diff --git a/lib/.gitignore b/lib/.gitignore
index cbeae7705..4f9ebba6a 100644
--- a/lib/.gitignore
+++ b/lib/.gitignore
@@ -1,2 +1,3 @@
 Makefile.lammps
 .depend
+Makefile.auto
diff --git a/lib/Install.py b/lib/Install.py
index 6b9025433..416a2319c 100644
--- a/lib/Install.py
+++ b/lib/Install.py
@@ -1,92 +1,100 @@
 #!/usr/bin/env python
 
 # install.py tool to do a generic build of a library
 # soft linked to by many of the lib/Install.py files
 # used to automate the steps described in the corresponding lib/README
 
 from __future__ import print_function
 import sys,os,subprocess
 
 # help message
 
 help = """
 Syntax from src dir: make lib-libname args="-m machine -e suffix"
 Syntax from lib dir: python Install.py -m machine -e suffix
 
 libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
 specify -m and optionally -e, order does not matter
 
   -m = peform a clean followed by "make -f Makefile.machine"
        machine = suffix of a lib/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
 
 Examples:
 
 make lib-poems args="-m g++"    # build COLVARS lib with GNU g++ compiler
 make lib-meam args="-m ifort"   # build MEAM lib with Intel ifort compiler
 """
 
 # print error message or help
 
 def error(str=None):
   if not str: print(help)
   else: print("ERROR",str)
   sys.exit()
 
 # parse args
 
 args = sys.argv[1:]
 nargs = len(args)
 if nargs == 0: error()
 
 machine = None
 extraflag = 0
 
 iarg = 0
 while iarg < nargs:
   if args[iarg] == "-m":
     if iarg+2 > nargs: error()
     machine = args[iarg+1]
     iarg += 2
   elif args[iarg] == "-e":
     if iarg+2 > nargs: error()
     extraflag = 1
     suffix = args[iarg+1]
     iarg += 2
   else: error()
 
 # set lib from working dir
 
 cwd = os.getcwd()
 lib = os.path.basename(cwd)
 
 # create Makefile.auto as copy of Makefile.machine
 # reset EXTRAMAKE if requested
 
 if not os.path.exists("Makefile.%s" % machine):
   error("lib/%s/Makefile.%s does not exist" % (lib,machine))
 
 lines = open("Makefile.%s" % machine,'r').readlines()
 fp = open("Makefile.auto",'w')
 
+has_extramake = False
 for line in lines:
   words = line.split()
-  if len(words) == 3 and extraflag and \
-        words[0] == "EXTRAMAKE" and words[1] == '=':
-    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
-  print >>fp,line,
+  if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
+    has_extramake = True
+    if extraflag:
+      line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+  fp.write(line)
 
 fp.close()
 
-# make the library via Makefile.auto
+# make the library via Makefile.auto optionally with parallel make
+
+try:
+  import multiprocessing
+  n_cpus = multiprocessing.cpu_count()
+except:
+  n_cpus = 1
 
 print("Building lib%s.a ..." % lib)
-cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
 txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
-print(txt)
+print(txt.decode('UTF-8'))
 
 if os.path.exists("lib%s.a" % lib): print("Build was successful")
 else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
-if not os.path.exists("Makefile.lammps"):
+if has_extramake and not os.path.exists("Makefile.lammps"):
   print("lib/%s/Makefile.lammps was NOT created" % lib)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.mpi
similarity index 83%
copy from lib/awpmd/Makefile.mpicc
copy to lib/awpmd/Makefile.mpi
index 4c289ad88..e4b424e77 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpi
@@ -1,69 +1,71 @@
 SHELL = /bin/sh
 
 # which file will be copied to Makefile.lammps
 
-EXTRAMAKE = Makefile.lammps.installed
+EXTRAMAKE = Makefile.lammps.linalg
 
 # ------ FILES ------
 
 SRC = \
     ivutils/src/logexc.cpp \
     systems/interact/TCP/wpmd.cpp \
     systems/interact/TCP/wpmd_split.cpp
 
 INC = \
     cerf.h \
     cerf2.h \
     cerf_octave.h \
     cvector_3.h \
     lapack_inter.h \
     logexc.h \
     pairhash.h \
     refobj.h \
     tcpdefs.h \
     vector_3.h \
     wavepacket.h \
     wpmd.h \
     wpmd_split.h
 
 # ------ DEFINITIONS ------
 
 LIB = libawpmd.a
 OBJ =   $(SRC:.cpp=.o)
 
 # ------ SETTINGS ------
 
 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with
 
-CC =	    mpic++ 
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
 ARCHIVE =	ar
 ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
 USRLIB =
 SYSLIB =
 
 # ------ MAKE PROCEDURE ------
 
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
 
 # ------ COMPILE RULES ------
 
 %.o:%.cpp
 	$(CC) $(CCFLAGS) -c $< -o $@
 %.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
 
 # ------ DEPENDENCIES ------
 
 DEPENDS = $(OBJ:.o=.d)
 
 # ------ CLEAN ------
 
 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.mpicc
index 4c289ad88..5cf6a75bd 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpicc
@@ -1,69 +1,71 @@
 SHELL = /bin/sh
 
 # which file will be copied to Makefile.lammps
 
 EXTRAMAKE = Makefile.lammps.installed
 
 # ------ FILES ------
 
 SRC = \
     ivutils/src/logexc.cpp \
     systems/interact/TCP/wpmd.cpp \
     systems/interact/TCP/wpmd_split.cpp
 
 INC = \
     cerf.h \
     cerf2.h \
     cerf_octave.h \
     cvector_3.h \
     lapack_inter.h \
     logexc.h \
     pairhash.h \
     refobj.h \
     tcpdefs.h \
     vector_3.h \
     wavepacket.h \
     wpmd.h \
     wpmd_split.h
 
 # ------ DEFINITIONS ------
 
 LIB = libawpmd.a
 OBJ =   $(SRC:.cpp=.o)
 
 # ------ SETTINGS ------
 
 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with
 
-CC =	    mpic++ 
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
 ARCHIVE =	ar
 ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
 USRLIB =
 SYSLIB =
 
 # ------ MAKE PROCEDURE ------
 
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
 
 # ------ COMPILE RULES ------
 
 %.o:%.cpp
 	$(CC) $(CCFLAGS) -c $< -o $@
 %.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
 
 # ------ DEPENDENCIES ------
 
 DEPENDS = $(OBJ:.o=.d)
 
 # ------ CLEAN ------
 
 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.serial
similarity index 85%
copy from lib/awpmd/Makefile.mpicc
copy to lib/awpmd/Makefile.serial
index 4c289ad88..f51714fc9 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.serial
@@ -1,69 +1,71 @@
 SHELL = /bin/sh
 
 # which file will be copied to Makefile.lammps
 
-EXTRAMAKE = Makefile.lammps.installed
+EXTRAMAKE = Makefile.lammps.linalg
 
 # ------ FILES ------
 
 SRC = \
     ivutils/src/logexc.cpp \
     systems/interact/TCP/wpmd.cpp \
     systems/interact/TCP/wpmd_split.cpp
 
 INC = \
     cerf.h \
     cerf2.h \
     cerf_octave.h \
     cvector_3.h \
     lapack_inter.h \
     logexc.h \
     pairhash.h \
     refobj.h \
     tcpdefs.h \
     vector_3.h \
     wavepacket.h \
     wpmd.h \
     wpmd_split.h
 
 # ------ DEFINITIONS ------
 
 LIB = libawpmd.a
 OBJ =   $(SRC:.cpp=.o)
 
 # ------ SETTINGS ------
 
 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with
 
-CC =	    mpic++ 
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+CC =	    g++
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -I../../src/STUBS
+
 ARCHIVE =	ar
 ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
 USRLIB =
 SYSLIB =
 
 # ------ MAKE PROCEDURE ------
 
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
 
 # ------ COMPILE RULES ------
 
 %.o:%.cpp
 	$(CC) $(CCFLAGS) -c $< -o $@
 %.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
 
 # ------ DEPENDENCIES ------
 
 DEPENDS = $(OBJ:.o=.d)
 
 # ------ CLEAN ------
 
 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index 2fc207710..01e70543f 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -1,142 +1,142 @@
 #!/usr/bin/env python
 
 # Install.py tool to do automate build of Colvars
 
 from __future__ import print_function
 import sys,os,subprocess
 
 # help message
 
 help = """
 Syntax from src dir: make lib-colvars args="-m machine -e suffix"
 Syntax from lib/colvars dir: python Install.py -m machine -e suffix
 
 specify -m and optionally -e, order does not matter
 
-  -m = peform a clean followed by "make -f Makefile.machine"
+  -m = delete all existing objects, followed by "make -f Makefile.machine"
        machine = suffix of a lib/colvars/Makefile.* or of a
          src/MAKE/MACHINES/Makefile.* file
   -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
        does not alter existing Makefile.machine
 
 Examples:
 
-make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-colvars args="-m mpi"     # build COLVARS lib with default mpi compiler wrapper
 """
 
 # print error message or help
 
 def error(str=None):
   if not str: print(help)
   else: print("ERROR",str)
   sys.exit()
 
 # parse args
 
 args = sys.argv[1:]
 nargs = len(args)
 if nargs == 0: error()
 
 machine = None
 extraflag = False
 
 iarg = 0
 while iarg < nargs:
   if args[iarg] == "-m":
     if iarg+2 > len(args): error()
     machine = args[iarg+1]
     iarg += 2  
   elif args[iarg] == "-e":
     if iarg+2 > len(args): error()
     extraflag = True
     suffix = args[iarg+1]
     iarg += 2  
   else: error()
 
 # set lib from working dir
 
 cwd = os.getcwd()
 lib = os.path.basename(cwd)
 
 def get_lammps_machine_flags(machine):
   """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""
   if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):
     error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
   lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,
                'r').readlines()
   machine_flags = {}
   for line in lines:
     line = line.partition('#')[0]
     line = line.rstrip()
     words = line.split()
     if (len(words) > 2):
       if ((words[0] == 'CC') or (words[0] == 'CCFLAGS') or
           (words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or
           (words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):
         machine_flags[words[0]] = ' '.join(words[2:])
   return machine_flags
 
 def gen_colvars_makefile_machine(machine, machine_flags):
   """Generate Makefile.machine for Colvars given the compiler flags"""
   machine_makefile = open("Makefile.%s" % machine, 'w')
   machine_makefile.write('''# -*- makefile -*- to build Colvars module with %s
 
 COLVARS_LIB = libcolvars.a
 COLVARS_OBJ_DIR =
 
 CXX =		%s
 CXXFLAGS =	%s %s
 AR =		%s
 ARFLAGS =	%s
 SHELL =		%s
 
 include Makefile.common
 
 .PHONY: default clean
 
 default: $(COLVARS_LIB) Makefile.lammps
 
 clean:
 	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
 ''' % (machine, machine_flags['CC'],
        machine_flags['CCFLAGS'], machine_flags['SHFLAGS'] ,
        machine_flags['ARCHIVE'], machine_flags['ARFLAGS'],
        machine_flags['SHELL']))
 
 if not os.path.exists("Makefile.%s" % machine):
   machine_flags = get_lammps_machine_flags(machine)
   gen_colvars_makefile_machine(machine, machine_flags)
 if not os.path.exists("Makefile.%s" % machine):
   error("lib/%s/Makefile.%s does not exist" % (lib,machine))
 
 # create Makefile.auto as copy of Makefile.machine
 # reset EXTRAMAKE if requested
 
 lines = open("Makefile.%s" % machine,'r').readlines()
 fp = open("Makefile.auto",'w')
 for line in lines:
   words = line.split()
   if len(words) == 3 and extraflag and \
         words[0] == "EXTRAMAKE" and words[1] == '=':
     line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
   fp.write(line)
 fp.close()
 
-# make the library via Makefile.auto
+# make the library via Makefile.auto optionally with parallel make
 
 try:
   import multiprocessing
   n_cpus = multiprocessing.cpu_count()
 except:
   n_cpus = 1
 
 print("Building lib%s.a ..." % lib)
 cmd = ["make -f Makefile.auto clean"]
-print(subprocess.check_output(cmd, shell=True).decode())
+print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
 cmd = ["make -f Makefile.auto -j%d" % n_cpus]
-print(subprocess.check_output(cmd, shell=True).decode())
+print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
 
 if os.path.exists("lib%s.a" % lib): print("Build was successful")
 else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
 if not os.path.exists("Makefile.lammps"):
   print("lib/%s/Makefile.lammps was NOT created" % lib)
diff --git a/lib/colvars/Makefile.lammps b/lib/colvars/Makefile.lammps
deleted file mode 100644
index 99f57b050..000000000
--- a/lib/colvars/Makefile.lammps
+++ /dev/null
@@ -1,5 +0,0 @@
-# Settings that the LAMMPS build will import when this package library is used
-
-colvars_SYSINC =
-colvars_SYSLIB =
-colvars_SYSPATH =
diff --git a/lib/colvars/Makefile.mingw32-cross b/lib/colvars/Makefile.mingw32-cross
deleted file mode 100644
index 29c64b26a..000000000
--- a/lib/colvars/Makefile.mingw32-cross
+++ /dev/null
@@ -1,31 +0,0 @@
-# -*- makefile -*- to build Colvars module with MinGW 32-bit
-
-EXTRAMAKE = Makefile.lammps.empty
-
-COLVARS_LIB = libcolvars.a
-COLVARS_OBJ_DIR = Obj_mingw64/
-
-CXX =		i686-w64-mingw32-g++
-CXXFLAGS =	-O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-fno-rtti -fno-exceptions -finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized
-AR =		i686-w64-mingw32-ar
-ARFLAGS =	-rscv
-SHELL =		/bin/sh
-
-.PHONY: default clean
-
-default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
-
-include Makefile.common
-
-$(COLVARS_OBJ_DIR):
-	mkdir $(COLVARS_OBJ_DIR)
-
-clean:
-	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-	-rmdir $(COLVARS_OBJ_DIR)
-
-Makefile.lammps:
-	-cp $(EXTRAMAKE) Makefile.lammps
diff --git a/lib/colvars/Makefile.mingw32-cross-mpi b/lib/colvars/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46..000000000
--- a/lib/colvars/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw32-cross
-	-rm -f Obj_mingw32-mpi
-	ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	-rm -f Obj_mingw32-mpi
-
diff --git a/lib/colvars/Makefile.mingw64-cross b/lib/colvars/Makefile.mingw64-cross
deleted file mode 100644
index 2fd1c6fc6..000000000
--- a/lib/colvars/Makefile.mingw64-cross
+++ /dev/null
@@ -1,31 +0,0 @@
-# -*- makefile -*- to build Colvars module with MinGW 32-bit
-
-EXTRAMAKE = Makefile.lammps.empty
-
-COLVARS_LIB = libcolvars.a
-COLVARS_OBJ_DIR = Obj_mingw32/
-
-CXX =		x86_64-w64-mingw32-g++
-CXXFLAGS =	-O2 -march=core2 -mtune=core2 -mpc64 -msse2		\
-		-fno-rtti -fno-exceptions -finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized
-AR =		x86_64-w64-mingw32-ar
-ARFLAGS =	-rscv
-SHELL =		/bin/sh
-
-.PHONY: default clean
-
-default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
-
-include Makefile.common
-
-$(COLVARS_OBJ_DIR):
-	mkdir $(COLVARS_OBJ_DIR)
-
-clean:
-	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-	-rmdir $(COLVARS_OBJ_DIR)
-
-Makefile.lammps:
-	-cp $(EXTRAMAKE) Makefile.lammps
diff --git a/lib/colvars/Makefile.mingw64-cross-mpi b/lib/colvars/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d4..000000000
--- a/lib/colvars/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw64-cross
-	-rm -f Obj_mingw64-mpi
-	ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	-rm -f Obj_mingw64-mpi
-
diff --git a/lib/colvars/Makefile.mpi b/lib/colvars/Makefile.mpi
new file mode 100644
index 000000000..6343ed7c0
--- /dev/null
+++ b/lib/colvars/Makefile.mpi
@@ -0,0 +1,25 @@
+# -*- makefile -*- to build Colvars module with default MPI compiler wrapper
+
+EXTRAMAKE = Makefile.lammps.empty
+
+COLVARS_LIB = libcolvars.a
+COLVARS_OBJ_DIR =
+
+CXX =		mpicxx
+CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops
+AR =		ar
+ARFLAGS =	-rscv
+SHELL =		/bin/sh
+
+.PHONY: default clean
+
+default: $(COLVARS_LIB) Makefile.lammps
+
+include Makefile.common
+
+clean:
+	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
+
+Makefile.lammps:
+	-cp $(EXTRAMAKE) Makefile.lammps
+
diff --git a/lib/colvars/Makefile.serial b/lib/colvars/Makefile.serial
new file mode 100644
index 000000000..556e39d07
--- /dev/null
+++ b/lib/colvars/Makefile.serial
@@ -0,0 +1,25 @@
+# -*- makefile -*- to build Colvars module with GNU compiler
+
+EXTRAMAKE = Makefile.lammps.empty
+
+COLVARS_LIB = libcolvars.a
+COLVARS_OBJ_DIR =
+
+CXX =		g++
+CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops
+AR =		ar
+ARFLAGS =	-rscv
+SHELL =		/bin/sh
+
+.PHONY: default clean
+
+default: $(COLVARS_LIB) Makefile.lammps
+
+include Makefile.common
+
+clean:
+	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
+
+Makefile.lammps:
+	-cp $(EXTRAMAKE) Makefile.lammps
+
diff --git a/lib/h5md/Makefile.h5cc b/lib/h5md/Makefile.h5cc
index bd3e8a978..9feed2d74 100644
--- a/lib/h5md/Makefile.h5cc
+++ b/lib/h5md/Makefile.h5cc
@@ -1,33 +1,38 @@
 EXTRAMAKE=Makefile.lammps.empty
 
 CC=h5cc
 
 # -DH5_NO_DEPRECATED_SYMBOLS is required here to ensure we are using
 # the v1.8 API when HDF5 is configured to default to using the v1.6 API.
 CFLAGS=-D_DEFAULT_SOURCE -O2 -DH5_NO_DEPRECATED_SYMBOLS  -Wall -fPIC
 HDF5_PATH=/usr
 INC=-I include
 AR=ar
 ARFLAGS=rc
-LIB=libch5md.a
+# need to build two libraries to not break compatibility and to support Install.py
+LIB=libh5md.a libch5md.a
 
 all: lib Makefile.lammps
 
 build:
 	mkdir -p build
+
 build/ch5md.o: src/ch5md.c | build
 	$(CC) $(INC) $(CFLAGS) -c $< -o $@
 
 Makefile.lammps:
 	cp $(EXTRAMAKE) $@
 
 .PHONY: all lib clean
 
-$(LIB): build/ch5md.o
-	$(AR) $(ARFLAGS) $(LIB) build/ch5md.o
+libch5md.a : build/ch5md.o
+	$(AR) $(ARFLAGS) $@ build/ch5md.o
+
+libh5md.a : build/ch5md.o
+	$(AR) $(ARFLAGS) $@ build/ch5md.o
 
 lib: $(LIB)
 
 clean:
 	rm -f build/*.o $(LIB)
 
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
deleted file mode 100644
index 560afecec..000000000
--- a/lib/linalg/Install.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-
-# install.py tool to do build of the linear algebra library
-# used to automate the steps described in the README file in this dir
-
-import sys,commands,os
-
-# help message
-
-help = """
-Syntax from src dir: make lib-linalg args="-m machine"
-Syntax from lib dir: python Install.py -m machine
-
-  -m = peform a clean followed by "make -f Makefile.machine"
-       machine = suffix of a lib/Makefile.* file
-
-Example:
-
-make lib-linalg args="-m gfortran"   # build with GNU Fortran compiler
-"""
-
-# print error message or help
-
-def error(str=None):
-  if not str: print help
-  else: print "ERROR",str
-  sys.exit()
-
-# parse args
-
-args = sys.argv[1:]
-nargs = len(args)
-if nargs == 0: error()
-
-machine = None
-
-iarg = 0
-while iarg < nargs:
-  if args[iarg] == "-m":
-    if iarg+2 > nargs: error()
-    machine = args[iarg+1]
-    iarg += 2  
-  else: error()
-
-# set lib from working dir
-
-cwd = os.getcwd()
-lib = os.path.basename(cwd)
-
-# make the library
-
-print "Building lib%s.a ..." % lib
-cmd = "make -f Makefile.%s clean; make -f Makefile.%s" % (machine,machine)
-txt = commands.getoutput(cmd)
-print txt
-
-if os.path.exists("lib%s.a" % lib): print "Build was successful"
-else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
diff --git a/lib/linalg/Makefile.gfortran b/lib/linalg/Makefile.gfortran
index 89b7f2d7a..7e1d97a5b 100644
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
@@ -1,54 +1,52 @@
 # -*- makefile -*-
 # *_________________________________________________________________________*
 # *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
 
 SHELL = /bin/sh
 
 # ------ FILES ------
 
 SRC =	$(wildcard *.f)
 
 FILES = $(SRC) Makefile.* README
 
 # ------ DEFINITIONS ------
 
 LIB = liblinalg.a
 OBJ =   $(SRC:.f=.o)
 
 # ------ SETTINGS ------
 
 FC =           gfortran
-FFLAGS =      -O3 -fPIC -march=native -mpc64  \
-         -ffast-math -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -fno-second-underscore
-FFLAGS0 =      -O0 -fPIC -march=native -mpc64  \
-         -Wall -W -Wno-uninitialized -fno-second-underscore
+FFLAGS =      -O3 -fPIC -ffast-math -fstrict-aliasing -fno-second-underscore
+FFLAGS0 =     -O0 -fPIC -fno-second-underscore
 ARCHIVE =	ar
 AR =	ar
 ARCHFLAG =	-rcs
 USRLIB =
 SYSLIB =
 
 # ------ MAKE PROCEDURE ------
 
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 
 # ------ COMPILE RULES ------
 
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 
 %.o:%.f
 	$(FC) $(FFLAGS) -c $<
 
 dlamch.o: dlamch.f
 	$(FC) $(FFLAGS0) -c $<
 
 # ------ CLEAN ------
 
 clean:
-	-rm *.o *.mod *~ $(LIB)
+	-rm -f *.o *.mod *~ $(LIB)
 
 tar:
 	-tar -czvf ../linalg.tar.gz $(FILES)
 
diff --git a/lib/linalg/Makefile.mingw32-cross b/lib/linalg/Makefile.mingw32-cross
deleted file mode 100644
index 02aa3f71a..000000000
--- a/lib/linalg/Makefile.mingw32-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# -*- makefile -*-
-# *_________________________________________________________________________*
-# *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
-
-SHELL = /bin/sh
-
-# ------ FILES ------
-
-SRC =	$(wildcard *.f)
-
-FILES = $(SRC) Makefile.* README
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32/
-LIB = $(DIR)liblinalg.a
-OBJ =   $(SRC:%.f=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-FC =    	i686-w64-mingw32-gfortran
-FFLAGS =	-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-ffast-math -funroll-loops -fstrict-aliasing -Wall -W	\
-		-Wno-uninitialized -fno-second-underscore
-FFLAGS0 =	-O0 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-Wall -W -Wno-uninitialized -fno-second-underscore
-ARCHIVE =	i686-w64-mingw32-ar
-AR =		i686-w64-mingw32-ar
-ARCHFLAG =	-rcs
-USRLIB =
-SYSLIB =
-
-.PHONY: default clean tar
-
-.SUFFIXES:
-.SUFFIXES: .F .f .o
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB)
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-
-$(DIR):
-	mkdir $(DIR)
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.F
-	$(F90) $(F90FLAGS) -c $< -o $@
-
-$(DIR)%.o:%.f
-	$(FC) $(FFLAGS) -c $< -o $@
-
-$(DIR)dlamch.o: dlamch.f
-	$(FC) $(FFLAGS0) -c $< -o $@
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-	-rmdir $(DIR)
-
-tar:
-	-tar -czvf ../linalg.tar.gz $(FILES)
-
diff --git a/lib/linalg/Makefile.mingw32-cross-mpi b/lib/linalg/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46..000000000
--- a/lib/linalg/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw32-cross
-	-rm -f Obj_mingw32-mpi
-	ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	-rm -f Obj_mingw32-mpi
-
diff --git a/lib/linalg/Makefile.mingw64-cross b/lib/linalg/Makefile.mingw64-cross
deleted file mode 100644
index ee6eef819..000000000
--- a/lib/linalg/Makefile.mingw64-cross
+++ /dev/null
@@ -1,67 +0,0 @@
-# -*- makefile -*-
-# *_________________________________________________________________________*
-# *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
-
-SHELL = /bin/sh
-
-# ------ FILES ------
-
-SRC =	$(wildcard *.f)
-
-FILES = $(SRC) Makefile.* README
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64/
-LIB = $(DIR)liblinalg.a
-OBJ =   $(SRC:%.f=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-FC =    	x86_64-w64-mingw32-gfortran
-FFLAGS =	-O3 -march=core2 -mtune=generic -msse2 -mpc64	\
-		-ffast-math -funroll-loops -fstrict-aliasing -Wall -W	\
-		-Wno-uninitialized -fno-second-underscore
-FFLAGS0 =	-O0 -march=core2 -mtune=generic -msse2 -mpc64	\
-		-Wall -W -Wno-uninitialized -fno-second-underscore
-ARCHIVE =	x86_64-w64-mingw32-ar
-AR =		x86_64-w64-mingw32-ar
-ARCHFLAG =	-rcs
-USRLIB =
-SYSLIB =
-
-.PHONY: default clean tar
-
-.SUFFIXES:
-.SUFFIXES: .F .f .o
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB)
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-
-$(DIR):
-	mkdir $(DIR)
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.F
-	$(F90) $(F90FLAGS) -c $< -o $@
-
-$(DIR)%.o:%.f
-	$(FC) $(FFLAGS) -c $< -o $@
-
-$(DIR)dlamch.o: dlamch.f
-	$(FC) $(FFLAGS0) -c $< -o $@
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-	-rmdir $(DIR)
-
-tar:
-	-tar -czvf ../linalg.tar.gz $(FILES)
-
diff --git a/lib/linalg/Makefile.mingw64-cross-mpi b/lib/linalg/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d4..000000000
--- a/lib/linalg/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw64-cross
-	-rm -f Obj_mingw64-mpi
-	ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	-rm -f Obj_mingw64-mpi
-
diff --git a/lib/linalg/Makefile.serial b/lib/linalg/Makefile.serial
new file mode 120000
index 000000000..c52fbcb98
--- /dev/null
+++ b/lib/linalg/Makefile.serial
@@ -0,0 +1 @@
+Makefile.gfortran
\ No newline at end of file