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Huy Tran edited this page Nov 7, 2024 · 66 revisions

SMOKE Installation Instructions

DISCLAIMER: The below instructions aim at helping inexperienced users in compiling SMOKE (and its prerequisite libraries and software). These instructions had been tested on limited number of Linux operating systems with their specific configurations, and so they may not work on all other systems.

  • Instructions for I/O API
  • Instructions for SMOKE
  • Required fortran compilers: intel fortran (preferred) or gfortran compilers
  • Prerequisite libraries (Skip to Installations instructions for required packages if they are not pre-installed):

The following instructions presumes all software will be installed under a parent directory with environmental name $MASTERDIR

NOTE

  1. Although these instructions are for both gcc/gfortran and intel compilers, using gcc/gfortran is NOT recommended due to inconsistency in gcc. Using intel compiler is highly recommended.
  2. In high-performance cluster system, it is a common practice to have software compiled on one computer system (e.g., login node) and executed in another system (e.g., compute node). There is potential conflict in CPU instruction set if the software was compiled on system with newer CPU (e.g., with Intel CPU Xeon 6140) and then executed on system with older CPU (e.g., Intel Xeon E5-2463). It is recommended to have the software compiled on system with older CPU to maximize compatibility.

I/O API

cd $MASTERDIR
git clone https://github.com/cjcoats/ioapi-3.2.git ioapi-3.2

  • Change into $MASTERDIR/ioapi-3.2
    cd $MASTERDIR/ioapi-3.2

NOTE This instruction assumes all required software packages are precompiled under $MASTERDIR/ioapi-3.2/dependencies. If this not the case, follow Installations instructions for required packages in the subsequent sections.

  • Create $MASTERDIR/ioapi-3.2/IOAPI.config.csh with the following content
#!/bin/tcsh

unsetenv BIN

switch ( $#argv )
  case 0:
     echo "SCRIPT ERROR: BIN parameter <Linux2_x86_64ifort|Linux2_x86_64> must be set"
     exit(1)
  breaksw
  case 1:
     setenv BIN $argv[1]
  breaksw
  case 2:
  case 3:
endsw

 setenv IOAPI_HOME $MASTERDIR/ioapi-3.2
 setenv IOAPI_BASE $IOAPI_HOME
 setenv IOAPILIBS  ${IOAPI_HOME}/${BIN}
 setenv IOAPIINCD  ${IOAPI_HOME}/${BIN}
 setenv IOBIN      ${IOAPI_HOME}/${BIN}

 setenv BASEDIR    ${PWD}
 setenv INSTALL    ${PWD}
 setenv LIBINST    ${INSTALL}/${BIN}
 setenv BININST    ${INSTALL}/${BIN}
 setenv CPLMODE    nocpl
 setenv IOAPIDEFS  "-DIOAPI_NCF4" 
 setenv PVMINCL 
 setenv VERSION    '3.2-${CPLMODE}'

if ( ${BIN} == 'Linux2_x86_64' || ${BIN} == 'Linux2_x86_64gfortran' ) then
     #module load gcc/9.1.0
     setenv NETCDFC ${IOAPI_HOME}/dependencies/netcdfc.4.9.2_gcc
     setenv NETCDFF ${IOAPI_HOME}/dependencies/netcdff.4.6.1_gcc
     setenv HDF5    ${IOAPI_HOME}/dependencies/hdf5.1.14.3_gcc
     setenv SZIP    ${IOAPI_HOME}/dependencies/szip.2.1.1_gcc
     setenv ZLIB    ${IOAPI_HOME}/dependencies/zlib.1.3.1_gcc
     setenv NCFLIBS "-L${NETCDFF}/lib -L${NETCDFC}/lib -L${HDF5}/lib -L${SZIP}/lib -L${ZLIB}/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lsz -ldl"
endif
if ( ${BIN} == 'Linux2_x86_64ifort' || ${BIN} == 'Linux2_x86_64ifort_mediumdbg' ) then
     #module load intel/19.4
     setenv NETCDFC ${IOAPI_HOME}/dependencies/netcdfc.4.9.2_intel
     setenv NETCDFF ${IOAPI_HOME}/dependencies/netcdff.4.6.1_intel
     setenv HDF5    ${IOAPI_HOME}/dependencies/hdf5.1.14.3_intel
     setenv SZIP    ${IOAPI_HOME}/dependencies/szip.2.1.1_intel
     setenv ZLIB    ${IOAPI_HOME}/dependencies/zlib.1.3.1_intel
     setenv NCFLIBS "-L${NETCDFF}/lib -lnetcdff -L${NETCDFC}/lib -L${HDF5}/lib -L${SZIP}/lib -L${ZLIB}/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lsz"
endif
  • Create $MASTERDIR/ioapi-3.2/compile.ioapi.csh with the following content
#!/bin/tcsh

# Select either gfortran or intel fortran compiler
#setenv BIN Linux2_x86_64       # Using gfortran compiler
setenv BIN Linux2_x86_64ifort   # Using intel fortran compiler (ifort)
source ./IOAPI.config.csh $BIN

cd $IOAPI_HOME
make clean
make all >& compile.$BIN.log
  • Create Makefile from provide Makefile.template
    cp $MASTERDIR/ioapi-3.2/Makefile.template $MASTERDIR/ioapi-3.2/Makefile
  • Modify $MASTERDIR/ioapi-3.2/Makefile as follow
#      ----------   I/O API Build System directory definitions  --------

VERSION    = 3.2-${CPLMODE}
#BASEDIR    = ${PWD}              # No longer need cause it is defined in $MASTERDIR/ioapi-3.2/IOAPI.config.csh
#NCFLIBS    = -lnetcdff -lnetcdf  # No longer need cause it is defined in $MASTERDIR/ioapi-3.2/IOAPI.config.csh
IODIR      = $(BASEDIR)/ioapi
FIXDIR     = $(IODIR)/fixed_src
HTMLDIR    = $(BASEDIR)/HTML
TOOLDIR    = $(BASEDIR)/m3tools
OBJDIR     = $(BASEDIR)/$(BIN)
  • Also comment out the ${IODIR}/Makefile ${TOOLDIR}/Makefile in configure section in the in the $MASTERDIR/ioapi-3.2/Makefile 
configure: #${IODIR}/Makefile ${TOOLDIR}/Makefile
	(cd $(IODIR)   ;  sed $(SEDCMD) < Makefile.$(CPLMODE).sed > Makefile )
	(cd $(TOOLDIR) ;  sed $(SEDCMD) < Makefile.$(CPLMODE).sed > Makefile )
  • Modify $MASTERDIR/ioapi-3.2/ioapi/Makefile.nocpl.sed as follow
# Architecture dependent stuff

MAKEINCLUDE.$(BIN)
 
#DEFINEFLAGS  =                $(ARCHFLAGS) $(PARFLAGS)
#DEFINEFLAGS = -DIOAPICPL=1   $(ARCHFLAGS) $(PARFLAGS)
#DEFINEFLAGS = -DIOAPI_PNCF=1 $(ARCHFLAGS) $(PARFLAGS)
DEFINEFLAGS = -DIOAPI_NCF4=1 $(ARCHFLAGS) $(PARFLAGS)
#DEFINEFLAGS = -DIOAPI_PNCF=1 -DIOAPI_NCF4=1 $(ARCHFLAGS) $(PARFLAGS)

#VFLAG  = -DVERSION='3.2-cpl'
#VFLAG  = -DVERSION='3.2-cpl-mpi'
#VFLAG  = -DVERSION='3.2-cpl-ncf4'
#VFLAG  = -DVERSION='3.2-cpl-ncf4-mpi'
#VFLAG  = -DVERSION='3.2-nocpl-mpi'
VFLAG  = -DVERSION='3.2-nocpl-ncf4'
#VFLAG  = -DVERSION='3.2-nocpl-ncf4-mpi'
#VFLAG   = -DVERSION='3.2-nocpl'

NOTE for using Intel Fortran Compiler

  • Intel® C++ Compiler Classic (icc) is removed in the oneAPI 2024.0 release (see this link). See instructions for using intel oneAPI in the bellow optional sections.
  • Modify the $MASTERDIR/ioapi-3.2/ioapi/Makeinclude.Linux2_x86_64ifort as follow:
#OMPFLAGS  = -openmp      # for Intel compilers, version 15 or earlier
#OMPLIBS   = -openmp
 OMPFLAGS  = -qopenmp
 OMPLIBS   = -qopenmp -qopenmp-link=static -static-intel

COPTFLAGS = -O3 ${MFLAGS}
FOPTFLAGS = -O3 -unroll -stack-temps -safe-cray-ptr \
  -convert big_endian -assume byterecl  ${MFLAGS}

##No change to the remaining lines

NOTE for using gfortran compiler

  • Executable files compiled with gfortran always check for version of glibc on the OS system upon execution, and will crash if there is discrepancy in glibc version the files were compiled with and the one the OS system that they are executed on. This practice makes gfortran-compiled executable files not portable (i.e., files compiled on one system can not be executed on another system). For portability, intel fortran compiler is recommended.
  • Modify the $MASTERDIR/ioapi-3.2/ioapi/Makeinclude.Linux2_x86_64 as follow:
AR   = ar
CC   = gcc
CXX  = g++
FC   = gfortran
M4   = m4
LINK = $(CC) -static

## Module-include-directory command
MODI = -I
E132 = -ffixed-line-length-132

MFLAGS    = -ffast-math -funroll-loops -m64 -static # -march=native -mtune=native

OMPFLAGS  = -fopenmp
OMPLIBS   = -fopenmp
COPTFLAGS = -O3 ${MFLAGS}
FOPTFLAGS = -O3 -std=legacy ${MFLAGS}
FPPFLAGS  = -DF90=1
FSFLAGS   = -fno-automatic
ARCHFLAGS = \
 -DAUTO_ARRAYS=1 \
 -DF90=1 -DFLDMN=1 \
 -DFSTR_L=int \
 -DIOAPI_NO_STDOUT=1 \
 -DNEED_ARGS=1
PARFLAGS  =
ARCHLIB   = -static -L/usr/lib64 -lm -lpthread -lc

M4DEFFILE = $(PVM_ROOT)/conf/$(PVM_ARCH).m4
PVMLIBS   = # -lpvm3

Now compile IOAPI
chmod 755 $MASTERDIR/ioapi-3.2/compile.ioapi.csh
$MASTERDIR/ioapi-3.2/compile.ioapi.csh

SMOKE

  • Clone latest release version of SMOKE (version 5.0 at the time of this instruction) from CMAS center
    cd $MASTERDIR
    git clone https://github.com/CEMPD/SMOKE.git SMOKE_v5.0
  • Create $MASTERDIR/SMOKE_v5.0/SMOKE_INSTALL.config.csh with content
#!/bin/tcsh

 setenv SMK_HOME $MASTERDIR/SMOKE_v5.0 
#setenv BIN Linux2_x86_64       # if using gfotran
 setenv BIN Linux2_x86_64ifort  # if using intel fortran
 #> source IOAPI config to get same variable $BIN and libraries that were used to compile IOAPI
source $MASTERDIR/ioapi-3.2/IOAPI.config.csh $BIN # source IOAPI config to get same variable $BIN and libraries
  • cd $MASTERDIR/SMOKE_v5.0
  • Create $MASTERDIR/SMOKE_v5.0/compile.SMOKE.csh with content
#!/bin/tcsh

 source ./SMOKE_INSTALL.config.csh

 mkdir -p $SMK_HOME/$BIN

#> Before compiling, update Makeinclude with the following:
#          point INSTDIR to correct path
#          point BASEDIR to correct path
#          point IOBASE to correct path
#          OBJDIR to correct path
#          EFLAG to correct compiler. eg., INtel, GNU, PGI

cd $SMK_HOME/src
make clean
make all # >& $SMK_HOME/LOG.compile.$BIN
  • If using intel compiler, modify $MASTERDIR/SMOKE_v5.0/src/Makeinclude as follow
BASEDIR = ${SMK_HOME}/src
INCDIR  = ${BASEDIR}/inc
OBJDIR  = ${SMK_HOME}/${BIN}

IOBASE  = ${IOAPI_HOME}
IODIR   = ${IOBASE}/ioapi
IOBIN   = ${IOBASE}/${BIN}
IOINC   = ${IODIR}/fixed_src

INSTDIR = ${SMK_HOME}/${BIN}

##  Architecture dependent stuff

include ${IODIR}/Makeinclude.${BIN}

F90 = $(FC)

 IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN} -traceback      #  Intel, Absoft, Pathscale, UNIX Fortran
# IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  GNU   Fortran
# IFLAGS = -I${IOINC} -I${INCDIR} -M${IOBIN}                #  Sun   Fortran
# IFLAGS = -I${IOINC} -I${INCDIR} -module ${OBJDIR} -module ${IOBIN}    #  PGI Fortran:  order *important*

 EFLAG = -extend-source 132 -zero -static-intel -debug  #  Intel Fortran
# EFLAG = -ffixed-line-length-132  -fno-backslash       #  GNU   Fortran
# EFLAG = -Mextend -Mbackslash                          #  PGI Fortran
# EFLAG = -e                                            #  Sun   Fortran
# EFLAG = -W132                                         #  Absoft   Fortran

FFLAGS  = ${IFLAGS} ${EFLAG} ${DEFINEFLAGS} ${PARFLAGS} ${FOPTFLAGS} ${ARCHFLAGS}

LDFLAGS = ${IFLAGS} ${DEFINEFLAGS} ${ARCHFLAGS}

ARFLAGS = rv

SMKLIB = -L${OBJDIR} -lsmoke

########  netCDF-4 needs "-lnetcdff -lnetcdf":

# IOLIB = -L$(IOBIN) -lioapi -lnetcdff -lnetcdf ${PVMLIBS}
# IOLIB = -L$(IOBIN) -lioapi -lnetcdff -lnetcdf  
  IOLIB = -L$(IOBIN) -lioapi ${NCFLIBS}
  • If using gfortran compiler, modify $MASTERDIR/SMOKE_v5.0/src/Makeinclude as follow
BASEDIR = ${SMK_HOME}/src
INCDIR  = ${BASEDIR}/inc
OBJDIR  = ${SMK_HOME}/${BIN}

IOBASE  = ${IOAPI_HOME}
IODIR   = ${IOBASE}/ioapi
IOBIN   = ${IOBASE}/${BIN}
IOINC   = ${IODIR}/fixed_src

INSTDIR = ${SMK_HOME}/${BIN}

##  Architecture dependent stuff

include ${IODIR}/Makeinclude.${BIN}

F90 = $(FC)

# IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  Intel, Absoft, Pathscale, UNIX Fortran
 IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  GNU   Fortran
# IFLAGS = -I${IOINC} -I${INCDIR} -M${IOBIN}                #  Sun   Fortran
# IFLAGS = -I${IOINC} -I${INCDIR} -module ${OBJDIR} -module ${IOBIN}    #  PGI Fortran:  order *important*

# EFLAG = -extend-source 132 -zero                      #  Intel Fortran
 EFLAG = -ffixed-line-length-132  -fno-backslash -fcheck=all -Wall -march=native -ffast-math -funroll-loops #  GNU   Fortran
# EFLAG = -Mextend -Mbackslash                          #  PGI Fortran
# EFLAG = -e                                            #  Sun   Fortran
# EFLAG = -W132                                         #  Absoft   Fortran

FFLAGS  = ${IFLAGS} ${EFLAG} ${DEFINEFLAGS} ${PARFLAGS} ${FOPTFLAGS} ${ARCHFLAGS}

LDFLAGS = ${IFLAGS} ${DEFINEFLAGS} ${ARCHFLAGS}

ARFLAGS = rv

SMKLIB = -L${OBJDIR} -lsmoke

########  netCDF-4 needs "-lnetcdff -lnetcdf":

# IOLIB = -L$(IOBIN) -lioapi -lnetcdff -lnetcdf ${PVMLIBS}
# IOLIB = -L$(IOBIN) -lioapi -lnetcdff -lnetcdf  
IOLIB = -L$(IOBIN) -lioapi ${NCFLIBS}

Now compile SMOKE
chmod 755 $MASTERDIR/SMOKE_v5.0/compile.SMOKE.csh
$MASTERDIR/SMOKE_v5.0/compile.SMOKE.csh

Installations instructions for required packages

  • Create C-shell script $MASTERDIR/config_support_softwares.csh with the following content
#!/bin/tcsh -f

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compiler argument must be set: <intel/gcc>"
      exit( 1 )
breaksw
   case 1:
breaksw
   case 2:
      echo "SCRIPT ERROR: too many input arguments. Abort!"
      exit( 1 )
breaksw
endsw

setenv compiler    "$argv[1]"

 if ($compiler == 'gcc') then
#    module load gcc/9.1.0
     setenv CC gcc
     setenv CXX g++
     setenv FC gfortran
     #setenv CFLAGS "-ffixed-line-length-132  -fno-backslash -fcheck=all -Wall -march=native -ffast-math -funroll-loops"
 else if ($compiler == 'intel') then
#    module load intel/19.4
     setenv CC icc
     setenv CXX icpc
     setenv FC ifort
 else
     echo "SCRIPT ERROR: compiler parameter is not recognized. Abort!"
     exit( 1 )
 endif


#> Critical Folder Locations for Installed Software
 setenv AUXILIARY $MASTERDIR/ioapi-3.2/dependencies 
 setenv HDF5      $AUXILIARY/hdf5.1.14.3_$compiler
 setenv NETCDFF   $AUXILIARY/netcdff.4.6.1_$compiler
 setenv NETCDFC   $AUXILIARY/netcdfc.4.9.2_$compiler
 setenv ZLIB      $AUXILIARY/zlib.1.3.1_$compiler
 setenv SZIP      $AUXILIARY/szip.2.1.1_$compiler

ZLIB

  • Download zlib:
    wget -P $MASTERDIR https://www.zlib.net/zlib-1.3.1.tar.gz
  • Decompress the downloaded package
    cd $MASTERDIR
    tar -xvzf zlib-1.3.1.tar.gz
    cd zlib-1.3.1
  • Create $MASTERDIR/zlib-1.3.1/compile.csh with the following content
#!/bin/tcsh

# Select either gfortran or intel fortran compiler
setenv compiler intel
#setenv compiler gcc
source $MASTERDIR/config_support_softwares.csh $compiler

mkdir -p $ZLIB

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compile script must have a valid option from the following:"
      echo "     <configure>        : generate configuration for compilation"
      echo "     <make_clean>       : uninstall previous build"
      echo "     <make_check>       : build and run check, not install yet"
      echo "     <make_install>     : finall installation; must be run after make_check"
      exit( 1 )
endsw

setenv RUN_TYPE    "$argv[1]"

if ( $RUN_TYPE == "configure" ) then
 ./configure --prefix=$ZLIB --64 --static
 #>IMPORTANT: After running configure, add -fPIC to CFLAGS in Makefile before compiling: CFLAGS=-O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -fPIC
endif

if ( $RUN_TYPE == "make_clean" ) then
make clean
make uninstall
endif

if ( $RUN_TYPE == "make" ) then
make >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_check" ) then
make test >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_install" ) then
make install >& log.$RUN_TYPE
endif

  • chmod u+x $MASTERDIR/zlib-1.3.1/compile.csh

  • Run $MASTERDIR/zlib-1.3.1/compile.csh <option> with <option> to be configure, make and make_install to compile zlib
    $MASTERDIR/zlib-1.3.1/compile.csh configure

  • NOTE: After running $MASTERDIR/zlib-1.3/compile.csh configure add -fPIC to the end of CFLAGS in Makefile before continue compiling
    $MASTERDIR/zlib-1.3.1/compile.csh make_clean (Optional; recommended when recompiling)
    $MASTERDIR/zlib-1.3.1/compile.csh make
    $MASTERDIR/zlib-1.3.1/compile.csh make_check (Optional; recommended when recompiling)
    $MASTERDIR/zlib-1.3.1/compile.csh make_install

  • If compiled successfully, zlib should be installed under $MASTERDIR/ioapi-3.2/dependencies/zlib.1.3.1_$compiler

SZIP

  • Download szip
    wget -P $MASTERDIR https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz
    cd $MASTERDIR
    tar -xvzf szip-2.1.1.tar.gz
    cd szip-2.1.1
  • Create $MASTERDIR/szip-2.1.1/compile.csh with the following content
#!/bin/tcsh

##Select either gfortran or intel fortran compiler
#setenv compiler gcc
setenv compiler intel 
source $MASTERDIR/config_support_softwares.csh $compiler

mkdir -p $SZIP

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compile script must have a valid option from the following:"
      echo "     <configure>        : generate configuration for compilation"
      echo "     <make_clean>       : uninstall previous build"
      echo "     <make_check>       : build and run check, not install yet"
      echo "     <make_install>     : finall installation; must be run after make_check"
      exit( 1 )
endsw

setenv RUN_TYPE    "$argv[1]"

if ( $RUN_TYPE == "configure" ) then
 ./configure --prefix=$SZIP --disable-shared --enable-static
 #>IMPORTANT: After running configure, add -fPIC to CFLAGS in Makefile
endif

if ( $RUN_TYPE == "make_clean" ) then
make clean
make uninstall
endif

if ( $RUN_TYPE == "make" ) then
make >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_check" ) then
make check >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_install" ) then
make install >& log.$RUN_TYPE
endif
  • chmod u+x $MASTERDIR/szip-2.1.1/compile.csh
  • Run $MASTERDIR/szip-2.1.1/compile.csh <option> with <option> to be configure, make and make_install to compile zlib
  • If compiled successfully, szip should be installed under $MASTERDIR/ioapi-3.2/dependencies/szip.2.1.1_$compiler

HDF5

  • Download hdf5
    wget -P $MASTERDIR https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_14_3/src/hdf5-1.14.3.tar.gz
    cd $MASTERDIR
    tar -xvzf hdf5-1.14.3.tar.gz
    cd hdf5-1.14.3
  • Create $MASTERDIR/hdf5-1.14.3/compile.csh with the following content
#!/bin/tcsh

##Select either gfortran or intel fortran compiler
#setenv compiler gcc
setenv compiler intel
source $MASTERDIR/config_support_softwares.csh $compiler

mkdir -p $HDF5

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compile script must have a valid option from the following:"
      echo "     <configure>        : generate configuration for compilation"
      echo "     <make_clean>       : uninstall previous build"
      echo "     <make_check>       : build and run check, not install yet"
      echo "     <make_install>     : finall installation; must be run after make_check"
      exit( 1 )
endsw

setenv RUN_TYPE    "$argv[1]"

if ( $RUN_TYPE == "configure" ) then
 if ( $compiler == 'gcc' ) then
 ./configure --prefix=$HDF5 --with-zlib=$ZLIB --with-szlib=$SZIP \
             --enable-static --disable-shared \
             --enable-static-exec \
             --enable-fortran --enable-cxx --enable-hl \
             --enable-fast-install \
             --enable-tests=no \
             --disable-sharedlib-rpath
 endif
 if ( $compiler == 'intel' ) then
 ./configure --prefix=$HDF5 --with-zlib=$ZLIB --with-szlib=$SZIP \
             CFLAGS="-diag-disable=10441 -fPIC -O3 -xHost -ip -align -static -static-intel" \
             FFLAGS="-fPIC -O3 -xHost -ip -align -static -static-intel" \
             CXXFLAGS="-fPIC -O3 -xHost -ip -align -static -static-intel" \
             --enable-static --disable-shared \
             --enable-static-exec \
             --enable-fortran --enable-cxx --enable-hl \
             --enable-tests=no \
             --disable-sharedlib-rpath
             #--enable-fast-install 
 endif
endif

if ( $RUN_TYPE == "make_clean" ) then
make clean
make uninstall
endif

if ( $RUN_TYPE == "make" ) then
make  >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_check" ) then
make test >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_install" ) then
make install >& log.$RUN_TYPE
endif
  • chmod u+x $MASTERDIR/hdf5-1.14.3/compile.csh
  • Run $MASTERDIR/hdf5-1.14.3/compile.csh <option> with <option> to be configure, make and make_install to compile hdf5
  • If compiled successfully, hdf5 should be installed under $MASTERDIR/ioapi-3.2/dependencies/hdf5.1.14.3_$compiler

NETCDF

  • Two NETCDF packages are required: netcdf-c and netcdf-fortran

netcdf-c

  • Download netcdf-c
    wget -P $MASTERDIR https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz
    cd $MASTERDIR
    tar -xvzf netcdf-c-4.9.2.tar.gz
    cd netcdf-c-4.9.2
  • Create $MASTERDIR/netcdf-c-4.9.2/compile.csh with the following content
#!/bin/tcsh

##Select either gfortran or intel fortran compiler
#setenv compiler gcc
setenv compiler intel
source $MASTERDIR/config_support_softwares.csh $compiler

mkdir -p $NETCDFC

setenv CPPFLAGS "-I${HDF5}/include -I${SZIP}/include -I${ZLIB}/include"
setenv LDFLAGS  "-L${HDF5}/lib -L${SZIP}/lib -L${ZLIB}/lib"
#setenv LIBS     "-lhdf5_hl -lhdf5 -lm -lz -lsz" # Does not need this

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compile script must have a valid option from the following:"
      echo "     <configure>        : generate configuration for compilation"
      echo "     <make_clean>       : uninstall previous build"
      echo "     <make_check>       : build and run check, not install yet"
      echo "     <make_install>     : finall installation; must be run after make_check"
      exit( 1 )
endsw

setenv RUN_TYPE    "$argv[1]"

if ( $RUN_TYPE == "configure" ) then
 if ( $compiler == 'gcc' ) then
 ./configure --prefix=$NETCDFC \
             --disable-dap \
             --disable-shared \
             --disable-examples \
             --enable-static \
             --disable-byterange \
             --disable-plugins \
	     CFLAGS='-static -static-libgcc -static-libgfortran' \
             --disable-libxml2
 endif
 if ( $compiler == 'intel' ) then
 ./configure --prefix=$NETCDFC \
             --disable-dap \
             --disable-examples \
             --disable-shared \
             --disable-byterange \
             --disable-libxml2 \
             --disable-plugins \
	     CFLAGS='-static -static-intel' \
             --enable-static
 endif
endif

if ( $RUN_TYPE == "make_clean" ) then
make clean
make uninstall
endif

if ( $RUN_TYPE == "make" ) then
make >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_check" ) then
make check >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_install" ) then
make install >& log.$RUN_TYPE
endif
  • chmod u+x $MASTERDIR/netcdf-c-4.9.2/compile.csh
  • Run $MASTERDIR/netcdf-c-4.9.2/compile.csh <option> with <option> to be configure, make and make_install to compile netcdf-c
  • If compiled successfully, netcdf-c should be installed under $MASTERDIR/ioapi-3.2/dependencies/netcdfc.4.9.2_$compiler

netcdf-fortran

  • Download netcdf-fortran
    wget -P $MASTERDIR https://downloads.unidata.ucar.edu/netcdf-fortran/4.6.1/netcdf-fortran-4.6.1.tar.gz
    cd $MASTERDIR
    tar -xvzf netcdf-fortran-4.6.1.tar.gz
    cd netcdf-fortran-4.6.1
  • Create $MASTERDIR/netcdf-fortran-4.6.1/compile.csh with the following content
#!/bin/tcsh

##Select either gfortran or intel fortran compiler
#setenv compiler gcc
setenv compiler intel
source $MASTERDIR/config_support_softwares.csh $compiler

mkdir -p $NETCDFF

setenv LIBS `${NETCDFC}/bin/nc-config --libs`
setenv CPPFLAGS "-I${NETCDFC}/include"

switch ( $#argv )
   case 0:
      echo "SCRIPT ERROR: compile script must have a valid option from the following:"
      echo "     <configure>        : generate configuration for compilation"
      echo "     <make_clean>       : uninstall previous build"
      echo "     <make_check>       : build and run check, not install yet"
      echo "     <make_install>     : finall installation; must be run after make_check"
      exit( 1 )
endsw

setenv RUN_TYPE    "$argv[1]"

if ( $RUN_TYPE == "configure" ) then
 ./configure --prefix=$NETCDFF CFLAGS='-static' \
             --disable-shared \
             --enable-static \
             --disable-zstandard-plugin \
             --enable-fast-install 
endif

if ( $RUN_TYPE == "make_clean" ) then
make clean
make uninstall
endif

if ( $RUN_TYPE == "make" ) then
make >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_check" ) then
make check >& log.$RUN_TYPE
endif

if ( $RUN_TYPE == "make_install" ) then
make install >& log.$RUN_TYPE
endif
  • chmod u+x $MASTERDIR/netcdf-fortran-4.6.1/compile.csh
  • Run $MASTERDIR/netcdf-fortran-4.6.1/compile.csh <option> with <option> to be configure, make and make_install to compile netcdf-c
  • If compiled successfully, netcdf-fortran should be installed under $MASTERDIR/ioapi-3.2/dependencies/netcdff.4.6.1_$compiler

OPTIONAL: Intel OneAPI installation and settings

Obtain and install Intel oneAPI Base Toolkit and Intel HPC Toolkit following instructions provided by Intel (Offline Installer is recommended)

In all of the instructions above and where intel compiler is applied, replace "icc" with "icx" and "icpc" with "icpx" (As of Intel HPC Toolkit 2024.1.0, classic fortran compiler "ifort" is still supported but it will be replaced by "ifx" in future versions).

One modification needed for compiling IOAPI: add stdlib.h header to $MASTERDIR/ioapi-3.2/ioapi/sortic.c so that it would look like:

#include  <string.h>  
#include  <stdint.h>  
#include "parms3.h"  
#include  <stdlib.h>

Addition Information All software installations under this instruction were tested on Red Hat Enterprise Linux 8 and Ubuntu operation systems with gcc version 9.1.0, 11.2, intel classic compiler version 19.4 and intel OneAPI version 2024.1.0

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