From 7cba3d1a7f6c41806f62216ae3b2977f2e542dd3 Mon Sep 17 00:00:00 2001
From: Michael Bynum <michaelbynum@users.noreply.github.com>
Date: Tue, 5 May 2020 13:47:44 -0600
Subject: [PATCH 1/5] working on cmake for pynumero hsl

---
 pyomo/contrib/pynumero/src/CMakeLists.txt     | 29 ++--------
 .../pynumero/src/hsl_interface/CMakeLists.txt | 23 ++++++++
 .../pynumero/src/hsl_interface/Makefile       | 54 -------------------
 .../pynumero/src/hsl_interface/Makefile.in    | 32 -----------
 4 files changed, 27 insertions(+), 111 deletions(-)
 create mode 100644 pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
 delete mode 100644 pyomo/contrib/pynumero/src/hsl_interface/Makefile
 delete mode 100644 pyomo/contrib/pynumero/src/hsl_interface/Makefile.in

diff --git a/pyomo/contrib/pynumero/src/CMakeLists.txt b/pyomo/contrib/pynumero/src/CMakeLists.txt
index 22c65b86e54..dacaae8fafe 100644
--- a/pyomo/contrib/pynumero/src/CMakeLists.txt
+++ b/pyomo/contrib/pynumero/src/CMakeLists.txt
@@ -139,31 +139,10 @@ IF( BUILD_ASL )
   ENDIF()
 ENDIF()
 
-set(PYNUMERO_MA27_SOURCES
-  "ma27Interface.cpp"
-  "ma27Interface.hpp"
-)
-
-IF( BUILD_MA27 )
-  ADD_LIBRARY( pynumero_MA27 SHARED ${PYNUMERO_MA27_SOURCES} )
-  TARGET_LINK_LIBRARIES( pynumero_MA27 ${HSL_LIBRARY} )
-  SET_TARGET_PROPERTIES( pynumero_MA27 PROPERTIES ENABLE_EXPORTS 1 )
-  INSTALL(TARGETS pynumero_MA27 LIBRARY DESTINATION lib
-    RUNTIME DESTINATION lib )
-ENDIF()
-
-set(PYNUMERO_MA57_SOURCES
-  "ma57Interface.cpp"
-  "ma57Interface.hpp"
-)
-
-IF( BUILD_MA57 )
-  ADD_LIBRARY( pynumero_MA57 SHARED ${PYNUMERO_MA57_SOURCES} )
-  TARGET_LINK_LIBRARIES( pynumero_MA57 ${HSL_LIBRARY} )
-  SET_TARGET_PROPERTIES( pynumero_MA57 PROPERTIES ENABLE_EXPORTS 1 )
-  INSTALL(TARGETS pynumero_MA57 LIBRARY DESTINATION lib
-    RUNTIME DESTINATION lib )
-ENDIF()
+#
+# build hsl interfaces
+#
+add_subdirectory(hsl_interface)
 
 #
 # build the tests for the interfaces
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt b/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
new file mode 100644
index 00000000000..c4998655ebd
--- /dev/null
+++ b/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
@@ -0,0 +1,23 @@
+set(PYNUMERO_MA27_SOURCES
+  "ma27Interface.c"
+)
+
+IF( BUILD_MA27 )
+  ADD_LIBRARY( pynumero_MA27 SHARED ${PYNUMERO_MA27_SOURCES} )
+  TARGET_LINK_LIBRARIES( pynumero_MA27 ${HSL_LIBRARY} )
+  SET_TARGET_PROPERTIES( pynumero_MA27 PROPERTIES ENABLE_EXPORTS 1 )
+  INSTALL(TARGETS pynumero_MA27 LIBRARY DESTINATION lib
+    RUNTIME DESTINATION lib )
+ENDIF()
+
+set(PYNUMERO_MA57_SOURCES
+  "ma57Interface.c"
+)
+
+IF( BUILD_MA57 )
+  ADD_LIBRARY( pynumero_MA57 SHARED ${PYNUMERO_MA57_SOURCES} )
+  TARGET_LINK_LIBRARIES( pynumero_MA57 ${HSL_LIBRARY} )
+  SET_TARGET_PROPERTIES( pynumero_MA57 PROPERTIES ENABLE_EXPORTS 1 )
+  INSTALL(TARGETS pynumero_MA57 LIBRARY DESTINATION lib
+    RUNTIME DESTINATION lib )
+ENDIF()
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/Makefile b/pyomo/contrib/pynumero/src/hsl_interface/Makefile
deleted file mode 100644
index 85911018ca8..00000000000
--- a/pyomo/contrib/pynumero/src/hsl_interface/Makefile
+++ /dev/null
@@ -1,54 +0,0 @@
-rootdir:=$(shell dirname $(realpath $(firstword $(MAKEFILE_LIST))))
-
-include $(rootdir)/Makefile.in
-
-all: libpynumero_MA27.so libpynumero_MA57.so
-
-
-ifeq ($(strip $(COINHSLDIR)),)
-
-# If libcoinhsl is not available, link with the ma27d.o object one gets from
-# compiling ma27, e.g. gfortran -O2 -fPIC -c -o ma27d.o ma27d.f
-libpynumero_MA27.so: ma27Interface.o $(MA27DIR)/ma27d.o
-	$(CL) $(CLFLAGS) $(OPTCL) $(OUTC) $@ $^ $(LIBGFORTRAN) $(LIBBLAS)
-
-LIBMA57 = -L$(MA57DIR) -lma57
-
-else
-
-# IF libcoinhsl is available, get ma27 by dynamically linking libcoinhsl
-libpynumero_MA27.so: ma27Interface.o
-	$(CL) $(CLFLAGS) $(OPTCL) $(OUTC) $@ $^ $(LIBCOINHSL) $(LIBGFORTRAN) $(LIBBLAS)
-
-LIBMA57 = $(LIBCOINHSL)
-
-endif
-
-ifeq ($(strip $(METISDIR)),)
-
-LIBMETIS =
-
-else
-
-# This assumes metis is locally installed
-# TODO: allow option to link metis installed to some system location
-#       (and option to link system-installed ma57, for that matter)
-LIBMETIS = -L$(METISDIR) -lmetis -lm
-
-endif
-
-libpynumero_MA57.so: ma57Interface.o
-	$(CL) $(CLFLAGS) $(OPTCL) $(OUTC) $@ $^ $(LIBMA57) $(LIBGFORTRAN) $(LIBBLAS) $(LIBMETIS)
-
-ma27Interface.o: ma27Interface.c
-	$(CC) $(CCFLAGS) $(OPTCC) $(OUTC) $@ $^
-
-ma57Interface.o: ma57Interface.c
-	$(CC) $(CCFLAGS) $(OPTCC) $(OUTC) $@ $^
-
-install: libpynumero_MA27.so libpynumero_MA57.so
-	$(CP) $^ $(INSTALLDIR)/lib/
-
-clean:
-	$(RM) *27*.o *27*.so *57*.o *57*.so
-
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/Makefile.in b/pyomo/contrib/pynumero/src/hsl_interface/Makefile.in
deleted file mode 100644
index 655dec5c834..00000000000
--- a/pyomo/contrib/pynumero/src/hsl_interface/Makefile.in
+++ /dev/null
@@ -1,32 +0,0 @@
-OUTC = -o
-OUTF = -o
-RM = /bin/rm -f
-CP = /bin/cp
-CC = gcc
-CL = gcc
-FC = gfortran
-FL = gfortran
-AR = ar vr
-LIBLAPACK = -llapack
-LIBBLAS = -lblas
-LIBGFORTRAN = -lgfortran
-
-CCFLAGS = -Wall -g -c -fPIC
-CLFLAGS = -Wall -g -shared
-FCFLAGS = 
-FLFLAGS =
-
-OPTFC = -O2
-OPTFL = -O2
-OPTCC = -O2
-OPTCL = -O2
-
-INSTALLDIR = $${HOME}/.pyomo
-
-METISDIR =
-COINHSLDIR =
-MA27DIR =
-MA57DIR =
-MA97DIR =
-
-LIBCOINHSL = -L$(COINHSLDIR) -lcoinhsl

From 52a73a4ddbb979f843378eb134bdb0239a1b1841 Mon Sep 17 00:00:00 2001
From: Michael Bynum <michaelbynum@users.noreply.github.com>
Date: Tue, 5 May 2020 14:38:25 -0600
Subject: [PATCH 2/5] updating pynumero hsl tests

---
 .../contrib/pynumero/extensions/tests/test_ma27_interface.py  | 4 +++-
 .../contrib/pynumero/extensions/tests/test_ma57_interface.py  | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/pyomo/contrib/pynumero/extensions/tests/test_ma27_interface.py b/pyomo/contrib/pynumero/extensions/tests/test_ma27_interface.py
index 335e03de0f0..495c463023d 100644
--- a/pyomo/contrib/pynumero/extensions/tests/test_ma27_interface.py
+++ b/pyomo/contrib/pynumero/extensions/tests/test_ma27_interface.py
@@ -10,7 +10,9 @@
 import sys
 import os
 import ctypes
-import numpy as np
+from pyomo.contrib.pynumero.dependencies import numpy as np, numpy_available
+if not numpy_available:
+    raise unittest.SkipTest('pynumero MA27 tests require numpy')
 import numpy.ctypeslib as npct
 import pyutilib.th as unittest
 from pyomo.contrib.pynumero.extensions.ma27_interface import *
diff --git a/pyomo/contrib/pynumero/extensions/tests/test_ma57_interface.py b/pyomo/contrib/pynumero/extensions/tests/test_ma57_interface.py
index 12d8cb0fe7a..869d69e07b5 100644
--- a/pyomo/contrib/pynumero/extensions/tests/test_ma57_interface.py
+++ b/pyomo/contrib/pynumero/extensions/tests/test_ma57_interface.py
@@ -10,7 +10,9 @@
 import sys
 import os
 import ctypes
-import numpy as np
+from pyomo.contrib.pynumero.dependencies import numpy as np, numpy_available
+if not numpy_available:
+    raise unittest.SkipTest('pynumero MA27 tests require numpy')
 import numpy.ctypeslib as npct
 import pyutilib.th as unittest
 from pyomo.contrib.pynumero.extensions.ma57_interface import *

From e405ca8cd96a00028ff7fafd076e11cae44e2227 Mon Sep 17 00:00:00 2001
From: Michael Bynum <michaelbynum@users.noreply.github.com>
Date: Tue, 5 May 2020 14:52:58 -0600
Subject: [PATCH 3/5] updating cmake for pynumero

---
 pyomo/contrib/pynumero/src/CMakeLists.txt     | 24 ++++++++++++++++++-
 .../pynumero/src/hsl_interface/CMakeLists.txt | 23 ------------------
 .../src/{hsl_interface => }/ma27Interface.c   |  0
 .../src/{hsl_interface => }/ma57Interface.c   |  0
 4 files changed, 23 insertions(+), 24 deletions(-)
 delete mode 100644 pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
 rename pyomo/contrib/pynumero/src/{hsl_interface => }/ma27Interface.c (100%)
 rename pyomo/contrib/pynumero/src/{hsl_interface => }/ma57Interface.c (100%)

diff --git a/pyomo/contrib/pynumero/src/CMakeLists.txt b/pyomo/contrib/pynumero/src/CMakeLists.txt
index dacaae8fafe..cf246d2e6f3 100644
--- a/pyomo/contrib/pynumero/src/CMakeLists.txt
+++ b/pyomo/contrib/pynumero/src/CMakeLists.txt
@@ -142,7 +142,29 @@ ENDIF()
 #
 # build hsl interfaces
 #
-add_subdirectory(hsl_interface)
+set(PYNUMERO_MA27_SOURCES
+  "ma27Interface.c"
+)
+
+IF( BUILD_MA27 )
+  ADD_LIBRARY( pynumero_MA27 SHARED ${PYNUMERO_MA27_SOURCES} )
+  TARGET_LINK_LIBRARIES( pynumero_MA27 ${HSL_LIBRARY} )
+  SET_TARGET_PROPERTIES( pynumero_MA27 PROPERTIES ENABLE_EXPORTS 1 )
+  INSTALL(TARGETS pynumero_MA27 LIBRARY DESTINATION lib
+    RUNTIME DESTINATION lib )
+ENDIF()
+
+set(PYNUMERO_MA57_SOURCES
+  "ma57Interface.c"
+)
+
+IF( BUILD_MA57 )
+  ADD_LIBRARY( pynumero_MA57 SHARED ${PYNUMERO_MA57_SOURCES} )
+  TARGET_LINK_LIBRARIES( pynumero_MA57 ${HSL_LIBRARY} )
+  SET_TARGET_PROPERTIES( pynumero_MA57 PROPERTIES ENABLE_EXPORTS 1 )
+  INSTALL(TARGETS pynumero_MA57 LIBRARY DESTINATION lib
+    RUNTIME DESTINATION lib )
+ENDIF()
 
 #
 # build the tests for the interfaces
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt b/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
deleted file mode 100644
index c4998655ebd..00000000000
--- a/pyomo/contrib/pynumero/src/hsl_interface/CMakeLists.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-set(PYNUMERO_MA27_SOURCES
-  "ma27Interface.c"
-)
-
-IF( BUILD_MA27 )
-  ADD_LIBRARY( pynumero_MA27 SHARED ${PYNUMERO_MA27_SOURCES} )
-  TARGET_LINK_LIBRARIES( pynumero_MA27 ${HSL_LIBRARY} )
-  SET_TARGET_PROPERTIES( pynumero_MA27 PROPERTIES ENABLE_EXPORTS 1 )
-  INSTALL(TARGETS pynumero_MA27 LIBRARY DESTINATION lib
-    RUNTIME DESTINATION lib )
-ENDIF()
-
-set(PYNUMERO_MA57_SOURCES
-  "ma57Interface.c"
-)
-
-IF( BUILD_MA57 )
-  ADD_LIBRARY( pynumero_MA57 SHARED ${PYNUMERO_MA57_SOURCES} )
-  TARGET_LINK_LIBRARIES( pynumero_MA57 ${HSL_LIBRARY} )
-  SET_TARGET_PROPERTIES( pynumero_MA57 PROPERTIES ENABLE_EXPORTS 1 )
-  INSTALL(TARGETS pynumero_MA57 LIBRARY DESTINATION lib
-    RUNTIME DESTINATION lib )
-ENDIF()
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/ma27Interface.c b/pyomo/contrib/pynumero/src/ma27Interface.c
similarity index 100%
rename from pyomo/contrib/pynumero/src/hsl_interface/ma27Interface.c
rename to pyomo/contrib/pynumero/src/ma27Interface.c
diff --git a/pyomo/contrib/pynumero/src/hsl_interface/ma57Interface.c b/pyomo/contrib/pynumero/src/ma57Interface.c
similarity index 100%
rename from pyomo/contrib/pynumero/src/hsl_interface/ma57Interface.c
rename to pyomo/contrib/pynumero/src/ma57Interface.c

From 575713279ba9440362a10656708415d81b495bde Mon Sep 17 00:00:00 2001
From: Michael Bynum <michaelbynum@users.noreply.github.com>
Date: Wed, 6 May 2020 06:27:31 -0600
Subject: [PATCH 4/5] removing main from hsl interfaces

---
 pyomo/contrib/pynumero/src/ma27Interface.c | 36 ----------------------
 pyomo/contrib/pynumero/src/ma57Interface.c | 26 ----------------
 2 files changed, 62 deletions(-)

diff --git a/pyomo/contrib/pynumero/src/ma27Interface.c b/pyomo/contrib/pynumero/src/ma27Interface.c
index 0cf2b8a6a50..c45d1757d8a 100644
--- a/pyomo/contrib/pynumero/src/ma27Interface.c
+++ b/pyomo/contrib/pynumero/src/ma27Interface.c
@@ -204,39 +204,3 @@ void free_memory(struct MA27_struct* ma27) {
 	}
 	free(ma27);
 }
-
-int main() {
-	
-	struct MA27_struct* ma27 = new_MA27_struct();
-
-	printf("ICNTL[1-1]: %i\n", get_icntl(ma27, 0));
-	printf("ICNTL[2-1]: %i\n", get_icntl(ma27, 1));
-	printf("ICNTL[3-1]: %i\n", get_icntl(ma27, 2));
-	printf("ICNTL[4-1]: %i\n", get_icntl(ma27, 3));
-
-	// Set print level
-	set_icntl(ma27, 2, 2);
-	printf("ICNTL[3-1]: %i\n", get_icntl(ma27, 2));
-
-	int N = 5, NZ = 7;
-	int IRN[7] = { 1, 1, 2, 2, 3, 3, 5 };
-	int ICN[7] = { 1, 2, 3, 5, 3, 4, 5 };
-	double* A = malloc(NZ*sizeof(double));
-	if (A == NULL) { abort_bad_memory(1); }
-//	A = { 2., 3., 4., 6., 1., 5., 1. };
-	A[0] = 2.;
-	A[1] = 3.;
-	A[2] = 4.;
-	A[3] = 6.;
-	A[4] = 1.;
-	A[5] = 5.;
-	A[6] = 1.;
-	double RHS[5] = { 8., 45., 31., 15., 17. };
-
-	do_symbolic_factorization(ma27, N, NZ, IRN, ICN);
-	do_numeric_factorization(ma27, N, NZ, IRN, ICN, A);
-	do_backsolve(ma27, N, RHS);
-	free_memory(ma27);
-	free(A);
-}
-
diff --git a/pyomo/contrib/pynumero/src/ma57Interface.c b/pyomo/contrib/pynumero/src/ma57Interface.c
index 8882baaf78a..830cf817e8a 100644
--- a/pyomo/contrib/pynumero/src/ma57Interface.c
+++ b/pyomo/contrib/pynumero/src/ma57Interface.c
@@ -315,29 +315,3 @@ void free_memory(struct MA57_struct* ma57) {
 	}
 	free(ma57);
 }
-
-int main() {
-	
-	struct MA57_struct* ma57 = new_MA57_struct();
-
-	printf("ICNTL[0]: %i\n", get_icntl(ma57, 0));
-	printf("ICNTL[1]: %i\n", get_icntl(ma57, 1));
-	printf("ICNTL[2]: %i\n", get_icntl(ma57, 2));
-	printf("ICNTL[3]: %i\n", get_icntl(ma57, 3));
-
-	// Set print level
-	set_icntl(ma57, 4, 3);
-	printf("ICNTL[4]: %i\n", get_icntl(ma57, 4));
-
-	int N = 5, NE = 7;
-	int IRN[7] = { 1, 1, 2, 2, 3, 3, 5 };
-	int JCN[7] = { 1, 2, 3, 5, 3, 4, 5 };
-	double A[7] = { 2., 3., 4., 6., 1., 5., 1. };
-	double RHS[5] = { 8., 45., 31., 15., 17. };
-
-	do_symbolic_factorization(ma57, N, NE, IRN, JCN);
-	do_numeric_factorization(ma57, N, NE, A);
-	do_backsolve(ma57, N, RHS);
-	free_memory(ma57);
-}
-

From 966cee111c849f64be5c0d3f1a54d03abff4108b Mon Sep 17 00:00:00 2001
From: Michael Bynum <michaelbynum@users.noreply.github.com>
Date: Wed, 6 May 2020 07:40:01 -0600
Subject: [PATCH 5/5] updating the pynumero installation instructions

---
 pyomo/contrib/pynumero/README.md | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/pyomo/contrib/pynumero/README.md b/pyomo/contrib/pynumero/README.md
index 593d4dc947b..28845d628e4 100644
--- a/pyomo/contrib/pynumero/README.md
+++ b/pyomo/contrib/pynumero/README.md
@@ -14,7 +14,7 @@ PyNumero libraries
 
 PyNumero relies on C/C++ extensions for expensive computing operations.
 
-If you installed Pyomo using Anaconda (from conda-forge), then you can
+If you installed Pyomo using conda (from conda-forge), then you can
 obtain precompiled versions of the redistributable interfaces
 (pynumero_ASL) using conda.  Through Pyomo 5.6.9 these libraries are
 available by installing the `pynumero_libraries` package from
@@ -27,7 +27,20 @@ interfaces, you can build the extensions locally one of three ways:
 1. By running the `build.py` Python script in this directory.  This
 script will automatically drive the `cmake` build harness to compile the
 libraries and install them into your local Pyomo configuration
-directory.
+directory. Cmake options may be specified in the command. For example,
+
+    python build.py -DBUILD_ASL=ON
+
+If you have compiled Ipopt, and you would like to link against the
+libraries built with Ipopt, you can. For example,
+
+    python build.py -DBUILD_ASL=ON -DBUILD_MA27=ON -DIPOPT_DIR=<path_to_ipopt_build>/lib/
+
+If you do so, you will likely need to update an environment variable
+for the path to shared libraries. For example, on Linux,
+
+    export LD_LIBRARY_PATH=<path_to_ipopt_build>/lib/
+
 2. By running `pyomo build-extensions`.  This will build all registered
 Pyomo binary extensions, including PyNumero (using the `build.py` script
 from option 1).
@@ -48,4 +61,6 @@ Prerequisites
      this library)
 
 2. `pynumero_MA27`:
-   - *TODO*
+   - cmake
+   - a C/C++ compiler
+   - MA27 library