Remove local complexify and use shared library and scripts (#302)

* Updating base makefile to clean complex build properly

* remove local complexify module and script

* update default config

* updating complex makefiles

* update doc and setup

* typo

* update docs

Makefile_CS

@@ -1,4 +1,4 @@
-# Master makefilefor complex ADflow. The actual makefile you want is 
+# Master makefile for complex ADflow. The actual makefile you want is
 # src/build/Makefile_CS
 default:
 # Check if the config.mk file is in the config dir.
@@ -17,29 +17,17 @@ default:
 
 
 clean:
-	rm -fr src_cs/build/*.mod
-	rm -fr src_cs/build/*.o
-	rm -fr src_cs/build/*.a
-	rm -fr src_cs/build/*.so
-	rm -fr src_cs/build/adflow_project.dep
-	rm -f *~ config.mk;
-# Completely nuke most of the directories
-	rm -fr src_cs/adjoint
-	rm -fr src_cs/ADT
-	rm -fr src_cs/bcdata
-	rm -fr src_cs/initFlow
-	rm -fr src_cs/inputParam
-	rm -fr src_cs/NKSolver
-	rm -fr src_cs/metis-4.0
-	rm -fr src_cs/output
-	rm -fr src_cs/overset
-	rm -fr src_cs/partitioning
-	rm -fr src_cs/slidingComm
-	rm -fr src_cs/solver
-	rm -fr src_cs/turbulence
-	rm -fr src_cs/utils
-	rm -fr src_cs/wallDistance
-	rm -fr src_cs/warping
+# The command will search "src_cs" finds and deletes anything (files and directories)
+# except what is listed here below. Note in order not to delete the parent directory
+# holding a file it needs to specified. Finally ! means "not".
+	find src_cs ! \( \
+	-wholename 'src_cs' \
+	-o -wholename 'src_cs/build' \
+	-o -wholename 'src_cs/build/Makefile' \
+	-o -wholename 'src_cs/build/Makefile1' \
+	-o -wholename 'src_cs/modules' \
+	-o -wholename 'src_cs/modules/precision.F90' \) \
+	-exec rm -rf {} +
 
 adflow_build:
 	ln -sf config/config.mk config.mk;

config/defaults/config.LINUX_GFORTRAN.mk

@@ -26,6 +26,10 @@ CC_REAL_PRECISION_FLAG      =
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
+# ------- Define complexify inlcude and linker flags -------------------------
+COMPLEXIFY_INCLUDE_FLAGS=-I$(COMPLEXIFY_DIR)/include
+COMPLEXIFY_LINKER_FLAGS=-L$(COMPLEXIFY_DIR)/lib -lcomplexify
+
 # ------- Define Compiler Flags ----------------------------------------
 FF77_FLAGS = -fPIC -fdefault-real-8 -fdefault-double-8 -march=native
 FF90_FLAGS = $(FF77_FLAGS) -std=f2008

config/defaults/config.LINUX_INTEL.mk

@@ -26,6 +26,10 @@ CC_REAL_PRECISION_FLAG      =
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
+# ------- Define complexify inlcude and linker flags -------------------------
+COMPLEXIFY_INCLUDE_FLAGS=-I$(COMPLEXIFY_DIR)/include
+COMPLEXIFY_LINKER_FLAGS=-L$(COMPLEXIFY_DIR)/lib -lcomplexify
+
 # ------- Define Compiler Flags ----------------------------------------
 FF77_FLAGS   = -fPIC -r8
 FF90_FLAGS = $(FF77_FLAGS) -std08

config/defaults/config.LINUX_INTEL_AVX2.mk

@@ -26,6 +26,10 @@ CC_REAL_PRECISION_FLAG      =
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
+# ------- Define complexify inlcude and linker flags -------------------------
+COMPLEXIFY_INCLUDE_FLAGS=-I$(COMPLEXIFY_DIR)/include
+COMPLEXIFY_LINKER_FLAGS=-L$(COMPLEXIFY_DIR)/lib -lcomplexify
+
 # ------- Define Compiler Flags ----------------------------------------
 FF77_FLAGS   = -fPIC -r8
 FF90_FLAGS = $(FF77_FLAGS) -std08

config/defaults/config.LINUX_INTEL_SAFE.mk

@@ -30,6 +30,10 @@ CC_REAL_PRECISION_FLAG      =
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
+# ------- Define complexify inlcude and linker flags -------------------------
+COMPLEXIFY_INCLUDE_FLAGS=-I$(COMPLEXIFY_DIR)/include
+COMPLEXIFY_LINKER_FLAGS=-L$(COMPLEXIFY_DIR)/lib -lcomplexify
+
 # ------- Define Compiler Flags ----------------------------------------
 FF77_FLAGS = -fPIC -r8
 FF90_FLAGS = $(FF77_FLAGS) -std08

config/defaults/config.OSX_GFORTRAN.mk

@@ -29,6 +29,10 @@ CC_REAL_PRECISION_FLAG      =
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
+# ------- Define complexify inlcude and linker flags -------------------------
+COMPLEXIFY_INCLUDE_FLAGS=-I$(COMPLEXIFY_DIR)/include
+COMPLEXIFY_LINKER_FLAGS=-L$(COMPLEXIFY_DIR)/lib -lcomplexify
+
 # ------- Define Compiler Flags ----------------------------------------
 FF77_FLAGS = -fPIC -fdefault-real-8 -fdefault-double-8 -march=native
 FF90_FLAGS = $(FF77_FLAGS) -std=f2008

doc/install.rst

@@ -8,9 +8,11 @@ It is therefore necessary to build this library before using ADflow.
 Requirements
 ------------
 ADflow requires the following dependencies:
+
 - CGNS Library
 - PETSc
 - MPI
+- Complexify (see the `Complex build`_ section)
 
 See the MDO Lab installation guide `here <https://mdolab-mach-aero.readthedocs-hosted.com/en/latest/installInstructions/install3rdPartyPackages.html>`_ for the supported versions and installation instructions.
 
@@ -21,14 +23,14 @@ To start, find a configuration file close to your current setup in::
 
     config/defaults
 
-and copy it to ''config/config.mk''. For example:
+and copy it to ``config/config.mk``. For example:
 
 .. prompt:: bash
 
     cp config/defaults/config.LINUX_GFORTRAN.mk config/config.mk
 
-If you are a beginner user installing the packages on a linux desktop, 
-you should use the ``config.LINUX_GFORTRAN`` versions of the configuration 
+If you are a beginner user installing the packages on a linux desktop,
+you should use the ``config.LINUX_GFORTRAN`` versions of the configuration
 files. The ``config.LINUX_INTEL`` versions are usually used on clusters.
 ADflow has been successfully compiled on LINUX with either
 ``ifort`` or ``gfortran``.
@@ -47,19 +49,18 @@ the screen (near the end)::
 
 If you don't see this, it will be necessary to configure the build manually.
 To configure manually, open ``config/config.mk`` and modify options as necessary.
-
-It is most likely that you need to modify the ``CGNS_INCLUDE_FLAGS`` and the ``CGNS_LINKER_FLAGS`` variables.
+Common issues are often that dependency variable paths, such as ``CGNS_INCLUDE_FLAGS`` and ``CGNS_LINKER_FLAGS``, point to an incorrect location and need to be updated.
 After changes to the configuration file, run ``make clean`` before attempting a new build.
 
 .. NOTE::
 
     Compiling ADflow on HPC clusters requires additional care, as some systems do not have a homogeneous CPU architecture across all nodes.
-    For example, the architecture of the login nodes may differ from the architecture of compute nodes available on the same cluster. 
+    For example, the architecture of the login nodes may differ from the architecture of compute nodes available on the same cluster.
 
     Compiling the code on/for a specific login node type may result in unexpected crashes if the compute nodes have an incompatible (newer) architecture.
-    You can append the ``-march=<HPC-ARCH>`` flag to the ``config.mk`` file to specify the architecture of the compute node and avoid such issues. 
-    To optimize the compiled code for a specific architecture, one can add the ``-mtune=<HPC-ARCH>`` flag. However, this is rarely needed. 
-    An example of the updated flags in the config file is:: 
+    You can append the ``-march=<HPC-ARCH>`` flag to the ``config.mk`` file to specify the architecture of the compute node and avoid such issues.
+    To optimize the compiled code for a specific architecture, one can add the ``-mtune=<HPC-ARCH>`` flag. However, this is rarely needed.
+    An example of the updated flags in the config file is::
 
         FF90_FLAGS = <normal-flags> -march=<HPC-ARCH> -mtune=<HPC-ARCH>
 
@@ -69,7 +70,7 @@ After changes to the configuration file, run ``make clean`` before attempting a
 
         FF90_FLAGS = <normal-flags> -march=sandybridge
 
-    We recommend to contact your local HPC team to get more information about hardware specific issues. 
+    We recommend to contact your local HPC team to get more information about hardware specific issues.
 
 Lastly, to build and install the Python interface, type:
 
@@ -105,30 +106,32 @@ Then in the root directory run:
 
 Complex Build
 -------------
-ADflow contains scripts to automatically build a "complexified"
-version of ADflow directly from the real version.
-
-ADflow_CS REQUIRES a complex build of petsc to build and run. The
-petsc configuration script must be re-run with the following
-options:
+Its possible to build a "complexified" version of ADflow directly from the real version.
+To do so, ADflow relies on the `Complexify <https://github.com/mdolab/complexify>`__ module and library, which needs to be compiled and installed first.
+Furthermore, complex ADflow **requires** a complex build of PETSc to build and run.
+The PETSc configuration script must be re-run with the following options:
 
 .. prompt:: bash
 
     ./configure --with-shared-libraries --download-superlu_dist=yes --download-parmetis=yes --download-metis=yes --with-fortran-interfaces=1 --with-debugging=yes --with-scalar-type=complex --PETSC_ARCH=complex-debug
 
 Follow instructions as before to complete complex build.
-
 Now, to build complex ADflow do:
 
 .. prompt:: bash
 
-    export PETSC_ARCH=complex-debug
+    export PETSC_ARCH=$PETSC_ARCH_COMPLEX
     make -f Makefile_CS
 
-Note that the correct, complex PETSC_ARCH MUST be set before the code is
-compiled and also must be set when running in complex mode.
+Note that, ``PETSC_ARCH``, **must** be set and point to the complex PETSc before the code is compiled, and must also be set when running in complex mode.
+In the above example, an intermediate convenience variable, ``PETSC_ARCH_COMPLEX``, defines the complex PETSc arch path.
+Once the library is built run the following to install the python module and library into your environment.
+
+.. prompt:: bash
+
+   pip install .[complex]
 
-To run the complex tests, first set the ``$PETSC_ARCH`` to the complex architecture.
+To run the complex tests, first set the ``PETSC_ARCH`` to the complex architecture.
 Then run:
 
 .. prompt:: bash

setup.py

@@ -37,6 +37,7 @@
         "docs": docs_require,
         "testing": ["parameterized", "testflo", "idwarp", "pygeo", "pyspline"],
         "mphys": ["openmdao", "mphys", "idwarp"],
+        "complex": ["complexify"],
     },
     classifiers=["Operating System :: Linux", "Programming Language :: Python, Fortran"],
 )

src_cs/build/Makefile

@@ -5,15 +5,16 @@ include ../../config/config.mk
 EXTRA_FF90_FLAGS = $(shell bash ../../config/compilerCheck.sh $(FF90))
 
 # Group all the fortran, C and compiler flags together.
-FF90_ALL_FLAGS_NO_OPT = $(FF90_FLAGS) $(EXTRA_FF90_FLAGS) $(CGNS_INCLUDE_FLAGS) -I. -DUSE_COMPLEX \
+FF90_ALL_FLAGS_NO_OPT = $(FF90_FLAGS) $(EXTRA_FF90_FLAGS) $(CGNS_INCLUDE_FLAGS) \
+		   -I. -DUSE_COMPLEX $(COMPLEXIFY_INCLUDE_FLAGS) \
 		   $(PETSC_CC_INCLUDES) $(FF90_PRECISION_FLAGS)
 
 FF90_ALL_FLAGS = $(FF90_ALL_FLAGS_NO_OPT) $(FFXX_OPT_FLAGS)
 
 CC_ALL_FLAGS     = $(C_FLAGS) -I../c_defines  -I../metis-4.0  $(PETSC_CC_INCLUDES) \
 		   $(CC_PRECISION_FLAGS)
 
-LINKER_ALL_FLAGS = $(CGNS_LINKER_FLAGS) $(PETSC_LIB) $(LINKER_FLAGS)
+LINKER_ALL_FLAGS = $(CGNS_LINKER_FLAGS) $(COMPLEXIFY_LINKER_FLAGS) $(PETSC_LIB) $(LINKER_FLAGS)
 
 # Include the full filelist
 include ../../src/build/fileList
@@ -40,9 +41,6 @@ include ../../src/build/rules
 dirs:=$(addprefix ../,$(dirs))
 VPATH:=$(dirs)
 
-# Add the special extra complexify module to the list of files:
-fortranFiles:=$(fortranFiles) modules/complexify.f90
-
 # Need to add the ../ to each of the file lists:
 fortranFilesNoOpt:=$(addprefix ../,$(fortranFilesNoOpt))
 fortranFiles:=$(addprefix ../,$(fortranFiles))

src_cs/build/Makefile1

@@ -27,11 +27,10 @@ complexify:
 	@for file in $(filesToComplexify); do \
 		realFile=$(addprefix ../../src/,$$file); \
 		cmplxFile=$(addprefix ../,$$file); \
-		echo Checking $$file $$realFile $$cmplxFile; \
+		echo Checking $$realFile $$cmplxFile; \
 		if [ $$realFile -nt $$cmplxFile -o ! -e $$cmplxFile ];  then \
-			python complexify.py $$realFile; \
-			echo Complexifying $$file $$realFile $$cmplxFile; \
-			mv newFile $$cmplxFile; \
+			echo Complexifying $$realFile $$cmplxFile; \
+			complexify $$realFile --outFileName $$cmplxFile; \
 		fi;\
 	done