ that will compile the code])
 
 # Checks for libraries.
+CXXFLAGS_CPY=$CXXFLAGS
+LDFLAGS_CPY=$LDFLAGS
+CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
+LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 AC_CHECK_LIB([m],[cos],[],[AC_MSG_ERROR([libm library not found])])
 AC_CHECK_LIB([gslcblas],[cblas_dgemm],[],
              [AC_MSG_ERROR([GSL CBLAS library not found])])
@@ -90,12 +91,8 @@ AC_CHECK_LIB([nlopt_cxx],[nlopt_create],
     [LIBS="$LIBS -lnlopt_cxx"],[])
 AM_CONDITIONAL([HAVE_NLOPT], [test x$have_nlopt = xtrue])
 AC_CHECK_LIB([hdf5_cpp],[H5Fopen],
-    [AC_DEFINE([HAVE_HDF5],
+    [LIBS="$LIBS -lhdf5_cpp -lhdf5"],
-    [1],
+    [AC_MSG_ERROR([HDF5 library not found])], [-lhdf5])
-    [Define to 1 if you have the `HDF5' library (-lhdf5_cpp).])]
-    [have_hdf5=true]
-    [LIBS="$LIBS -lhdf5_cpp -lhdf5"],[],[-lhdf5])
-AM_CONDITIONAL([HAVE_HDF5], [test x$have_hdf5 = xtrue])
 SAVED_LDFLAGS=$LDFLAGS
 LDFLAGS="$LDFLAGS -lMinuit2"
 AC_MSG_CHECKING([for ROOT::Minuit2::BasicMinimumError in -lMinuit2]);
@@ -123,24 +120,44 @@ AC_LINK_IFELSE(
     [AC_MSG_RESULT([no])]
     [AC_MSG_ERROR([LatCore library not found])])
 LDFLAGS=$SAVED_LDFLAGS
+CXXFLAGS=$CXXFLAGS_CPY
+LDFLAGS=$LDFLAGS_CPY
 
 # Checks for header files.
 AC_HEADER_STDC
 
+cwd=`pwd -P`; cd ${srcdir}; abs_srcdir=`pwd -P`; cd ${cwd}
+LATAN_CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
+LATAN_LDFLAGS="$AM_LDFLAGS $LDFLAGS"
+LATAN_LIBS=$LIBS
+LATAN_SHORT_SHA=`git rev-parse --short HEAD`
+LATAN_SHA=`git rev-parse HEAD`
+LATAN_BRANCH=`git rev-parse --abbrev-ref HEAD`
+AM_CXXFLAGS="-I${abs_srcdir}/lib $AM_CXXFLAGS"
+AM_CFLAGS="-I${abs_srcdir}/lib $AM_CFLAGS"
+CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
+LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 AC_SUBST([LIBS])
-AC_SUBST([AM_CFLAGS])
+AC_SUBST([AM_CXXFLAGS])
 AC_SUBST([AM_LDFLAGS])
+AC_SUBST([LATAN_CXXFLAGS])
+AC_SUBST([LATAN_LDFLAGS])
+AC_SUBST([LATAN_LIBS])
+AC_SUBST([LATAN_SHA])
+AC_SUBST([LATAN_BRANCH])
 
-AC_CONFIG_FILES([Makefile lib/Makefile utils/Makefile physics/Makefile 
+AC_CONFIG_FILES([latan-config], [chmod +x latan-config])
-                 examples/Makefile])
+AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([lib/Makefile])
+AC_CONFIG_FILES([utils/Makefile])
+AC_CONFIG_FILES([physics/Makefile])
+AC_CONFIG_FILES([examples/Makefile])
 AC_OUTPUT
 
 echo "*********************************************"
 echo "* ${PACKAGE_NAME} v${VERSION}" build options
 echo "*********************************************"
 echo "* C++ compiler     : $CXX"
-echo "* HDF5 support     : `test x$HAVE_HDF5_TRUE = 'x'   && echo yes \
-                                                          || echo no`"
 echo "* Minuit minimizers: `test x$HAVE_MINUIT_TRUE = 'x' && echo yes \
                                                           || echo no`"
 echo "* NLopt minimizers : `test x$HAVE_NLOPT_TRUE = 'x'  && echo yes \

latan-config.in

@@ -0,0 +1,79 @@
+#! /bin/sh
+
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+includedir=@includedir@
+
+usage()
+{
+  cat <<EOF
+Usage: latan-config [OPTION]
+
+Known values for OPTION are:
+
+  --prefix     show LatAnalyze installation prefix
+  --cxxflags   print pre-processor and compiler flags
+  --ldflags    print library linking flags
+  --libs       print library linking information
+  --help       display this help and exit
+  --version    output version information
+  --git        print git revision
+
+EOF
+  
+  exit $1
+}
+
+if test $# -eq 0; then
+  usage 1
+fi
+
+cflags=false
+libs=false
+
+while test $# -gt 0; do
+  case "$1" in
+    -*=*) optarg=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;;
+    *) optarg= ;;
+  esac
+  
+  case "$1" in
+    --prefix)
+      echo $prefix
+    ;;
+    
+    --version)
+      echo @VERSION@
+      exit 0
+    ;;
+    
+    --git)
+      echo "@LATAN_BRANCH@ @LATAN_SHA@"
+      exit 0
+    ;;
+    
+    --help)
+      usage 0
+    ;;
+    
+    --cxxflags)
+      echo @LATAN_CXXFLAGS@
+    ;;
+    
+    --ldflags)
+      echo @LATAN_LDFLAGS@
+    ;;
+    
+    --libs)
+      echo @LIBS@
+    ;;
+    
+    *)
+      usage
+      exit 1
+    ;;
+  esac
+  shift
+done
+
+exit 0

lib/FitInterface.cpp

@@ -200,6 +200,7 @@ double FitInterface::getSvdTolerance(void) const
 void FitInterface::setSvdTolerance(const double &tol)
 {
     svdTol_ = tol;
+    scheduleLayoutInit();
 }
 
 VarName & FitInterface::xName(void)

lib/Io.cpp

@@ -20,9 +20,7 @@
 #include <LatAnalyze/Io.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <LatAnalyze/AsciiFile.hpp>
-#ifdef HAVE_HDF5
 #include <LatAnalyze/Hdf5File.hpp>
-#endif
 
 using namespace std;
 using namespace Latan;
@@ -42,12 +40,10 @@ unique_ptr<File> Io::open(const std::string &fileName, const unsigned int mode)
     {
         return unique_ptr<File>(new AsciiFile(fileName, mode));
     }
-#ifdef HAVE_HDF5
     else if (ext == "h5")
     {
         return unique_ptr<File>(new Hdf5File(fileName, mode));
     }
-#endif
     else
     {
         LATAN_ERROR(Io, "unknown file extension '" + ext + "'");

lib/Makefile.am

@@ -35,6 +35,7 @@ libLatAnalyze_la_SOURCES = \
     GslHybridRootFinder.cpp\
     GslMinimizer.cpp       \
     GslQagsIntegrator.cpp  \
+    Hdf5File.cpp           \
     Histogram.cpp          \
     includes.hpp           \
     Io.cpp                 \
@@ -69,6 +70,7 @@ libLatAnalyze_la_HEADERS = \
     GslHybridRootFinder.hpp\
     GslMinimizer.hpp       \
     GslQagsIntegrator.hpp  \
+    Hdf5File.hpp           \
     Histogram.hpp          \
     Integrator.hpp         \
     Io.hpp                 \
@@ -87,10 +89,6 @@ libLatAnalyze_la_HEADERS = \
     StatArray.hpp          \
     XYSampleData.hpp       \
     XYStatData.hpp
-if HAVE_HDF5
-    libLatAnalyze_la_SOURCES += Hdf5File.cpp
-    libLatAnalyze_la_HEADERS += Hdf5File.hpp
-endif
 if HAVE_MINUIT
     libLatAnalyze_la_SOURCES += MinuitMinimizer.cpp
     libLatAnalyze_la_HEADERS += MinuitMinimizer.hpp

physics/2pt-fit.cpp

@@ -30,7 +30,7 @@ int main(int argc, char *argv[])
     opt.addOption("s", "shift"    , OptParser::OptType::value  , true,
                   "time variable shift", "0");
     opt.addOption("m", "model"    , OptParser::OptType::value  , true,
-                  "fit model (exp|exp2|exp3|cosh|cosh2|cosh3|<interpreter code>)", "cosh");
+                  "fit model (exp|exp2|exp3|cosh|cosh2|cosh3|explin|<interpreter code>)", "cosh");
     opt.addOption("" , "nPar"     , OptParser::OptType::value  , true,
                   "number of model parameters for custom models "
                   "(-1 if irrelevant)", "-1");
@@ -117,7 +117,7 @@ int main(int argc, char *argv[])
     
     // make model //////////////////////////////////////////////////////////////
     DoubleModel mod;
-    bool        coshModel = false;
+    bool        coshModel = false, linearModel = false;
     
     if ((model == "exp") or (model == "exp1"))
     {
@@ -174,6 +174,15 @@ int main(int argc, char *argv[])
                                  + p[5]*(exp(-p[2]*x[0])+exp(-p[4]*(nt-x[0])));
                         }, 1, nPar);
     }
+    else if (model == "explin")
+    {
+        linearModel = true;
+        nPar        = 2;
+        mod.setFunction([](const double *x, const double *p)
+                        {
+                            return p[1] - p[0]*x[0];
+                        }, 1, nPar);
+    }
     else
     {
         if (nPar > 0)
@@ -210,8 +219,16 @@ int main(int argc, char *argv[])
         mod.parName().setName(p, "E_" + strFrom(p/2));
         mod.parName().setName(p + 1, "Z_" + strFrom(p/2));
     }
-    init(0) = log(data.y(nt/4, 0)[central]/data.y(nt/4 + 1, 0)[central]);
+    if (linearModel)
-    init(1) = data.y(nt/4, 0)[central]/(exp(-init(0)*nt/4));
+    {
+        init(0) = data.y(nt/4, 0)[central] - data.y(nt/4 + 1, 0)[central];
+        init(1) = data.y(nt/4, 0)[central] + nt/4*init(0);
+    }
+    else
+    {
+        init(0) = log(data.y(nt/4, 0)[central]/data.y(nt/4 + 1, 0)[central]);
+        init(1) = data.y(nt/4, 0)[central]/(exp(-init(0)*nt/4));
+    }
     for (Index p = 2; p < nPar; p += 2)
     {
         init(p)     = 2*init(p - 2);
@@ -219,11 +236,19 @@ int main(int argc, char *argv[])
     }
     for (Index p = 0; p < nPar; p += 2)
     {
-        globMin.setLowLimit(p, 0.);
+        if (linearModel)
-        globMin.setHighLimit(p, 10.*init(p));
+        {
-        globMin.setLowLimit(p + 1, -10.*init(p + 1));
+            globMin.setLowLimit(p, -10.*fabs(init(p)));
-        globMin.setHighLimit(p + 1, 10.*init(p + 1));
+            globMin.setHighLimit(p, 10.*fabs(init(p)));
-        locMin.setLowLimit(p, 0.);
+        }
+        else
+        {
+            globMin.setLowLimit(p, 0.);
+            locMin.setLowLimit(p, 0.);
+            globMin.setHighLimit(p, 10.*init(p));
+        }
+        globMin.setLowLimit(p + 1, -10.*fabs(init(p + 1)));
+        globMin.setHighLimit(p + 1, 10.*fabs(init(p + 1)));
     }
     globMin.setPrecision(0.001);
     globMin.setMaxIteration(100000);
@@ -264,7 +289,10 @@ int main(int argc, char *argv[])
         double     e0, e0Err;
         
         p << PlotRange(Axis::x, 0, nt - 1);
-        p << LogScale(Axis::y);
+        if (!linearModel)
+        {
+            p << LogScale(Axis::y);
+        }
         p << Color("rgb 'blue'") << PlotPredBand(fit.getModel(_), 0, nt - 1);
         p << Color("rgb 'blue'") << PlotFunction(fit.getModel(), 0, nt - 1);
         p << Color("rgb 'red'") << PlotData(data.getData());
@@ -285,6 +313,16 @@ int main(int argc, char *argv[])
                 }
             }
         }
+        else if (linearModel)
+        {
+            FOR_STAT_ARRAY(effMass, s)
+            {
+                for (Index t = 0; t < nt - 1; ++t)
+                {
+                    effMass[s](t) = corr[s](t) - corr[s](t+1);
+                }
+            }
+        }
         else
         {
             FOR_STAT_ARRAY(effMass, s)
@@ -302,7 +340,6 @@ int main(int argc, char *argv[])
         p << Color("rgb 'blue'") << PlotHLine(e0);
         p << Color("rgb 'red'") << PlotData(effMassT, effMass);
         p.display();
-        p.save("test");
     }
     if (doHeatmap)
     {

utils/resample.cpp

@@ -25,12 +25,7 @@
 #ifndef DEF_NSAMPLE
 #define DEF_NSAMPLE "100"
 #endif
-
-#ifdef HAVE_HDF5
 #define DEF_FMT "h5"
-#else
-#define DEF_FMT "sample"
-#endif
 
 using namespace std;
 using namespace Latan;