updated packages

cfg/packages.yaml

@@ -88,11 +88,15 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  bzip2:
-    externals:
-    - spec: [email protected]
-      prefix: /
+  #bzip2:
+  #  externals:
+  #  - spec: [email protected]
+  #    prefix: /
   tar:
     externals:
     - spec: [email protected]
       prefix: /
+  cpio:
+    externals:
+    - spec: [email protected]
+      prefix: /

packages/compss/package.py

@@ -37,7 +37,7 @@ class Compss(Package):
     version('2.10',       sha256='0795ca7674f1bdd0faeac950fa329377596494f64223650fe65a096807d58a60', preferred=True)
 
     # dependencies. 
-    depends_on('python')
+    depends_on('python@3.6')
     depends_on('openjdk')
     depends_on('boost')
     depends_on('libxml2')

packages/fesom2/package.py

@@ -43,21 +43,33 @@ class Fesom2(CMakePackage):
     depends_on('blas')
 
     variant('hecuba', default=False, description='Builds a MPI version of the library')
-    def setup_build_environment(self, env):
-        env.set('CC', self.spec['mpi'].mpicc)
-        env.set('FC',self.spec['mpi'].mpifc) 
-        env.set('CXX', self.spec['mpi'].mpicxx)
-        env.set('F77', self.spec['mpi'].mpif77)
+
+    #def setup_build_environment(self, env):
+        #env.set('CC', self.spec['mpi'].mpicc)
+        #env.set('FC',self.spec['mpi'].mpifc) 
+        #env.set('CXX', self.spec['mpi'].mpicxx)
+        #env.set('F77', self.spec['mpi'].mpif77)
+        #env.prepend_path('LD_LIBRARY_PATH', str(self.spec['blas'].libs.directories[0]))
+        #env.prepend_path('C_INCLUDE_PATH', str(self.spec['blas'].headers.directories[0]))
+        #env.append_flags('LD_FLAGS',self.spec['blas'].libs.ld_flags)
 
     @run_after('install')
     def copy_fesom(self):
-        #print("***** Calling super install ****") 
+        #pmrint("***** Calling super install ****") 
         #super().install(spec, prefix)
         print("***** Coping fesom binary to bin ****")
         mkdirp(self.prefix.bin)
         install(self.stage.source_path+'/bin/fesom.x', self.prefix.bin)
+    def patch(self):
+        microarch = self.spec.target
+        comp = self.spec.compiler
+        filter_file("-march=native", microarch.optimization_flags(comp.name, str(comp.version)),
+                "Makefile.in_gnu_impi")
+        filter_file("-march=native", microarch.optimization_flags(comp.name, str(comp.version)),
+                "src/CMakeLists.txt")
 
     def cmake_args(self):
+        spec = self.spec
         # FIXME: Add arguments other than
         # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
         # FIXME: If not needed delete this function
@@ -66,4 +78,37 @@ def cmake_args(self):
             args.append('-DUSE_HECUBA=ON')
         else:
             args.append('-DUSE_HECUBA=OFF')
+        args.append(self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc))
+        args.append(self.define('CMAKE_CXX_COMPILER', spec['mpi'].mpicxx))
+        args.append(self.define('CMAKE_Fortran_COMPILER', spec['mpi'].mpifc))
+        if ('^intel-mkl' in spec or '^intel-parallel-studio+mkl' in spec):
+            args.extend([self.define("BLA_VENDOR", "Intel10_64ilp")])
+        elif '^netlib-lapack' in spec:
+            args.extend([self.define("BLA_VENDOR", "Generic")])
+        elif '^openblas' in spec:
+            args.extend([self.define("BLA_VENDOR", "OpenBLAS")])
+        microarch = self.spec.target
+        comp = self.spec.compiler
+        math_libs = self.spec['blas'].libs
+        args.extend([self.define("CMAKE_C_FLAGS",microarch.optimization_flags(comp.name, str(comp.version)) +" "+self.spec['blas'].headers.include_flags)])
+        args.extend([self.define("CMAKE_CXX_FLAGS",microarch.optimization_flags(comp.name, str(comp.version))+ " "+self.spec['blas'].headers.include_flags)])
+        args.extend([self.define("CMAKE_Fortran_FLAGS",microarch.optimization_flags(comp.name, str(comp.version))+" "+self.spec['blas'].headers.include_flags)])
+        #args.append('-DBLA_VENDOR=Intel10_64ilp')
+        #args.append('-DBLA_STATIC=ON')
+        #args.append('-DBLA_VENDOR=OpenBLAS')
+        """
+        blas = self.spec['blas'].libs
+        args.extend([
+          '-DBLAS_LIBRARY_NAMES={0}'.format(';'.join(blas.names)),
+          '-DBLAS_LIBRARY_DIRS={0}'.format(';'.join(blas.directories))])
+        math_libs = self.spec['blas'].libs
+        args.append(
+          '-DMATH_LIBS:STRING={0}'.format(math_libs.ld_flags)
+        )
+        """
+
+        args.append(
+          '-DBLAS_LIBRARIES={0}'.format("-L"+self.spec['blas'].libs.directories[0]+" -Wl,--no-as-needed -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl")
+        )
         return args
+

packages/kratos/fom.json

@@ -0,0 +1,14 @@
+{
+	"execution" : {
+		"type":"task"
+	},
+	"constraints" : {
+		"computing_units": "$KRATOS_CUS"
+	},
+	"parameters" : {
+    		"returns" : 1,
+		"model" : "IN",
+		"parameters" : "IN",
+		"sample" : "IN"
+  	}
+}

packages/kratos/model.json

@@ -0,0 +1,13 @@
+{
+	"execution" : {
+		"type":"task"
+	},
+	"constraints" : {
+		"computing_units": "$KRATOS_CUS"
+	},
+	"parameters" : {
+    		"returns" : 2,
+		"model_file" : "FILE_IN",
+		"parameters" : "IN"
+  	}
+}

packages/kratos/package.py

@@ -40,14 +40,17 @@ class Kratos(CMakePackage):
 
     # FIXME: Add dependencies if required.
     depends_on('boost')
-    depends_on('python@3:')
-
+    depends_on('[email protected]:')
+    depends_on('blas')
+
     #variant
     variant('mpi', default=False, description='Builds a MPI version of the library')
     depends_on('mpi', when='+mpi')
     variant('mmg', default=False, description='Builds a MMG version of the library')
     depends_on('mmg', when='+mmg')
     variant('apps', default='none', multi=True, description='Builds apps version of the library')
+    variant('eigen_mkl', default=False, description='Builds a Eigen_mkl version of the library')
+    depends_on('intel-mkl', when='+eigen_mkl')
 
     def url_for_version(self, version):
         url = "https://github.com/KratosMultiphysics/Kratos/archive/refs/tags/v{0}.tar.gz"
@@ -61,20 +64,25 @@ def setup_build_environment(self, env):
             for app in apps:
                 kratos_apps = kratos_apps + os.path.join(applications_path,  app) + ";"
             env.set('KRATOS_APPLICATIONS', kratos_apps)
+        print("PYTHON_EXECUTABLE:" + str(self.spec['python'].prefix.bin + "/python3"))
+        env.set('PYTHON_EXECUTABLE',self.spec['python'].prefix.bin + "/python3")
 
     def setup_run_environment(self, env):
         env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
         env.prepend_path('PYTHONPATH', self.prefix)
 
+
     def cmake_args(self):
         # Add arguments other than
         # CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
         args = []
         if self.spec.variants['mpi'].value == True:
-            args.append('USE_MPI=ON')
+            args.append('-DUSE_MPI=ON')
         else:
-            args.append('USE_MPI=OFF')
+            args.append('-DUSE_MPI=OFF')
         if self.spec.variants['mmg'].value == True:
-            args.append('USE_MMG=ON')
+            args.append('-DUSE_MMG=ON')
+        if self.spec.variants['eigen_mkl'].value == True:
+            args.append('-DUSE_EIGEN_MKL=ON')
         return args
 

packages/kratos/rom.json

@@ -0,0 +1,15 @@
+{
+	"execution" : {
+		"type":"task"
+	},
+	"constraints" : {
+		"computing_units": "$KRATOS_CUS"
+	},
+	"parameters" : {
+    		"returns" : 1,
+		"model" : "IN",
+		"parameters" : "IN",
+		"sample": "IN",
+		"rom" : "FILE_IN"
+  	}
+}

packages/py-dislib/dislib.json

@@ -0,0 +1,7 @@
+
+{
+	"execution": {
+		"type":"workflow"
+	}
+}
+

packages/py-dislib/package.py

@@ -42,9 +42,9 @@ class PyDislib(PythonPackage):
     # FIXME: Add dependencies if required. Only add the python dependency
     # if you need specific versions. A generic python dependency is
     # added implicity by the PythonPackage class.
-    depends_on('python@3:', type=('build', 'run'))
+    depends_on('python@3.6', type=('build', 'run'))
     #depends_on('py-setuptools', type='build')
-    depends_on('[email protected]^[email protected]^[email protected]', type=('run'))
+    depends_on('[email protected].2^[email protected]^[email protected].5', type=('run'))
     #depends_on('py-scikit-learn', type=('run'))
     #depends_on('py-cvxpy', type=('run'))