From 83162b9aa1219b634adff7840404b71c5a13259e Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Thu, 1 Aug 2019 15:40:29 -0700
Subject: [PATCH 1/8] New configure/build process that finds what external
 libraries that MFEM is using and just copies them.

This means we don't have to separately configure Hypre, Metis,
Suitesparse, etc.
---
 .gitignore     |   1 +
 CMakeLists.txt |  58 ++++++---------------
 parsemk.py     | 138 +++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 154 insertions(+), 43 deletions(-)
 create mode 100644 parsemk.py

diff --git a/.gitignore b/.gitignore
index c409e787..e0c43e7f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ generated-docs/
 *.md~
 *.swp
 
+out.cmake
 GPATH
 GRTAGS
 GTAGS
diff --git a/CMakeLists.txt b/CMakeLists.txt
index d758f752..0eebcfc4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,9 +33,7 @@ set(${PROJECT_NAME}_GRAPHDATA ${PROJECT_SOURCE_DIR}/graphdata)
 
 #####
 # set up external dependencies
-# (this is a mess, seems to work, but I don't know what
-#  I'm doing and I'm sure it can be greatly simplified)
-# (also should take some directory hints from config.sh)
+# (we outsource a lot of this to MFEM)
 #####
 
 # This is a list of TPLs that are used by all targets
@@ -44,7 +42,7 @@ set(TPL_LIBRARIES "")
 # This is a list of linker flags to be used with TPLs for all targets
 set(TPL_LINKER_FLAGS "")
 
-# SAAMGE_PARALLEL
+# SAAMGE
 option(USE_SAAMGE "Should SAAMGE be enabled?" OFF)
 if(USE_SAAMGE)
   find_path(SAAMGE_INCLUDE_PATH saamge.hpp
@@ -64,6 +62,14 @@ else()
   set(${PROJECT_NAME}_USE_SAAMGE 0)
 endif()
 
+# MPI
+find_package(MPI REQUIRED)
+include_directories(${MPI_INCLUDE_PATH})
+list(APPEND TPL_LIBRARIES ${MPI_LIBRARIES})
+if(MPI_CXX_COMPILE_FLAGS)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_COMPILE_FLAGS}")
+endif()
+
 # MFEM
 find_path(MFEM_INCLUDE_PATH mfem.hpp
           HINTS ${MFEM_DIR}/include)
@@ -75,38 +81,11 @@ add_library(MFEM_LIB STATIC IMPORTED)
 set_property(TARGET MFEM_LIB PROPERTY IMPORTED_LOCATION ${MFEM_LIBRARY_PATH}/${MFEM_LIB_NAME})
 list(APPEND TPL_LIBRARIES ${MFEM_LIBRARY_PATH}/${MFEM_LIB_NAME})
 
-# Hypre
-find_path(HYPRE_INCLUDE_PATH HYPRE.h
-          HINTS ${HYPRE_DIR}/include)
-include_directories(${HYPRE_INCLUDE_PATH})
-set(HYPRE_LIB_NAME libHYPRE.a)
-find_library(HYPRE_LIB HYPRE
-  ${HYPRE_DIR}/lib)
-list(APPEND TPL_LIBRARIES ${HYPRE_LIB})
-
-# MPI
-find_package(MPI REQUIRED)
-include_directories(${MPI_INCLUDE_PATH})
-list(APPEND TPL_LIBRARIES ${MPI_LIBRARIES})
-if(MPI_CXX_COMPILE_FLAGS)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_COMPILE_FLAGS}")
-endif()
-
-# Metis
-find_path(METIS_INCLUDE_PATH metis.h
-  HINTS ${METIS_DIR}/include)
-set(METIS_LIB_NAME libmetis.a)
-find_path(METIS_LIBRARY_PATH ${METIS_LIB_NAME}
-  ${METIS_DIR}/lib)
-include_directories(${METIS_INCLUDE_PATH})
-add_library(METIS_LIB STATIC IMPORTED)
-set_property(TARGET METIS_LIB PROPERTY IMPORTED_LOCATION ${METIS_LIBRARY_PATH}/${METIS_LIB_NAME})
-list(APPEND TPL_LIBRARIES ${METIS_LIBRARY_PATH}/${METIS_LIB_NAME})
-
-# SuiteSparse
-find_package(SuiteSparse REQUIRED UMFPACK KLU AMD BTF CHOLMOD COLAMD CAMD CCOLAMD config)
-include_directories(${SuiteSparse_INCLUDE_DIRS})
-list(APPEND TPL_LIBRARIES ${SuiteSparse_LIBRARIES})
+# steal all of MFEM's dependencies
+execute_process(COMMAND python parsemk.py ${MFEM_DIR}/share/mfem/config.mk WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+include("out.cmake")
+include_directories(${MK_INCLUDES})
+list(APPEND TPL_LIBRARIES ${MK_LIBRARIES})
 
 # ARPACK
 # there are several sources for ARPACK, I recommend
@@ -135,13 +114,6 @@ else()
   set(${PROJECT_NAME}_USE_ARPACK 0)
 endif()
 
-# BLAS/LAPACK
-find_package(BLAS REQUIRED)
-find_package(LAPACK REQUIRED)
-list(APPEND TPL_LIBRARIES ${LAPACK_LIBRARIES})
-list(APPEND TPL_LIBRARIES ${BLAS_LIBRARIES})
-list(APPEND TPL_LIBRARIES "gfortran")
-
 list(REMOVE_DUPLICATES TPL_LIBRARIES)
 
 # SPE10 data (not a package, but we want it for testing)
diff --git a/parsemk.py b/parsemk.py
new file mode 100644
index 00000000..87478071
--- /dev/null
+++ b/parsemk.py
@@ -0,0 +1,138 @@
+# BHEADER ####################################################################
+#
+# Copyright (c) 2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+# LLNL-CODE-745247. All Rights reserved. See file COPYRIGHT for details.
+#
+# This file is part of smoothG. For more information and source code
+# availability, see https://www.github.com/llnl/smoothG.
+#
+# smoothG is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+#
+#################################################################### EHEADER #
+
+"""
+This essentially translates the config.mk file from MFEM
+into a out.cmake file to import the dependencies that MFEM
+uses into our configuration process.
+"""
+from __future__ import print_function
+from __future__ import division
+
+import sys
+
+
+def matchopencheck(item, op):
+    if len(item) > len(op) and item[:len(op)] == op:
+        return True
+    else:
+        return False
+
+
+def matchopen(item, op, l):
+    b = matchopencheck(item, op)
+    if b:
+        l.append(item[len(op):])
+    return b
+
+
+def name_package(p, expected_names):
+    """
+    loop order here together with order of
+    expected_names expresses the naming preference I want
+    (ie, I want ["HYPRE", "lapack", "blas"] to be named "HYPRE", not "lapack")
+    """
+    for en in expected_names:
+        for l in p["libraries"]:
+            if en == l:
+                p["name"] = en
+                return
+    p["name"] = "unexpected:" + p["libraries"][0]
+
+
+def parse_packages(filename="config.mk", verbose=False):
+    # print("Opening", filename)
+    rpathopen = "-Wl,-rpath,"
+    linkpathopen = "-L"
+    libraryopen = "-l"
+    other = []
+    packages = []
+    includes = []
+    status = "library"  # switch *from* library to rpath triggers new package
+    with open(filename, "r") as fd:
+        for line in fd:
+            p = line.split()
+            if len(p) > 0 and p[0] == "MFEM_TPLFLAGS":
+                for item in p[2:]:
+                    if len(item) > 2 and item[0:2] == "-I":
+                        includes.append(item[2:])
+            if len(p) > 0 and p[0] == "MFEM_EXT_LIBS":
+                # print("Found MFEM_EXT_LIBS.")
+                for item in p[2:]:
+                    b = False
+                    rp = matchopencheck(item, rpathopen)
+                    if status == "library" and rp:
+                        packages.append({"rpaths": [],
+                                         "linkpaths": [],
+                                         "libraries": []})
+                        status = "rpath"
+                    b = b or matchopen(item, rpathopen, packages[-1]["rpaths"])
+                    lp = matchopen(item, linkpathopen, packages[-1]["linkpaths"])
+                    if lp:
+                        status = "library"
+                    b = b or lp
+                    b = b or matchopen(item, libraryopen, packages[-1]["libraries"])
+                    if not b:
+                        other.append(item)
+    if len(other) > 0:
+        print("WARNING: could not parse MFEM_EXT_LIBS: did not understand following tokens:")
+        for o in other:
+            print("  ", o)
+    expected_names = ["HYPRE", "metis", "suitesparseconfig",
+                      "unwind", "z", "lapack"]
+    for p in packages:
+        name_package(p, expected_names)
+    if verbose:
+        print("packages:")
+        for p in packages:
+            print("\n  ", p["name"])
+            print("  ", "rpaths:")
+            for r in p["rpaths"]:
+                print("    ", r)
+            print("  ", "linkpaths:")
+            for l in p["linkpaths"]:
+                print("    ", l)
+            print("  ", "libraries:")
+            for l in p["libraries"]:
+                print("    ", l)
+    return packages, includes
+
+
+def save_cmake_packages(packages, includes, filename="out.cmake"):
+    with open(filename, "w") as fd:
+        fd.write('set(MK_INCLUDES "")\n\n')
+        for i in includes:
+            fd.write("list(APPEND MK_INCLUDES " + i + ")\n")
+        fd.write("\n")
+        fd.write('set(MK_LIBRARIES "")\n\n')
+        for p in packages:
+            fd.write("# " + p["name"] + "\n")
+            for l in p["libraries"]:
+                cmake_name = l + "_LIB"
+                fd.write("find_library(" + cmake_name + " " + l + " PATHS ")
+                for lp in p["linkpaths"]:
+                    fd.write(lp + " ")
+                fd.write(")\n")
+                fd.write("list(APPEND MK_LIBRARIES ${" + cmake_name + "})\n")
+            fd.write("\n")
+        fd.write("list(REMOVE_DUPLICATES MK_LIBRARIES)\n")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) > 1:
+        packages, includes = parse_packages(filename=sys.argv[1], verbose=False)
+    else:
+        packages, includes = parse_packages(verbose=False)
+    save_cmake_packages(packages, includes)

From f27bce0078d88a029b0a433b4e6e603709ee8408 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Thu, 1 Aug 2019 15:43:42 -0700
Subject: [PATCH 2/8] Modify example configure scripts to reflect new
 configure/build system.

---
 config/example_config_debug.sh               | 5 -----
 config/example_config_release.sh             | 5 -----
 config/example_config_release_with_arpack.sh | 5 -----
 3 files changed, 15 deletions(-)

diff --git a/config/example_config_debug.sh b/config/example_config_debug.sh
index 4b0e836b..30b59e44 100755
--- a/config/example_config_debug.sh
+++ b/config/example_config_debug.sh
@@ -33,9 +33,6 @@ rm -rf CMakeFiles
 
 cmake \
     -DMFEM_DIR=/path/to/the/directory/where/mfem/is/installed \
-    -DMETIS_DIR=/path/to/the/directory/where/metis/is/installed \
-    -DHYPRE_DIR=/path/to/the/directory/where/hypre/is/installed \
-    -DSuiteSparse_DIR=/path/to/the/directory/where/SuiteSparse/is/installed \
     -DSPE10_DIR=/path/to/the/directory/where/spe_perm.dat/is/located \
     \
     -DMEMORYCHECK_COMMAND=/path/to/valgrind/binary \
@@ -44,8 +41,6 @@ cmake \
     -DUSE_ARPACK=OFF \
     \
     -DCMAKE_BUILD_TYPE=Debug \
-    -DBLAS_LIBRARIES=/path/to/the/blas/library/file \
-    -DLAPACK_LIBRARIES=/path/to/the/lapack/library/file \
     \
     ${EXTRA_ARGS} \
     ${BASE_DIR}
diff --git a/config/example_config_release.sh b/config/example_config_release.sh
index 7517a69a..9a7883ce 100755
--- a/config/example_config_release.sh
+++ b/config/example_config_release.sh
@@ -33,9 +33,6 @@ rm -rf CMakeFiles
 
 cmake \
     -DMFEM_DIR=/path/to/the/directory/where/mfem/is/installed \
-    -DMETIS_DIR=/path/to/the/directory/where/metis/is/installed \
-    -DHYPRE_DIR=/path/to/the/directory/where/hypre/is/installed \
-    -DSuiteSparse_DIR=/path/to/the/directory/where/SuiteSparse/is/installed \
     -DSPE10_DIR=/path/to/the/directory/where/spe_perm.dat/is/located \
     \
     -DMEMORYCHECK_COMMAND=/path/to/valgrind/binary \
@@ -44,8 +41,6 @@ cmake \
     -DUSE_ARPACK=OFF \
     \
     -DCMAKE_BUILD_TYPE=Release \
-    -DBLAS_LIBRARIES=/path/to/the/blas/library/file \
-    -DLAPACK_LIBRARIES=/path/to/the/lapack/library/file \
     \
     ${EXTRA_ARGS} \
     ${BASE_DIR}
diff --git a/config/example_config_release_with_arpack.sh b/config/example_config_release_with_arpack.sh
index 4dade9f6..58dda7ce 100755
--- a/config/example_config_release_with_arpack.sh
+++ b/config/example_config_release_with_arpack.sh
@@ -33,9 +33,6 @@ rm -rf CMakeFiles
 
 cmake \
     -DMFEM_DIR=/path/to/the/directory/where/mfem/is/installed \
-    -DMETIS_DIR=/path/to/the/directory/where/metis/is/installed \
-    -DHYPRE_DIR=/path/to/the/directory/where/hypre/is/installed \
-    -DSuiteSparse_DIR=/path/to/the/directory/where/SuiteSparse/is/installed \
     -DSPE10_DIR=/path/to/the/directory/where/spe_perm.dat/is/located \
     \
     -DUSE_ARPACK=ON \
@@ -43,8 +40,6 @@ cmake \
     -DARPACKPP_DIR=/path/to/the/root/directory/of/arpackpp \
     \
     -DCMAKE_BUILD_TYPE=Release \
-    -DBLAS_LIBRARIES=/path/to/the/blas/library/file \
-    -DLAPACK_LIBRARIES=/path/to/the/lapack/library/file \
     \
     ${EXTRA_ARGS} \
     ${BASE_DIR}

From aa52c2b41af34a0da8adb36c7e8d313900ff39f2 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Thu, 1 Aug 2019 15:47:17 -0700
Subject: [PATCH 3/8] Modify .travis.yml for new config/build setup.

---
 .travis.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index df69900b..d692df59 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -160,9 +160,6 @@ script:
    - cd build;
    - |
        CC=mpicc CXX=mpic++ cmake -DMFEM_DIR="/home/travis/build/LLNL/mfem-install" \
-       -DHYPRE_DIR="/home/travis/build/LLNL/hypre-install" \
-       -DSuiteSparse_DIR="/home/travis/build/LLNL/SuiteSparse-install" \
-       -DMETIS_DIR="/home/travis/build/LLNL/metis-install" \
        -DUSE_ARPACK=OFF -DCMAKE_BUILD_TYPE=Debug \
        -DSPE10_PERM="/home/travis/build/LLNL/spe10-install/spe_perm.dat" \
        -DSMOOTHG_TEST_PROCS=2 ..;

From d477c6c3058cd3bd3d593b85124f7695c657ee62 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Fri, 2 Aug 2019 11:09:11 -0700
Subject: [PATCH 4/8] config: better search for MFEM's config.mk

---
 CMakeLists.txt | 4 +++-
 parsemk.py     | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0eebcfc4..739a0694 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -82,7 +82,9 @@ set_property(TARGET MFEM_LIB PROPERTY IMPORTED_LOCATION ${MFEM_LIBRARY_PATH}/${M
 list(APPEND TPL_LIBRARIES ${MFEM_LIBRARY_PATH}/${MFEM_LIB_NAME})
 
 # steal all of MFEM's dependencies
-execute_process(COMMAND python parsemk.py ${MFEM_DIR}/share/mfem/config.mk WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+find_path(MFEM_CONFIG_PATH config.mk
+    PATHS ${MFEM_DIR}/share/mfem ${MFEM_DIR})
+execute_process(COMMAND python parsemk.py ${MFEM_CONFIG_PATH}/config.mk WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 include("out.cmake")
 include_directories(${MK_INCLUDES})
 list(APPEND TPL_LIBRARIES ${MK_LIBRARIES})
diff --git a/parsemk.py b/parsemk.py
index 87478071..f9e3e3eb 100644
--- a/parsemk.py
+++ b/parsemk.py
@@ -92,6 +92,8 @@ def parse_packages(filename="config.mk", verbose=False):
             print("  ", o)
     expected_names = ["HYPRE", "metis", "suitesparseconfig",
                       "unwind", "z", "lapack"]
+    if len(packages) == 0 or len(includes) == 0:
+        print("WARNING: could not parse config.mk!")
     for p in packages:
         name_package(p, expected_names)
     if verbose:

From c4aeae1b1bd1393d84ec6504db04d4e059794744 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Mon, 5 Aug 2019 07:58:26 -0700
Subject: [PATCH 5/8] More robust parsemk.py

Really I am trying to debug the Travis build, which is kind of a
pain.
---
 parsemk.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/parsemk.py b/parsemk.py
index f9e3e3eb..72286ee7 100644
--- a/parsemk.py
+++ b/parsemk.py
@@ -58,9 +58,11 @@ def parse_packages(filename="config.mk", verbose=False):
     linkpathopen = "-L"
     libraryopen = "-l"
     other = []
-    packages = []
+    packages = [{"rpaths": [],
+                 "linkpaths": [],
+                 "libraries": []}]
     includes = []
-    status = "library"  # switch *from* library to rpath triggers new package
+    status = "begin"  # switch *from* library to rpath triggers new package
     with open(filename, "r") as fd:
         for line in fd:
             p = line.split()
@@ -69,14 +71,16 @@ def parse_packages(filename="config.mk", verbose=False):
                     if len(item) > 2 and item[0:2] == "-I":
                         includes.append(item[2:])
             if len(p) > 0 and p[0] == "MFEM_EXT_LIBS":
-                # print("Found MFEM_EXT_LIBS.")
+                print("Found MFEM_EXT_LIBS.")
                 for item in p[2:]:
+                    print("  parsing", item)
                     b = False
                     rp = matchopencheck(item, rpathopen)
                     if status == "library" and rp:
                         packages.append({"rpaths": [],
                                          "linkpaths": [],
                                          "libraries": []})
+                    if rp:
                         status = "rpath"
                     b = b or matchopen(item, rpathopen, packages[-1]["rpaths"])
                     lp = matchopen(item, linkpathopen, packages[-1]["linkpaths"])

From 6ef84b367081f7c48582fb72dbfa27042e864166 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Mon, 5 Aug 2019 08:12:35 -0700
Subject: [PATCH 6/8] parsemk.py: less verbose output

---
 parsemk.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/parsemk.py b/parsemk.py
index 72286ee7..5d19721d 100644
--- a/parsemk.py
+++ b/parsemk.py
@@ -71,9 +71,8 @@ def parse_packages(filename="config.mk", verbose=False):
                     if len(item) > 2 and item[0:2] == "-I":
                         includes.append(item[2:])
             if len(p) > 0 and p[0] == "MFEM_EXT_LIBS":
-                print("Found MFEM_EXT_LIBS.")
+                print("parsemk.py: Found MFEM_EXT_LIBS.")
                 for item in p[2:]:
-                    print("  parsing", item)
                     b = False
                     rp = matchopencheck(item, rpathopen)
                     if status == "library" and rp:

From bafae30d7bc5922f6c28d45dbadba8fc3794232a Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Tue, 13 Aug 2019 08:29:27 -0700
Subject: [PATCH 7/8] parsemk.py: now handles different versions of MFEM's
 config.mk

---
 parsemk.py | 60 ++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 40 insertions(+), 20 deletions(-)

diff --git a/parsemk.py b/parsemk.py
index 5d19721d..c20c313c 100644
--- a/parsemk.py
+++ b/parsemk.py
@@ -52,47 +52,67 @@ def name_package(p, expected_names):
     p["name"] = "unexpected:" + p["libraries"][0]
 
 
-def parse_packages(filename="config.mk", verbose=False):
-    # print("Opening", filename)
+def parse_lib_line(line, status, packages, other):
     rpathopen = "-Wl,-rpath,"
     linkpathopen = "-L"
     libraryopen = "-l"
+    for item in line:
+        b = False
+        rp = matchopencheck(item, rpathopen)
+        if status == "library" and rp:
+            packages.append({"rpaths": [],
+                             "linkpaths": [],
+                             "libraries": []})
+        if rp:
+            status = "rpath"
+        b = b or matchopen(item, rpathopen, packages[-1]["rpaths"])
+        lp = matchopen(item, linkpathopen, packages[-1]["linkpaths"])
+        if lp:
+            status = "library"
+        b = b or lp
+        b = b or matchopen(item, libraryopen, packages[-1]["libraries"])
+        if item == "$(MFEM_EXT_LIBS)":
+            b = True
+        if not b:
+            other.append(item)
+
+
+def parse_packages(filename="config.mk", verbose=False):
     other = []
     packages = [{"rpaths": [],
                  "linkpaths": [],
                  "libraries": []}]
+    alt_packages = [{"rpaths": [],
+                     "linkpaths": [],
+                     "libraries": []}]
     includes = []
     status = "begin"  # switch *from* library to rpath triggers new package
+    found_ext_libs = False
     with open(filename, "r") as fd:
+        print("parsemk.py: Found config file", filename)
         for line in fd:
             p = line.split()
             if len(p) > 0 and p[0] == "MFEM_TPLFLAGS":
+                print("parsemk.py: Found MFEM_TPLFLAGS")
                 for item in p[2:]:
                     if len(item) > 2 and item[0:2] == "-I":
                         includes.append(item[2:])
             if len(p) > 0 and p[0] == "MFEM_EXT_LIBS":
+                found_ext_libs = True
                 print("parsemk.py: Found MFEM_EXT_LIBS.")
-                for item in p[2:]:
-                    b = False
-                    rp = matchopencheck(item, rpathopen)
-                    if status == "library" and rp:
-                        packages.append({"rpaths": [],
-                                         "linkpaths": [],
-                                         "libraries": []})
-                    if rp:
-                        status = "rpath"
-                    b = b or matchopen(item, rpathopen, packages[-1]["rpaths"])
-                    lp = matchopen(item, linkpathopen, packages[-1]["linkpaths"])
-                    if lp:
-                        status = "library"
-                    b = b or lp
-                    b = b or matchopen(item, libraryopen, packages[-1]["libraries"])
-                    if not b:
-                        other.append(item)
+                parse_lib_line(p[2:], status, packages, other)
+            if len(p) > 0 and p[0] == "MFEM_LIBS":
+                print("parsemk.py: Found MFEM_LIBS.")
+                parse_lib_line(p[2:], status, alt_packages, other)
+    if not found_ext_libs:
+        packages = alt_packages
     if len(other) > 0:
-        print("WARNING: could not parse MFEM_EXT_LIBS: did not understand following tokens:")
+        print("WARNING: could not parse external MFEM libraries: "
+              "did not understand following tokens:")
         for o in other:
             print("  ", o)
+    if len(packages) == 0:
+        print("WARNING: did not find any external MFEM libraries!")
     expected_names = ["HYPRE", "metis", "suitesparseconfig",
                       "unwind", "z", "lapack"]
     if len(packages) == 0 or len(includes) == 0:

From 8f013ba04867bbc8eef0dd4683148af193113ad6 Mon Sep 17 00:00:00 2001
From: "Andrew T. Barker" <barker29@llnl.gov>
Date: Tue, 10 Sep 2019 16:33:32 -0700
Subject: [PATCH 8/8] cmake: make adopting of MFEM dependencies optional.

---
 CMakeLists.txt                   | 25 ++++++++++------
 config/example_config_debug.sh   |  2 ++
 config/example_config_release.sh |  2 ++
 explicitdependencies.cmake       | 51 ++++++++++++++++++++++++++++++++
 parsemk.py                       |  7 ++++-
 5 files changed, 77 insertions(+), 10 deletions(-)
 create mode 100644 explicitdependencies.cmake

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 739a0694..f2f45410 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,3 @@
-#!/bin/sh
 # BHEADER ####################################################################
 #
 # Copyright (c) 2018, Lawrence Livermore National Security, LLC.
@@ -81,16 +80,24 @@ add_library(MFEM_LIB STATIC IMPORTED)
 set_property(TARGET MFEM_LIB PROPERTY IMPORTED_LOCATION ${MFEM_LIBRARY_PATH}/${MFEM_LIB_NAME})
 list(APPEND TPL_LIBRARIES ${MFEM_LIBRARY_PATH}/${MFEM_LIB_NAME})
 
-# steal all of MFEM's dependencies
-find_path(MFEM_CONFIG_PATH config.mk
-    PATHS ${MFEM_DIR}/share/mfem ${MFEM_DIR})
-execute_process(COMMAND python parsemk.py ${MFEM_CONFIG_PATH}/config.mk WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
-include("out.cmake")
-include_directories(${MK_INCLUDES})
-list(APPEND TPL_LIBRARIES ${MK_LIBRARIES})
+option(ADOPT_MFEM_DEPENDENCIES "Take include and link paths from MFEM installation?" ON)
+if(ADOPT_MFEM_DEPENDENCIES)
+  # steal all of MFEM's dependencies
+  find_path(MFEM_CONFIG_PATH config.mk
+      PATHS ${MFEM_DIR}/share/mfem ${MFEM_DIR})
+  execute_process(COMMAND python parsemk.py ${MFEM_CONFIG_PATH}/config.mk
+      WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+  include("out.cmake")
+  include_directories(${MK_INCLUDES})
+  list(APPEND TPL_LIBRARIES ${MK_LIBRARIES})
+else()
+  include("explicitdependencies.cmake")
+  include_directories(${EI_INCLUDES})
+  list(APPEND TPL_LIBRARIES ${EI_LIBRARIES})
+endif()
 
 # ARPACK
-# there are several sources for ARPACK, I recommend
+# there are several sources for ARPACK, we recommend
 #    https://github.com/opencollab/arpack-ng.git
 # and
 #    https://github.com/m-reuter/arpackpp.git
diff --git a/config/example_config_debug.sh b/config/example_config_debug.sh
index 30b59e44..3ea6e4a7 100755
--- a/config/example_config_debug.sh
+++ b/config/example_config_debug.sh
@@ -32,6 +32,8 @@ rm CMakeCache.txt
 rm -rf CMakeFiles
 
 cmake \
+    -DADOPT_MFEM_DEPENDENCIES=ON \
+    \
     -DMFEM_DIR=/path/to/the/directory/where/mfem/is/installed \
     -DSPE10_DIR=/path/to/the/directory/where/spe_perm.dat/is/located \
     \
diff --git a/config/example_config_release.sh b/config/example_config_release.sh
index 9a7883ce..34cbc241 100755
--- a/config/example_config_release.sh
+++ b/config/example_config_release.sh
@@ -32,6 +32,8 @@ rm CMakeCache.txt
 rm -rf CMakeFiles
 
 cmake \
+    -DADOPT_MFEM_DEPENDENCIES=ON \
+    \
     -DMFEM_DIR=/path/to/the/directory/where/mfem/is/installed \
     -DSPE10_DIR=/path/to/the/directory/where/spe_perm.dat/is/located \
     \
diff --git a/explicitdependencies.cmake b/explicitdependencies.cmake
new file mode 100644
index 00000000..7c59a5a9
--- /dev/null
+++ b/explicitdependencies.cmake
@@ -0,0 +1,51 @@
+# BHEADER ####################################################################
+#
+# Copyright (c) 2018, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+# LLNL-CODE-745247. All Rights reserved. See file COPYRIGHT for details.
+#
+# This file is part of smoothG. For more information and source code
+# availability, see https://www.github.com/llnl/smoothG.
+#
+# smoothG is free software; you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License (as published by the Free
+# Software Foundation) version 2.1 dated February 1999.
+#
+#################################################################### EHEADER #
+
+set(EI_INCLUDES "")
+set(EI_LIBRARIES "")
+
+# Hypre
+find_path(HYPRE_INCLUDE_PATH HYPRE.h
+          HINTS ${HYPRE_DIR}/include)
+list(APPEND EI_INCLUDES ${HYPRE_INCLUDE_PATH})
+set(HYPRE_LIB_NAME libHYPRE.a)
+find_library(HYPRE_LIB HYPRE
+  ${HYPRE_DIR}/lib)
+list(APPEND EI_LIBRARIES ${HYPRE_LIB})
+
+# Metis
+find_path(METIS_INCLUDE_PATH metis.h
+  HINTS ${METIS_DIR}/include)
+set(METIS_LIB_NAME libmetis.a)
+find_path(METIS_LIBRARY_PATH ${METIS_LIB_NAME}
+  ${METIS_DIR}/lib)
+list(APPEND EI_INCLUDES ${METIS_INCLUDE_PATH})
+add_library(METIS_LIB STATIC IMPORTED)
+set_property(TARGET METIS_LIB PROPERTY IMPORTED_LOCATION ${METIS_LIBRARY_PATH}/${METIS_LIB_NAME})
+list(APPEND EI_LIBRARIES ${METIS_LIBRARY_PATH}/${METIS_LIB_NAME})
+
+# SuiteSparse
+find_package(SuiteSparse REQUIRED UMFPACK KLU AMD BTF CHOLMOD COLAMD CAMD CCOLAMD config)
+list(APPEND EI_INCLUDES ${SuiteSparse_INCLUDE_DIRS})
+list(APPEND EI_LIBRARIES ${SuiteSparse_LIBRARIES})
+
+# BLAS/LAPACK
+find_package(BLAS REQUIRED)
+find_package(LAPACK REQUIRED)
+list(APPEND EI_LIBRARIES ${LAPACK_LIBRARIES})
+list(APPEND EI_LIBRARIES ${BLAS_LIBRARIES})
+list(APPEND EI_LIBRARIES "gfortran")
+
+list(REMOVE_DUPLICATES EI_LIBRARIES)
diff --git a/parsemk.py b/parsemk.py
index c20c313c..bc2a61ed 100644
--- a/parsemk.py
+++ b/parsemk.py
@@ -17,6 +17,11 @@
 This essentially translates the config.mk file from MFEM
 into a out.cmake file to import the dependencies that MFEM
 uses into our configuration process.
+
+This was originally written to divide libraries/includes into
+'packages' that were understandable by a human. At some point
+we gave up on that and just threw everything into a pile of
+include and link flags.
 """
 from __future__ import print_function
 from __future__ import division
@@ -86,7 +91,7 @@ def parse_packages(filename="config.mk", verbose=False):
                      "linkpaths": [],
                      "libraries": []}]
     includes = []
-    status = "begin"  # switch *from* library to rpath triggers new package
+    status = "begin"
     found_ext_libs = False
     with open(filename, "r") as fd:
         print("parsemk.py: Found config file", filename)