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Improve efficiency when reading and writing TAS slices. First, the fits_write_subset() call can do a lot of file seeking and reading. Instead, and if the image to be written is contiguous in memory, use the fits_write_img() call. Second, cache the desirable parts of the fits file header. If you don't do this, and then you request something like bitpix from cfitsio, it might have to seek to the header part of the file and re-read in the bitpix part of the header. This could happen easily as cfitsio buffers file access, and the number of buffers is small. cfitsio doesn't save the header in a structure - it lives only in these ephemeral buffers.

VPATH  = $(SRCDIR)
STATIC = 
DBNAME = POSTGRESQL

# This optional file has custom definitions created by the configure script
-include $(SRCDIR)/custom.mk

# USED BY NEITHER linux_x86_64 nor linux_ia32
PGIPATH	= /usr/include/pgsql	

ifeq ($(JSOC_MACHINE), mac_osx) 
COMPILER = gcc
else
COMPILER = icc
endif

# Check for debug vs. release build - release is default.
#   To do a debug build, either set the environment variable JSOC_DEBUG to 1, OR
#   modify the following line so that DEBUG = 1.  The environment variable takes precedence.
DEBUG = 1

ifdef JSOC_DEBUG
ifeq ($(JSOC_DEBUG), 1)
DEBUG = 1
else
DEBUG = 0
endif
endif

# No warnings are displayed, by default, for a release build.
WARN = 0

# Builder can request warnings via environment variable (setenv JSOC_WARN 1).  The
#   environment variable takes precedence.
ifdef JSOC_WARN
ifeq ($(JSOC_WARN), 1)
WARN = 1
else
WARN = 0
endif
endif

# Warnings are always displayed for a debug build.
ifeq ($(DEBUG), 1)
WARN = 1
endif

_JSOCROOT_ = ..

ifeq ($(JSOC_MACHINE), mac_osx) 
F77 = f77
else
F77 = ifort
endif

# if fortran compiler
D_GCC_FORT = 
ifeq ($(F77), ifort)
  D_GCC_FORT = -DINTEL_FORTRAN
endif

ifeq ($(JSOC_MACHINE), linux_x86_64)
  F77 = ifort -mcmodel=medium
endif

# Path to 3rd-party library headers
FMATHLIBSH = -I$(_JSOCROOT_)/lib_third_party/include
CFITSIOH = -I$(_JSOCROOT_)/lib_third_party/include
GSLH = -I$(_JSOCROOT_)/lib_third_party/include

ifeq ($(JSOC_MACHINE), linux_x86_64) 
#    FMATHLIBS = -lmkl_lapack -lmkl -L$(_JSOCROOT_)/lib_third_party/lib/linux-x86_64/ -lfftw3f -lcfitsio
  # Path to 64-bit 3rd-party libraries
  FMATHLIBSL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_x86_64/
  CFITSIOL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_x86_64/
  GSLL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_x86_64/
  ECPGL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_x86_64/
endif
ifeq ($(JSOC_MACHINE), linux_ia32) 
#    FMATHLIBS = -lmkl_lapack -lmkl -L$(_JSOCROOT_)/lib_third_party/lib/linux-ia32/ -lfftw3f -lcfitsio
  # Path to 32-bit 3rd-party libraries
  FMATHLIBSL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_ia32/
  CFITSIOL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_ia32/
  GSLL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_ia32/
  ECPGL = -L$(_JSOCROOT_)/lib_third_party/lib/linux_ia32/
endif
ifeq ($(JSOC_MACHINE), mac_osx) 
#    FMATHLIBS = -lmkl_lapack -lmkl -L$(_JSOCROOT_)/lib_third_party/lib/linux-ia32/ -lfftw3f -lcfitsio
  # Path to 32-bit 3rd-party libraries
  FMATHLIBSL = -L$(_JSOCROOT_)/lib_third_party/lib/mac_osx/
  CFITSIOL = -L$(_JSOCROOT_)/lib_third_party/lib/mac_osx/
  GSLL = -L$(_JSOCROOT_)/lib_third_party/lib/mac_osx/
  ECPGL = -L$(_JSOCROOT_)/lib_third_party/lib/mac_osx/
endif

# All 3rd-party math libraries - local rules can define a subset
FMATHLIBS = $(FMATHLIBSL) -lfftw3f -lcfitsio
CFITSIOLIBS = $(CFITSIOL) -lcfitsio

ifeq ($(COMPILER), gcc)
	ifeq ($(JSOC_MACHINE), linux_x86_64) 
		ifneq ($(CFITSIOFNAME_GCC_X86_64),)
			FMATHLIBS = $(FMATHLIBSL) -lfftw3f -l$(CFITSIOFNAME_GCC_X86_64)
			CFITSIOLIBS = $(CFITSIOL) -l$(CFITSIOFNAME_GCC_X86_64)
		endif
	endif
endif

GSLLIBS = $(GSLL) -lgsl -lgslcblas 

### Build flags for all targets
#
LL_ALL		= $(SYSLIBS)

GCC_LF_ALL	= $(STATIC) -g 
ifeq ($(JSOC_MACHINE), linux_ia64)
  ICC_LF_ALL	= $(STATIC)
else
  ICC_LF_ALL	= $(STATIC) -xW
endif

GCC_CF_GCCCOMP  = -DGCCCOMP $(D_GCC_FORT)
ICC_CF_ICCCOMP  = -DICCCOMP $(D_GCC_FORT)

# Disable several warnings/remarks when compiling with icc - icc's Wall is a bit picky, it 
# complains about extern declarations in .c files.
#   1418 (remark) - external function definition with no prior declaration
#   1419 (warning) - external declaration in primary source file
#   310 (remark) - old style function declaration (pre-ANSI)
#   981 (remark) - operands are evaluted in unspecified order

ifeq ($(WARN), 1)
# Show warnings (always true for a debug build).
ICC_WARN = -Winline -Wall -wd1418 -wd1419 -wd310 -wd279 -wd981 -Wno-comment
GCC_WARN = -Winline -Wall -Wno-comment
F77_WARN =
else
# Don't show warnings.
ICC_WARN = -w0 -vec-report0 -Wno-comment
GCC_WARN = -Wno-comment
F77_WARN = -vec-report0
endif

# can't figure out how to get stupid make to do if/else if/else
ifeq ($(DEBUG), 0)
  GCC_CF_ALL	= -I$(SRCDIR)/base/include -std=gnu99 -O2 $(GCC_WARN) $(GCC_CF_GCCCOMP)
  ICC_CF_ALL = -I$(SRCDIR)/base/include -std=c99 -xW $(ICC_WARN) $(ICC_CF_ICCCOMP)

  ifeq ($(JSOC_MACHINE), linux_x86_64)
    GCC_CF_ALL	= -I$(SRCDIR)/base/include -std=gnu99 -O2 -march=opteron $(GCC_WARN) $(GCC_CF_GCCCOMP)
  endif

  ifeq ($(JSOC_MACHINE), linux_ia64)
    GCC_CF_ALL	= -I$(SRCDIR)/base/include -std=gnu99 -O2 $(GCC_WARN) $(GCC_CF_GCCCOMP)
    ICC_CF_ALL	= -I$(SRCDIR)/base/include -std=c99 $(ICC_WARN) $(ICC_CF_ICCCOMP)
  endif

  ifeq ($(JSOC_MACHINE), linux_ia32)
    GCC_CF_ALL	= -I$(SRCDIR)/base/include -std=gnu99 -O2 -march=i686 $(GCC_WARN) $(GCC_CF_GCCCOMP)
  endif	

else

  GCC_CF_ALL = -I$(SRCDIR)/base/include -std=gnu99 -g $(GCC_WARN) $(GCC_CF_GCCCOMP)
  ICC_CF_ALL = -I$(SRCDIR)/base/include -std=c99 -g $(ICC_WARN) $(ICC_CF_ICCCOMP)

endif

# Fortran global LINK flags
F_LF_ALL	= -nofor_main -no-ipo

# Fortran global COMPILE flags
ifeq ($(DEBUG), 0)
FF_ALL		= -xW -ftrapuv $(F77_WARN)
else
FF_ALL		= -ftrapuv $(F77_WARN)
endif

### Build tools
# 
# The C compiler named here must output full (header) dependencies in $(@).d.
# It may be necessary to create a script similar to ccd-gcc for your compiler.
# 
GCC_CMPLR	= $(SRCDIR)/build/ccd-gcc
ICC_CMPLR	= $(SRCDIR)/build/ccd-icc
ARCHIVE		= ar crus $@ $^

ECPG		= ecpg -o $@ -c $<
SWIG		= swig -perl5 -o $@ $<

GCC_COMP	= $(GCC_CMPLR) $(GCC_CF_ALL) $(CF_TGT) -o $@ -c $<
ICC_COMP	= $(ICC_CMPLR) $(ICC_CF_ALL) $(CF_TGT) -o $@ -c $<

GCC_LINK	= $(GCC_CMPLR) $(GCC_LF_ALL) $(LF_TGT) -o $@ $^ $(LL_TGT) $(LL_ALL)
ICC_LINK	= $(ICC_CMPLR) $(ICC_LF_ALL) $(LF_TGT) -o $@ $^ $(LL_TGT) $(LL_ALL)

GCC_COMPLINK	= $(GCC_CMPLR) $(GCC_CF_ALL) $(CF_TGT) $(GCC_LF_ALL) $(LF_TGT) -o $@ $< $(LL_TGT) $(LL_ALL)
ICC_COMPLINK	= $(ICC_CMPLR) $(GCC_CF_ALL) $(CF_TGT) $(ICC_LF_ALL) $(LF_TGT) -o $@ $< $(LL_TGT) $(LL_ALL)

ifneq ($(COMPILER), icc)
  COMP 		= $(GCC_COMP)
  LINK		= $(GCC_LINK)
  COMPLINK	= $(GCC_COMPLINK)
else
  COMP 		= $(ICC_COMP)
  LINK		= $(ICC_LINK)
  COMPLINK	= $(ICC_COMPLINK)
endif

FCOMP		= $(F77) $(FF_ALL) $(FF_TGT) -o $@ -c $<
FLINK		= $(F77) $(F_LF_ALL) $(LF_TGT) -o $@ $^ $(LL_TGT) $(LL_ALL)

SLBIN           = ln -sf ../../_$(JSOC_MACHINE)/$@ ../bin/$(JSOC_MACHINE)/
SLLIB		= ln -sf ../../_$(JSOC_MACHINE)/$@ ../lib/$(JSOC_MACHINE)/

ALL_LIBS_FPIC = $(LIBDRMSCLIENT_FPIC) $(LIBDBCLIENT_FPIC) $(LIBCMDPARAMS_FPIC) $(LIBTHREADUTIL_FPIC) $(LIBRICECOMP_FPIC) $(LIBDEFS_FPIC) $(LIBDSTRUCT_FPIC) $(LIBMISC_FPIC) $(LIBTIMEIO_FPIC) $(LIBFITSRW_FPIC) 

### Standard parts
#
include	$(SRCDIR)/Rules.mk

# Libraries from src/util linked with all programs.
ifneq ($(COMPILER), icc)
  SYSLIBS = -lz -ldl -lpthread -lm
else
  SYSLIBS = -lz -ldl -lpthread
endif
SRCLIBS = $(LIBTHREADUTIL) $(LIBRICECOMP) $(LIBCMDPARAMS) $(LIBDEFS) $(LIBDSTRUCT) $(LIBTIMEIO) $(LIBFITSRW) $(LIBERRLOG) $(LIBMISC)
FSRCLIBS = $(LIBTHREADUTIL) $(LIBRICECOMP) $(LIBCMDPARAMSF) $(LIBDEFS) $(LIBDSTRUCT) $(LIBTIMEIO) $(LIBFITSRW) $(LIBERRLOG) $(LIBMISC)

########## Libraries to link for server executables,    ##############
########## standalone executables and pipeline modules. ##############

# SERVERLIBS: Libraries linked with "server" programs that 
# need direct access to the DRMS databases.
SERVERLIBS = $(LIBDRMS) $(LIBDB) $(LIBSUMSAPI) $(SRCLIBS)

# EXELIBS: Libraries linked with standalone executables.
EXELIBS = $(LIBDRMSCLIENT) $(LIBDBCLIENT) $(SRCLIBS)

# MODLIBS: Libraries linked with DRMS modules.
MODLIBS = $(LIBJSOC_MAIN) $(SERVERLIBS)

# MODLIBS_SOCK: Libraries linked with DRMS modules with socket connection to a drms_server
MODLIBS_SOCK = $(LIBJSOC_MAIN_SOCK) $(LIBDRMSCLIENT) $(LIBDBCLIENT) $(SRCLIBS)

# FMODLIBS: Libraries linked with DRMS Fortran modules
FMODLIBS_SOCK = $(LIBJSOC_MAIN_SOCK_F) $(LIBINTHANDLESF) $(LIBDRMSCLIENT) $(LIBDBCLIENT) $(FSRCLIBS)

MATHLIBS =  $(LIBLSQR) $(LIBBLAS) $(LIBLAPACK)

# Make rules that apply to all projects outside of the base DRMS/SUMS system
-include $(SRCDIR)/proj/make_basic.mk

# Make rules that apply to all projects, inside and outside of the base DRMS/SUMS system
$(CEXE):	%:	%.o $(EXELIBS)
		$(LINK)
		$(SLBIN)

$(FEXE):	%:	%.o $(MATHLIBS)
		$(FLINK)
		$(SLBIN)

$(SERVEREXE):   LL_TGT := $(LL_TGT) -lpq $(CFITSIOLIBS)
$(SERVEREXE):	%:	%.o $(SERVERLIBS)
			$(LINK)
			$(SLBIN)

$(MODEXE):      LL_TGT := $(LL_TGT) -lpq $(CFITSIOLIBS)
$(MODEXE):	%:	%.o $(MODLIBS)
			$(LINK)
			$(SLBIN)

$(MODEXE_SOCK):	LL_TGT := $(LL_TGT) $(CFITSIOLIBS)
$(MODEXE_SOCK): %_sock: %.o $(MODLIBS_SOCK)
			$(LINK)
			$(SLBIN)

$(FMODEXE):	LL_TGT := $(LL_TGT) $(CFITSIOLIBS)
$(FMODEXE):     %_sock:	%.o $(FMODLIBS_SOCK)
			$(FLINK)
			$(SLBIN)

$(MODEXE_USEF):	LL_TGT := $(LL_TGT) -lpq $(CFITSIOLIBS)
$(MODEXE_USEF):     %:	%.o $(MODLIBS)
			$(FLINK)
			$(SLBIN)

$(MODEXE_USEF_SOCK):	LL_TGT := $(LL_TGT) $(CFITSIOLIBS)
$(MODEXE_USEF_SOCK): %_sock: %.o $(MODLIBS_SOCK)
			$(FLINK)
			$(SLBIN)