Merge pull request #9 from rikigigi/devel

fixed macos compilation, added ci for macos, fixed return value of cl…

.github/workflows/cmake.yml

@@ -16,11 +16,19 @@ jobs:
     # well on Windows or Mac.  You can convert this to a matrix build if you need
     # cross-platform coverage.
     # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
 
+    strategy:
+        matrix:
+            os: [ubuntu-latest, macos-latest ]
+            python-version: [ "3.7" ] 
     steps:
     - uses: actions/checkout@v2
-
+    - name: Setup python
+      uses: actions/setup-python@v2
+      with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
     - name: Configure CMake
       # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
       # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
@@ -32,7 +40,7 @@ jobs:
         cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
         sudo -E ${{github.workspace}}/install/install_python.sh
       env:
-        SP_DIR: /usr/lib/python3/dist-packages
+        SP_DIR: ${{github.workspace}}/tests
         SOURCE_DIR: ${{github.workspace}}
         BUILD_DIR: ${{github.workspace}}/build
 
@@ -43,10 +51,11 @@ jobs:
       run: |
         ctest -C ${{env.BUILD_TYPE}}
         ../install/install_test.sh
-        cd ../tests/ && pytest -sv .
+        cd ../tests/ && python -m pytest -sv .
     - name: TestCli
       run: |
         ${{github.workspace}}/tests/test_cli.sh
       env:
         SOURCE_DIR: ${{github.workspace}}
         BUILD_DIR: ${{github.workspace}}/build
+        PYTHONPATH: /usr/lib/python${{ matrix.python-version }}/dist-packages

analisi/main.cpp

@@ -239,6 +239,8 @@ int main(int argc, char ** argv)
 
         if (argc<=1 || ( (output_conversion!="" || output_conversion_gro.size()>0 ) && input=="") ||vm.count("help")|| (vm.count("loginput")==0 && ( debug2 || heat_coeff ) ) || skip<=0 || stop_acf<0 || final<0 || (!sub_mean && (sub_mean_start!=0) ) || sub_mean_start<0 || !(kk_l.size()==0 || kk_l.size()==2)){
             std::cout << options << "\n";
+            if (vm.count("help"))
+                return 0;
             return 1;
         }
 

lib/include/calcolamultithread.h

@@ -28,16 +28,16 @@ template <class T, int FLAGS_T = CalcolaMultiThread_Flags::PARALLEL_SPLIT_AVERAG
 class CalcolaMultiThread
 {
 public:
-    CalcolaMultiThread(unsigned int nthreads=0, unsigned int skip=0, int natoms=0) : nthreads{nthreads},skip{skip},ntimesteps{0},natoms{natoms}
+    CalcolaMultiThread(ssize_t nthreads=0, ssize_t skip=0, size_t natoms=0) : nthreads{nthreads},skip{skip},ntimesteps{0},natoms{natoms}
 {
     if (nthreads==0) nthreads=1;
     if (skip==0) skip=1;
 
 }
     static constexpr int FLAGS=FLAGS_T;
 
-    std::pair<int,int> splitter(int ith, int nthreads, int primo) const {
-        std::pair<int,int> res;
+    std::pair<size_t,size_t> splitter(size_t ith, size_t primo) const {
+        std::pair<size_t,size_t> res;
         res.first=ith*npassith;
         if (ith==nthreads-1) {
             res.second=end;
@@ -73,7 +73,7 @@ class CalcolaMultiThread
         }
     }
 
-    void calcola(unsigned int primo){
+    void calcola(size_t primo){
         init_split();
         if constexpr (!!(FLAGS & CalcolaMultiThread_Flags::CALL_CALC_INIT)) {
             static_cast<T*>(this)->calc_init(primo);
@@ -83,7 +83,7 @@ class CalcolaMultiThread
             for (ssize_t i=i0;i<i1;i+=skip){ //loop over trajectory. Can be a loop over a single value if disabled
                 for (unsigned int ith=0;ith<nthreads;++ith){
                     threads.push_back(std::thread([&,ith,t,i](){
-                        auto range=splitter(ith,nthreads,primo);
+                        auto range=splitter(ith,primo);
                         // calculate given start and stop timestep. note that & captures everything, user must take care of multithread safety of calc_single_th function
                         // select a different signature of the calculation function depending on where the loops (if present) are parallelized
                         if constexpr (FLAGS & CalcolaMultiThread_Flags::PARALLEL_LOOP_AVERAGE && (FLAGS & CalcolaMultiThread_Flags::PARALLEL_LOOP_TIME)) {
@@ -144,8 +144,7 @@ class CalcolaMultiThread
     ssize_t nthreads,skip,ntimesteps, leff;
 
 private:
-    size_t npassith,end;
-    ssize_t natoms;
+    size_t npassith,end, natoms;
     ssize_t t0,t1,i0,i1;
 };
 

tests/src/test_sh.cpp

@@ -15,7 +15,8 @@ struct ShFixture{
     ~ShFixture(){}
     TrajSetup traj;
     unsigned int nbin;
-    int natoms,ntypes;
+    size_t natoms;
+    int ntypes;
     SphericalCorrelations<l,double,Traiettoria> sh;
     DataRegression<double> data;
     double  workspace[(l+1)*(l+1)], cheby[(l+1)*2];

tests/test_cli.sh

@@ -31,6 +31,7 @@ TESTS=( "MSD_normal_full"   "-i $INPUT -Q"
 N_arr=${#TESTS[@]}
 N=$(( N_arr - 1 ))
 RETURN=0
+FLIST=""
 for i in $(seq 0 2 $N )
 do
     ip=$(( i + 1 ))
@@ -41,12 +42,16 @@ do
     if [ -f "$FTEST" ]
     then
         OUTPUT_F="`cat $FTEST`"
-
-        if [ -z "`diff <(echo "$OUTPUT") <(echo "$OUTPUT_F")`" ]
+        #the sign of nan is not defined by the standard
+        DIFF="`diff <(echo "$OUTPUT" | sed 's/-nan/nan/g') <(echo "$OUTPUT_F" | sed 's/-nan/nan/g') || true `" 
+        if [ -z "$DIFF" ]
         then
             echo SUCCESS $NAME
         else
             echo FAILED $NAME
+            echo "$DIFF"
+            FLIST="$FLIST
+FAILED $NAME"
             RETURN=$(( RETURN + 1 ))
         fi
     else
@@ -55,4 +60,5 @@ do
     fi
 
 done
+echo "$FLIST"
 exit $RETURN