diff --git a/.gitmodules b/.gitmodules
index cab59ea7b..9131d0ff2 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,7 +1,3 @@
-[submodule "nems/lib/ParallelIO"]
-	path = nems/lib/ParallelIO
-	url = https://github.com/NCAR/ParallelIO.git
-	branch = master
 [submodule "nems/lib/genf90"]
 	path = nems/lib/genf90
 	url = https://github.com/PARALLELIO/genf90
diff --git a/Makefile b/Makefile
index 1ddc4f357..169bf8228 100644
--- a/Makefile
+++ b/Makefile
@@ -22,9 +22,6 @@ endif
 MEDIATOR_DIR := $(BASE_DIR)/mediator
 LIBRARY_MEDIATOR := $(MEDIATOR_DIR)/libcmeps.a
 LIBRARY_UTIL := $(BASE_DIR)/nems/util/libcmeps_util.a
-PIO_INSTALL_DIR := $(BASE_DIR)/nems/lib/ParallelIO/install
-PIO_INSTALL_LIBS := $(PIO_INSTALL_DIR)/lib/libpiof.a
-PIO_INCLUDE_DIR := $(PIO_INSTALL_DIR)/include
 
 all default: install
 
@@ -39,11 +36,9 @@ else
 	@echo "ESMF_DEP_FRONT     = MED" >> cmeps.mk.install
 	@echo "ESMF_DEP_INCPATH   = $(INSTALLDIR)/include" >> cmeps.mk.install
 	@echo "ESMF_DEP_CMPL_OBJS = " >> cmeps.mk.install
-	@echo "ESMF_DEP_LINK_OBJS = $(INSTALLDIR)/libcmeps.a $(INSTALLDIR)/libcmeps_util.a $(INSTALLDIR)/libpiof.a $(INSTALLDIR)/libpioc.a $(PNETCDF_LD_OPTS)" >> cmeps.mk.install
+	@echo "ESMF_DEP_LINK_OBJS = $(INSTALLDIR)/libcmeps.a $(INSTALLDIR)/libcmeps_util.a $(PIO_ROOT)/lib/libpiof.a $(PIO_ROOT)/lib/libpioc.a $(PNETCDF_LD_OPTS)" >> cmeps.mk.install
 	mkdir -p $(INSTALLDIR)
 	mkdir -p $(INSTALLDIR)/include
-	cp -f $(PIO_INSTALL_DIR)/lib/*.a $(INSTALLDIR)
-	cp -f $(PIO_INSTALL_DIR)/include/* $(INSTALLDIR)/include
 	cp -f $(LIBRARY_UTIL) $(INSTALLDIR)
 	cp -f $(LIBRARY_MEDIATOR) $(INSTALLDIR)
 	cp -f mediator/*.mod $(INSTALLDIR)/include
@@ -53,23 +48,16 @@ endif
 
 $(LIBRARY_MEDIATOR): $(LIBRARY_UTIL) .FORCE
 	cd mediator ;\
-	exec $(MAKE) PIO_INCLUDE_DIR=$(PIO_INCLUDE_DIR) INTERNAL_PIO_INIT=1
+	exec $(MAKE) INTERNAL_PIO_INIT=1
 
-$(LIBRARY_UTIL): $(PIO_INSTALL_LIBS) .FORCE
+$(LIBRARY_UTIL): .FORCE
 	cd nems/util ;\
-	exec $(MAKE) PIO_INCLUDE_DIR=$(PIO_INCLUDE_DIR) 
-
-$(PIO_INSTALL_LIBS):
-	cd nems/lib ;\
-	exec $(MAKE) install FC="$(FC)" CC="$(CC)" CXX="$(CXX)" PIO_INSTALL_DIR=$(PIO_INSTALL_DIR)
+	exec $(MAKE)
 
 .FORCE:
 
 clean:
 	cd mediator; \
-	exec $(MAKE) clean PIO_INCLUDE_DIR=$(PIO_INCLUDE_DIR)
+	exec $(MAKE) clean
 	cd nems/util; \
-	exec $(MAKE) clean PIO_INCLUDE_DIR=$(PIO_INCLUDE_DIR)
-	cd nems/lib; \
-	exec $(MAKE) clean PIO_INSTALL_DIR=$(PIO_INSTALL_DIR)
-
+	exec $(MAKE) clean
diff --git a/mediator/Makefile b/mediator/Makefile
index d40272a19..517749140 100644
--- a/mediator/Makefile
+++ b/mediator/Makefile
@@ -5,10 +5,6 @@ endif
 include $(ESMFMKFILE)
 CPPDEFS += -DESMF_VERSION_MAJOR=$(ESMF_VERSION_MAJOR) -DESMF_VERSION_MINOR=$(ESMF_VERSION_MINOR)
 
-ifndef PIO_INCLUDE_DIR
-$(error PIO_INCLUDE_DIR not set)
-endif
-
 ifdef INTERNAL_PIO_INIT
 CPPDEFS += -DINTERNAL_PIO_INIT
 endif
@@ -23,7 +19,7 @@ $(LIBRARY): $(OBJ)
 	$(AR) $(ARFLAGS) $@ $?
 
 %.o: %.F90 
-	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) $(CPPDEFS) -I${PIO_INCLUDE_DIR} -I../nems/util $*.F90
+	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) $(CPPDEFS) -I$(PIO_ROOT)/include -I../nems/util $*.F90
 
 clean:
 	$(RM) -f $(LIBRARY) *.i90 *.o *.mod
diff --git a/nems/lib/Makefile b/nems/lib/Makefile
deleted file mode 100644
index 0da2ec4e0..000000000
--- a/nems/lib/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-ifndef NETCDF
-ifndef PNETCDF
-$(error NETCDF or PNETCDF must be set to build PIO)
-endif
-endif
-
-ifndef PIO_INSTALL_DIR
-$(error PIO_INSTALL_DIR must be set)
-endif
-
-BASE_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
-PIO_SRC_DIR := "$(BASE_DIR)/ParallelIO"
-PIO_BUILD_DIR := "$(BASE_DIR)/ParallelIO/build"
-
-CMAKE_ENV_VARS := CC="$(CC)"   \
-                  CXX="$(CXX)" \
-                  FC="$(FC)"
-
-CMAKE_OPTS := -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON \
-              -D PIO_ENABLE_TESTS:BOOL=OFF \
-              -D PIO_ENABLE_TIMING:BOOL=OFF \
-              -D PIO_USE_MALLOC:BOOL=ON \
-              -D GENF90_PATH=$(BASE_DIR)/genf90 \
-              -D USER_CMAKE_MODULE_PATH=$(PIO_SRC_DIR)/cmake \
-              -D CMAKE_INSTALL_PREFIX=$(PIO_INSTALL_DIR)  
-
-ifdef NETCDF
-CMAKE_OPTS += -D NetCDF_PATH:PATH=$(NETCDF)
-endif
-
-ifdef PNETCDF
-CMAKE_OPTS += -D PnetCDF_PATH:STRING=$(PNETCDF)
-else
-CMAKE_OPTS += -D WITH_PNETCDF=OFF
-endif
-
-.PHONY: install build clean
-
-install: build
-
-build: $(PIO_BUILD_DIR)/Makefile
-	cd $(PIO_BUILD_DIR); \
-	exec $(MAKE) install
-
-$(PIO_BUILD_DIR)/Makefile:
-	mkdir -p $(PIO_BUILD_DIR); \
-	cd $(PIO_BUILD_DIR); \
-	$(CMAKE_ENV_VARS) cmake $(CMAKE_OPTS) ../
-
-clean:
-	rm -rf $(PIO_BUILD_DIR)
-	rm -rf $(PIO_INSTALL_DIR)
diff --git a/nems/lib/ParallelIO b/nems/lib/ParallelIO
deleted file mode 160000
index 86ad4463a..000000000
--- a/nems/lib/ParallelIO
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 86ad4463ab46e706aca632c2c4c2ffd48854113b
diff --git a/nems/util/Makefile b/nems/util/Makefile
index 665bcb136..58b97df4f 100644
--- a/nems/util/Makefile
+++ b/nems/util/Makefile
@@ -4,10 +4,6 @@ endif
 
 include $(ESMFMKFILE)
 
-ifndef PIO_INCLUDE_DIR
-$(error PIO_INCLUDE_DIR should point to PIO include directory.)
-endif
-
 LIBRARY  = libcmeps_util.a
 
 OBJ1= \
@@ -30,10 +26,10 @@ $(LIBRARY): $(OBJ1)
 
 %.o: %.F90.in
 	perl genf90.pl $< > $(@:.o=.F90)
-	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) -I$(PIO_INCLUDE_DIR) -DFORTRANUNDERSCORE -DCPRINTEL $(@:.o=.F90)
+	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) -I$(PIO_ROOT)/include -DFORTRANUNDERSCORE -DCPRINTEL $(@:.o=.F90)
 
 %.o: %.F90
-	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) -I$(PIO_INCLUDE_DIR) -I. $*.F90
+	$(ESMF_F90COMPILER) -c $(ESMF_F90COMPILEOPTS) $(ESMF_F90COMPILEPATHS) -I$(PIO_ROOT)/include -I. $*.F90
 
 clean:
 	$(RM) -f $(LIBRARY) *.f90 *.i90 *.o *.mod