Simulink cross-compilation succeeded, application not working - c

Question

I am currently trying to compile a Simulink model for a SoC board that is running a Linux OS. I am able to compile and run applications successfully for this board making my own makefiles, which are really very simple.
The cross-compiler I am using is the
environment-setup-cortexa8hf-vfp-neon-poky-linux-gnueabi
Also, generating c code from a Simulink model and applying my makefile works as well. (With very simple simulink models)
The problem is when I try to generate code and also compile the simulink model with the following options:
ert.tcl
toolchain: automatic (GNU)
for: faster builds
This generates a binary that is working but I have to modify the makefile in order to compile the code with my cross-compiler. The cross-compilation works but when I try to run the application in the SoC board I get the following error:
-sh. ./application file not found
Here is the makefile:
###########################################################################
## Makefile generated for Simulink model 'simmod'.
##
## Makefile : simmod.mk
## Generated on : Tue Sep 11 14:57:43 2018
## MATLAB Coder version: 4.0 (R2018a)
##
## Build Info:
##
## Final product: $(RELATIVE_PATH_TO_ANCHOR)/simmod
## Product type : executable
## Build type : Top-Level Standalone Executable
##
###########################################################################
###########################################################################
## MACROS
###########################################################################
# Macro Descriptions:
# PRODUCT_NAME Name of the system to build
# MAKEFILE Name of this makefile
# COMPUTER Computer type. See the MATLAB "computer" command.
PRODUCT_NAME = simmod
MAKEFILE = simmod.mk
COMPUTER = GLNXA64
MATLAB_ROOT = /opt/MATLAB/R2018a
MATLAB_BIN = /opt/MATLAB/R2018a/bin
MATLAB_ARCH_BIN = $(MATLAB_BIN)/glnxa64
MASTER_ANCHOR_DIR =
START_DIR = /home/hector/Documents/Qt/DA_AMiRo/Devices/Reflective_Operator/Matlab_Reflective_Operator/temp
ARCH = glnxa64
SOLVER =
SOLVER_OBJ =
CLASSIC_INTERFACE = 0
TGT_FCN_LIB = ISO_C
MODEL_HAS_DYNAMICALLY_LOADED_SFCNS = 0
MODELREF_LINK_RSPFILE_NAME = simmod_ref.rsp
RELATIVE_PATH_TO_ANCHOR = ..
C_STANDARD_OPTS = -mfloat-abi=hard -std=gnu99 -pedantic -fwrapv #-std=c99
CPP_STANDARD_OPTS = -fwrapv
###########################################################################
## TOOLCHAIN SPECIFICATIONS
###########################################################################
# Toolchain Name: GNU gcc/g++ v4.4.x | gmake (64-bit Linux)
# Supported Version(s): 4.4.x
# ToolchainInfo Version: R2018a
# Specification Revision: 1.0
#
#-------------------------------------------
# Macros assumed to be defined elsewhere
#-------------------------------------------
# C_STANDARD_OPTS
# CPP_STANDARD_OPTS
#-----------
# MACROS
#-----------
WARN_FLAGS = -Wall -W -Wwrite-strings -Winline -Wstrict-prototypes -Wnested-externs -Wpointer-arith -Wcast-align
WARN_FLAGS_MAX = $(WARN_FLAGS) -Wcast-qual -Wshadow
CPP_WARN_FLAGS = -Wall -W -Wwrite-strings -Winline -Wpointer-arith -Wcast-align
CPP_WARN_FLAGS_MAX = $(CPP_WARN_FLAGS) -Wcast-qual -Wshadow
TOOLCHAIN_SRCS =
TOOLCHAIN_INCS =
TOOLCHAIN_LIBS =
#------------------------
# BUILD TOOL COMMANDS
#------------------------
# C Compiler: GNU C Compiler
CC = arm-poky-linux-gnueabi-gcc #gcc
# Linker: GNU Linker
LD = arm-poky-linux-gnueabi-g++ #g++
# C++ Compiler: GNU C++ Compiler
CPP = arm-poky-linux-gnueabi-g++ #g++
# C++ Linker: GNU C++ Linker
CPP_LD = arm-poky-linux-gnueabi-g++ #g++
# Archiver: GNU Archiver
AR = ar
# MEX Tool: MEX Tool
MEX_PATH = $(MATLAB_ARCH_BIN)
MEX = "$(MEX_PATH)/mex"
# Download: Download
DOWNLOAD =
# Execute: Execute
EXECUTE = $(PRODUCT)
# Builder: GMAKE Utility
MAKE_PATH = %MATLAB%/bin/glnxa64
MAKE = "$(MAKE_PATH)/gmake"
#-------------------------
# Directives/Utilities
#-------------------------
CDEBUG = -g
C_OUTPUT_FLAG = -o
LDDEBUG = -g
OUTPUT_FLAG = -o
CPPDEBUG = -g
CPP_OUTPUT_FLAG = -o
CPPLDDEBUG = -g
OUTPUT_FLAG = -o
ARDEBUG =
STATICLIB_OUTPUT_FLAG =
MEX_DEBUG = -g
RM = #rm -f
ECHO = #echo
MV = #mv
RUN =
#----------------------------------------
# "Faster Builds" Build Configuration
#----------------------------------------
ARFLAGS = ruvs
CFLAGS = -c $(C_STANDARD_OPTS) -fPIC \
-O0
CPPFLAGS = -c $(CPP_STANDARD_OPTS) -fPIC \
-O0
CPP_LDFLAGS = -Wl,-rpath,"$(MATLAB_ARCH_BIN)",-L"$(MATLAB_ARCH_BIN)"
CPP_SHAREDLIB_LDFLAGS = -shared -Wl,-rpath,"$(MATLAB_ARCH_BIN)",-L"$(MATLAB_ARCH_BIN)" -Wl,--no-undefined
DOWNLOAD_FLAGS =
EXECUTE_FLAGS =
LDFLAGS = -Wl,-rpath,"$(MATLAB_ARCH_BIN)",-L"$(MATLAB_ARCH_BIN)"
MEX_CPPFLAGS = -R2018a -MATLAB_ARCH=$(ARCH) $(INCLUDES) \
\
CXXOPTIMFLAGS="$(C_STANDARD_OPTS) \
-O0 \
$(DEFINES)" \
\
-silent
MEX_CPPLDFLAGS = LDFLAGS=='$$LDFLAGS'
MEX_CFLAGS = -R2018a -MATLAB_ARCH=$(ARCH) $(INCLUDES) \
\
COPTIMFLAGS="$(C_STANDARD_OPTS) \
-O0 \
$(DEFINES)" \
\
-silent
MEX_LDFLAGS = LDFLAGS=='$$LDFLAGS'
MAKE_FLAGS = -f $(MAKEFILE)
SHAREDLIB_LDFLAGS = -shared -Wl,-rpath,"$(MATLAB_ARCH_BIN)",-L"$(MATLAB_ARCH_BIN)" -Wl,--no-undefined
#--------------------
# File extensions
#--------------------
H_EXT = .h
OBJ_EXT = .o
C_EXT = .c
EXE_EXT =
SHAREDLIB_EXT = .so
HPP_EXT = .hpp
OBJ_EXT = .o
CPP_EXT = .cpp
EXE_EXT =
SHAREDLIB_EXT = .so
STATICLIB_EXT = .a
MEX_EXT = .mexa64
MAKE_EXT = .mk
###########################################################################
## OUTPUT INFO
###########################################################################
PRODUCT = $(RELATIVE_PATH_TO_ANCHOR)/simmod
PRODUCT_TYPE = "executable"
BUILD_TYPE = "Top-Level Standalone Executable"
###########################################################################
## INCLUDE PATHS
###########################################################################
INCLUDES_BUILDINFO = -I$(START_DIR) -I$(START_DIR)/simmod_ert_rtw -I$(MATLAB_ROOT)/extern/include -I$(MATLAB_ROOT)/simulink/include -I$(MATLAB_ROOT)/rtw/c/src -I$(MATLAB_ROOT)/rtw/c/src/ext_mode/common -I$(MATLAB_ROOT)/rtw/c/ert
INCLUDES = $(INCLUDES_BUILDINFO)
###########################################################################
## DEFINES
###########################################################################
DEFINES_BUILD_ARGS = -DCLASSIC_INTERFACE=0 -DALLOCATIONFCN=0 -DTERMFCN=1 -DONESTEPFCN=1 -DMAT_FILE=0 -DMULTI_INSTANCE_CODE=0 -DINTEGER_CODE=0 -DMT=0
DEFINES_IMPLIED = -DTID01EQ=0
DEFINES_STANDARD = -DMODEL=simmod -DNUMST=1 -DNCSTATES=0 -DHAVESTDIO -DMODEL_HAS_DYNAMICALLY_LOADED_SFCNS=0 -DUNIX
DEFINES = $(DEFINES_BUILD_ARGS) $(DEFINES_IMPLIED) $(DEFINES_STANDARD)
###########################################################################
## SOURCE FILES
###########################################################################
SRCS = $(START_DIR)/simmod_ert_rtw/simmod.c
MAIN_SRC = $(START_DIR)/simmod_ert_rtw/ert_main.c
ALL_SRCS = $(SRCS) $(MAIN_SRC)
###########################################################################
## OBJECTS
###########################################################################
OBJS = simmod.o
MAIN_OBJ = ert_main.o
ALL_OBJS = $(OBJS) $(MAIN_OBJ)
###########################################################################
## PREBUILT OBJECT FILES
###########################################################################
PREBUILT_OBJS =
###########################################################################
## LIBRARIES
###########################################################################
LIBS =
###########################################################################
## SYSTEM LIBRARIES
###########################################################################
SYSTEM_LIBS = -lm
###########################################################################
## ADDITIONAL TOOLCHAIN FLAGS
###########################################################################
#---------------
# C Compiler
#---------------
CFLAGS_BASIC = $(DEFINES) $(INCLUDES)
CFLAGS += $(CFLAGS_BASIC)
#-----------------
# C++ Compiler
#-----------------
CPPFLAGS_BASIC = $(DEFINES) $(INCLUDES)
CPPFLAGS += $(CPPFLAGS_BASIC)
###########################################################################
## INLINED COMMANDS
###########################################################################
###########################################################################
## PHONY TARGETS
###########################################################################
.PHONY : all build buildobj clean info prebuild download execute
all : build
#echo "### Successfully generated all binary outputs."
build : prebuild $(PRODUCT)
buildobj : prebuild $(OBJS) $(PREBUILT_OBJS)
#echo "### Successfully generated all binary outputs."
prebuild :
download : build
execute : download
#echo "### Invoking postbuild tool "Execute" ..."
$(EXECUTE) $(EXECUTE_FLAGS)
#echo "### Done invoking postbuild tool."
###########################################################################
## FINAL TARGET
###########################################################################
#-------------------------------------------
# Create a standalone executable
#-------------------------------------------
$(PRODUCT) : $(OBJS) $(PREBUILT_OBJS) $(MAIN_OBJ)
#echo "### Creating standalone executable "$(PRODUCT)" ..."
$(LD) $(LDFLAGS) -o $(PRODUCT) $(OBJS) $(MAIN_OBJ) $(SYSTEM_LIBS) $(TOOLCHAIN_LIBS)
#echo "### Created: $(PRODUCT)"
###########################################################################
## INTERMEDIATE TARGETS
###########################################################################
#---------------------
# SOURCE-TO-OBJECT
#---------------------
%.o : %.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : %.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
%.o : $(RELATIVE_PATH_TO_ANCHOR)/%.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : $(RELATIVE_PATH_TO_ANCHOR)/%.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
%.o : $(MATLAB_ROOT)/rtw/c/src/%.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : $(MATLAB_ROOT)/rtw/c/src/%.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
%.o : $(MATLAB_ROOT)/simulink/src/%.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : $(MATLAB_ROOT)/simulink/src/%.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
%.o : $(START_DIR)/%.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : $(START_DIR)/%.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
%.o : $(START_DIR)/simmod_ert_rtw/%.c
$(CC) $(CFLAGS) -o "$#" "$<"
%.o : $(START_DIR)/simmod_ert_rtw/%.cpp
$(CPP) $(CPPFLAGS) -o "$#" "$<"
###########################################################################
## DEPENDENCIES
###########################################################################
$(ALL_OBJS) : $(MAKEFILE) rtw_proj.tmw
###########################################################################
## MISCELLANEOUS TARGETS
###########################################################################
info :
#echo "### PRODUCT = $(PRODUCT)"
#echo "### PRODUCT_TYPE = $(PRODUCT_TYPE)"
#echo "### BUILD_TYPE = $(BUILD_TYPE)"
#echo "### INCLUDES = $(INCLUDES)"
#echo "### DEFINES = $(DEFINES)"
#echo "### ALL_SRCS = $(ALL_SRCS)"
#echo "### ALL_OBJS = $(ALL_OBJS)"
#echo "### LIBS = $(LIBS)"
#echo "### MODELREF_LIBS = $(MODELREF_LIBS)"
#echo "### SYSTEM_LIBS = $(SYSTEM_LIBS)"
#echo "### TOOLCHAIN_LIBS = $(TOOLCHAIN_LIBS)"
#echo "### CFLAGS = $(CFLAGS)"
#echo "### LDFLAGS = $(LDFLAGS)"
#echo "### SHAREDLIB_LDFLAGS = $(SHAREDLIB_LDFLAGS)"
#echo "### CPPFLAGS = $(CPPFLAGS)"
#echo "### CPP_LDFLAGS = $(CPP_LDFLAGS)"
#echo "### CPP_SHAREDLIB_LDFLAGS = $(CPP_SHAREDLIB_LDFLAGS)"
#echo "### ARFLAGS = $(ARFLAGS)"
#echo "### MEX_CFLAGS = $(MEX_CFLAGS)"
#echo "### MEX_CPPFLAGS = $(MEX_CPPFLAGS)"
#echo "### MEX_LDFLAGS = $(MEX_LDFLAGS)"
#echo "### MEX_CPPLDFLAGS = $(MEX_CPPLDFLAGS)"
#echo "### DOWNLOAD_FLAGS = $(DOWNLOAD_FLAGS)"
#echo "### EXECUTE_FLAGS = $(EXECUTE_FLAGS)"
#echo "### MAKE_FLAGS = $(MAKE_FLAGS)"
clean :
$(ECHO) "### Deleting all derived files..."
$(RM) $(PRODUCT)
$(RM) $(ALL_OBJS)
$(ECHO) "### Deleted all derived files."