using intel static MKL library for conda packages by default as it se…

…ems to be cross-platform

conda.recipe/build.sh

@@ -1,6 +1,11 @@
 #!/usr/bin/env bash
 set -ex
 
+sed -i "s^use_MKL=^use_MKL=True^g" setup.cfg
+sed -i "s^MKLROOT=^MKLROOT=${CONDA_PREFIX}/lib^g" setup.cfg
+
+
 # Install the Python package, but without dependencies,
 # because Conda takes care of that
-$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
+$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
+sed -i "s^MKLROOT=${CONDA_PREFIX}/lib^MKLROOT=^g" setup.cfg

conda.recipe/conda_build_config.yaml

@@ -3,3 +3,7 @@ python:
     - 3.9
     - 3.10
     - 3.11
+
+mpi:
+    - mpich    # [not win]
+    - msmpi    # [win]

conda.recipe/meta.yaml

@@ -18,13 +18,14 @@ requirements:
     - pip
     - setuptools
     - numpy
-    - blas-devel
-    - liblapack
     - mpi4py
+    - {{ mpi }}
+    - mkl-static
   build:
     - make                       # [not win]
     - {{ compiler('c') }}
     - {{ compiler('fortran') }}  # [not win]
+    - cmake
   run:
     - python
     - {{ pin_compatible('numpy') }}
@@ -36,5 +37,5 @@ about:
   description: |
     pyPDAF is a python interface to the Fortran-based PDAF library
   license: GPL
-  doc_url: https://github.com/BoldingBruggeman/eat/wiki
-  dev_url: https://github.com/BoldingBruggeman/eat
+  doc_url: https://yumengch.github.io/pyPDAF/index.html
+  dev_url: https://github.com/yumengch/pyPDAF

setup.cfg

@@ -24,5 +24,14 @@ CPP_DEFS = -DUSE_PDAF
 [pyPDAF]
 pwd = /home/runner/work/pyPDAF/pyPDAF/
 CC = mpicc
+# if MKL is used, give the path to the static MKL library
+use_MKL=
+MKLROOT=
+# if dynamic/shared liblapack and libblas library is used,
+# give the library path and flags
 LAPACK_PATH=
-LAPACK_Flag=lapack,blas
+LAPACK_Flag=
+# GIVE MPI information
+MPI_INC_PATH=
+MPI_MOD_PATH=
+MPI_LIB_PATH=

setup.py

@@ -45,6 +45,7 @@
 if not os.path.isabs(PDAFdir):
     PDAFdir = os.path.join(pwd, PDAFdir)
     print ('input PDAF directory is not absolute path, changing to: ', PDAFdir)
+
 # set up C compiler for cython and Python
 if os.name == 'nt':
     compiler = 'msvc'
@@ -67,78 +68,80 @@
     else:
         print ('....using GNU compiler....')
 
-# compiler options for cython
 extra_compile_args=[]
+extra_link_args = []
+extra_objects = []
+library_dirs=[]
+libraries = []
+
+# compiler options for cython
 if compiler == 'gnu':
     extra_compile_args+=['-Wno-unreachable-code-fallthrough']
+
 # linking static PDAF library and interface objects
-extra_objects = []
-if sys.platform == 'darwin':
-    extra_objects+=['-Wl,-force_load', f'{PDAFdir}/lib/libpdaf-var.a',
-                   '-Wl,-force_load', f'{pwd}/lib/libPDAFc.a',]
-elif os.name != 'nt':
-    extra_objects+=['-Wl,--whole-archive', f'{PDAFdir}/lib/libpdaf-var.a',
-                   f'{pwd}/lib/libPDAFc.a', '-Wl,--no-whole-archive']
+if os.name == 'nt':
+    library_dirs+=[os.path.join(PDAFdir, 'lib', 'Release'),
+                   os.path.join(pwd, 'pyPDAF', 'fortran', 'build', 'Release'),
+                   ]
+    libraries += ['pdaf-var', 'pdafc']
+else:
+    if sys.platform == 'darwin':
+        extra_objects+=['-Wl,-force_load', f'{PDAFdir}/lib/libpdaf-var.a',
+                       '-Wl,-force_load', f'{pwd}/lib/libPDAFc.a',]
+    else:
+        extra_objects+=['-Wl,--whole-archive', f'{PDAFdir}/lib/libpdaf-var.a',
+                       f'{pwd}/lib/libPDAFc.a', '-Wl,--no-whole-archive']
 
-if compiler == 'intel':
+# linking BLAS/LAPACK
+use_MKL=dist.get_option_dict('pyPDAF')['use_MKL'][1]
+if use_MKL == 'True':
     MKLROOT=dist.get_option_dict('pyPDAF')['MKLROOT'][1]
-    extra_objects+=['-Wl,--start-group', 
-                    f'{MKLROOT}/lib/intel64/libmkl_intel_lp64.a',
-                    f'{MKLROOT}/lib/intel64/libmkl_sequential.a',
-                    f'{MKLROOT}/lib/intel64/libmkl_core.a',
-                    '-Wl,--end-group']
+    if os.name == 'nt':
+        extra_objects+=['-Wl,--start-group', 
+                        f'{MKLROOT}/libmkl_intel_lp64.a',
+                        f'{MKLROOT}/libmkl_sequential.a',
+                        f'{MKLROOT}/libmkl_core.a',
+                        '-Wl,--end-group']
+    else:
+        library_dirs+=[MKLROOT,]
+        libraries = ['mkl_core', 'mkl_sequential', 'mkl_intel_lp64']
+else:
+    # setup library to MPI-fortran 
+    LAPACK_PATH=dist.get_option_dict('pyPDAF')['LAPACK_PATH'][1]
+    if LAPACK_PATH != '': library_dirs += LAPACK_PATH.split(',')
+    LAPACK_Flag=dist.get_option_dict('pyPDAF')['LAPACK_Flag'][1]
+    print ('LAPACK_Flag', LAPACK_Flag)
+    if LAPACK_Flag != '': libraries += LAPACK_Flag.split(',')
 
-# PDAF library contains multiple same .o files
-# multiple-definition is thus necessary 
-extra_link_args = []
-# setup library to MPI-fortran 
-LAPACK_PATH=dist.get_option_dict('pyPDAF')['LAPACK_PATH'][1]
-print ('LAPACK_PATH', LAPACK_PATH)
-library_dirs=[]
-if LAPACK_PATH != '': library_dirs += LAPACK_PATH.split(',')
 # add mpi library path
-if os.name != 'nt':
-    if compiler == 'intel':
-        result = subprocess.run(['mpiifort', '-show'], stdout=subprocess.PIPE)
-    else:
-        result = subprocess.run(['mpifort', '-show'], stdout=subprocess.PIPE)
+if os.name == 'nt':
+    MPI_LIB_PATH=dist.get_option_dict('pyPDAF')['MPI_LIB_PATH'][1]
+    library_dirs+=[MPI_LIB_PATH,]
+    libraries += ['msmpi', 'msmpifec']
+else:
+    mpifortran = 'mpiifort' if compiler == 'intel' else 'mpifort'
+    result = subprocess.run([mpifortran, '-show'], stdout=subprocess.PIPE)
     result = result.stdout.decode()[:-1].split(' ')
     s = [l[2:].replace('"', '') for l in result if l[:2] == '-L']
     if len(s) > 0: library_dirs += s
-    # add gfortran library path
-    if sys.platform == 'darwin':
-        result = subprocess.run(['gfortran', '--print-file', 'libgfortran.dylib'], stdout=subprocess.PIPE)
-        result = result.stdout.decode()[:-18]
-    else:
-        result = subprocess.run(['gfortran', '--print-file', 'libgfortran.so'], stdout=subprocess.PIPE)
-        result = result.stdout.decode()[:-15]
-    library_dirs+=[result,]
-    library_dirs+=['/usr/lib', ]
-else:
-    library_dirs+=[os.path.join(PDAFdir, 'lib', 'Release'),
-                   os.path.join(pwd, 'pyPDAF', 'fortran', 'build', 'Release'),
-                   ]
-print ('library_dirs', library_dirs)
+    s = [l[2:] for l in result if l[:2] == '-l']
+    if len(s) > 0: libraries += s
 
+# add fortran library to the linking
 if os.name != 'nt':
-    if compiler == 'intel':
-        # somehow gfortran is always necessary
-        libraries = ['ifcore', 'ifcoremt', 'gfortran', 'm']
-    else:
-        libraries=['gfortran', 'm']
+    suffix = 'dylib' if sys.platform == 'darwin' else 'so'
+    result = subprocess.run(['gfortran', '--print-file', 'libgfortran.'+suffix], stdout=subprocess.PIPE)
+    result = result.stdout.decode()[:-18] if sys.platform == 'darwin' else result.stdout.decode()[:-15]
+    library_dirs+=[result,]
+    library_dirs+=['/usr/lib', ]
+    # somehow gfortran is always necessary
+    libraries += ['gfortran', 'm']
+    if compiler == 'intel': libraries += ['ifcore', 'ifcoremt']
 
-    if compiler == 'intel':
-        result = subprocess.run(['mpiifort', '-show'], stdout=subprocess.PIPE)
-    else:
-        result = subprocess.run(['mpifort', '-show'], stdout=subprocess.PIPE)
-    result = result.stdout.decode()[:-1].split(' ')
-    s = [l[2:] for l in result if l[:2] == '-l']
-    if len(s) > 0: libraries += s
-else:
-    libraries = ['msmpi', 'msmpifec', 'pdaf-var', 'pdafc', 'mkl_core', 'mkl_sequential', 'mkl_intel_lp64']
-LAPACK_Flag=dist.get_option_dict('pyPDAF')['LAPACK_Flag'][1]
-print ('LAPACK_Flag', LAPACK_Flag)
-if LAPACK_Flag != '': libraries += LAPACK_Flag.split(',')
+print ('extra_compile_args', extra_compile_args)
+print ('extra_link_args', extra_link_args)
+print ('extra_objects', extra_objects)
+print ('library_dirs', library_dirs)
 print ('libraries', libraries)
 
 def compilePDAFLibraryInterface():

setup_mac.cfg

@@ -35,5 +35,14 @@ CPP_DEFS = -DUSE_PDAF
 [pyPDAF]
 pwd = /Users/runner/work/pyPDAF/pyPDAF/
 CC = mpicc
+# if MKL is used, give the path to the static MKL library
+use_MKL=
+MKLROOT=
+# if dynamic/shared liblapack and libblas library is used,
+# give the library path and flags
 LAPACK_PATH=
-LAPACK_Flag=lapack,blas
+LAPACK_Flag=
+# GIVE MPI information
+MPI_INC_PATH=
+MPI_MOD_PATH=
+MPI_LIB_PATH=