# Error when installing CMAQ5.0.2-ISAM

**URL:** <https://forum.cmascenter.org/t/error-when-installing-cmaq5-0-2-isam/2281>\
**Category:** CMAQ\
**Created:** [April 21, 2021, 1:17am UTC](https://forum.cmascenter.org/t/error-when-installing-cmaq5-0-2-isam/2281 "2021-04-21T01:17:36Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![liuxin](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.cmascenter.org/liuxin/32/1934_2.png) [@liuxin](https://forum.cmascenter.org/u/liuxin)\
**Post date:** [April 21, 2021, 1:17am UTC](https://forum.cmascenter.org/t/error-when-installing-cmaq5-0-2-isam/2281/1 "2021-04-21T01:17:36Z")

</div>

Hello，  
I have installed CMAQ5.0.2-CCTM and running successfully with netcdf3.6.1, IOAPI3.2 and MPICH2.1.4. The following error occurred when I tried to install ISAM. What can I do to solve it ? 😷

 ![1](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/0/0c3ee859ce7afadeacca52666be25d47ed896764.png)

```
#!/bin/csh -f

# ====================== CCTMv5.0.2 Build Script ======================= #
# Usage: bldit.cctm >&! bldit.cctm.log #
# Requirements: I/O API & netCDF libs, a Fortran compiler, #
# and MPI for multiprocessor computing #
# Note that this script is configured/tested for Red Hat Linux O/S #
# The following environment variables must be set for this script to #
# build an executable. #
# setenv M3MODEL <source code repository> #
# setenv M3LIB <code libraries> #
# To report problems or request help with this script/program: #
# http://www.cmascenter.org/html/help.html #
# ====================================================================== #

#> Source the config.cmaq file to set the build environment
 source ../config.cmaq

#> Check for M3HOME and M3LIB settings:
 if ( ! -e $M3HOME || ! -e $M3LIB ) then
echo " $M3HOME or $M3LIB directory not found"
exit 1
 endif
 echo " Model repository base path: $M3HOME"
 echo " library path: $M3LIB"

#> If $M3MODEL not set, default to $M3HOME
 if ( $?M3MODEL ) then
echo " Model repository path: $M3MODEL"
 else
setenv M3MODEL $M3HOME
echo " default Model repository path: $M3MODEL"
 endif

 set BLD_OS = `uname -s` ## Script set up for Linux only 
 if ($BLD_OS != 'Linux') then
echo " $BLD_OS -> wrong bldit script for host!"
exit 1
 endif

 set echo

#:#:#:#:#:#:#:#:#:#:#:# Begin User Input Section #:#:#:#:#:#:#:#:#:#:#:#

#> user choices: Git repository
 set GlobInc = $M3MODEL/CCTM_ISAM/ICL
 set Mechs = $M3MODEL/CCTM_ISAM/MECHS
 
 setenv REPOROOT $M3MODEL/CCTM_ISAM

#> user choices: base working directory, application string
 set Base = $cwd
 set APPL = ISAM
 set MODEL = CCTM_${APPL}_$EXEC_ID
 set CFG = cfg.$MODEL

#set Local # do NOT copy the source files into the BLD directory -
         # comment out to copy the source files (default if not set)

 set build_twoway = 0 # 0 - not to build, 1 - to build WRF-CMAQ twoway

#> The "BLD" directory for checking out and compiling source code
 set Bld = $Base/BLD_${APPL}
 if ( ! -e "$Bld" ) then
mkdir $Bld
 else
if ( ! -d "$Bld" ) then
   echo " ***target exists, but not a directory***"
   exit 1
endif
 endif

 cd $Bld

#> user choices: bldmake command
#set MakeFileOnly # builds a Makefile to make the model, but does not compile -
                # comment out to also compile the model (default if not set)

#> user choices: single or multiple processors
 set ParOpt # set for multiple PE's; comment out for single PE

#> user choices: various modules

  if ( $build_twoway ) then
 set Twoway = twoway
  endif

 set ModDriver = driver/wrf
#set ModDriver = driver/yamo

 set ModGrid = grid/cartesian

 if ( $?ParOpt ) then
# set ModPar = par/par_nodistr
set ModPar = par/mpi
 else
set ModPar = par/par_noop
 endif 

 set ModInit = init/yamo

#set ModAdjc = ( // yamo option does not need denrate )

 set ModCpl = couple/gencoor_wrf
#set ModCpl = couple/gencoor

 set ModHadv = hadv/yamo

 set ModVadv = vadv/wrf
#set ModVadv = vadv/yamo

 set ModHdiff = hdiff/multiscale

 set ModVdiff = vdiff/acm2
#set ModVdiff = vdiff/acm2_mp

 set ModDepv = depv/m3dry
#set ModDepv = depv/m3dry_mp

set ModEmis = emis/emis

 set ModBiog = biog/beis3
 
 set ModPlmrs = plrise/smoke

 set ModCgrds = spcs/cgrid_spcs_nml
#set ModCgrds = spcs/cgrid_spcs_icl

 set ModPhot = phot/phot_inline
#set ModPhot = phot/phot_table

#set ModGas = gas/smvgear
#set ModGas = gas/ros3
#set ModGas = gas/ebi_cb05cl
 set ModGas = gas/ebi_cb05tucl
#set ModGas = gas/ebi_cb05tump
#set ModGas = gas/ebi_saprc99
#set ModGas = gas/ebi_saprc07tb
#set ModGas = gas/ebi_saprc07tc

#set ModAero = aero/aero5
 set ModAero = aero/aero6
#set ModAero = aero/aero6_mp

#set ModCloud = cloud/cloud_acm_ae5
 set ModCloud = cloud/cloud_acm_ae6
#set ModCloud = cloud/cloud_acm_ae6_mp

 set ISAM = isam
 set sens = ( -Disam )

 set ModPa = procan/pa

 set ModUtil = util/util

#> user choices: mechanism
#set Mechanism = cb05cl_ae5_aq
#set Mechanism = cb05tucl_ae5_aq
 set Mechanism = cb05tucl_ae6_aq
#set Mechanism = cb05tump_ae6_aq
#set Mechanism = saprc99_ae5_aq
#set Mechanism = saprc99_ae6_aq
#set Mechanism = saprc07tb_ae6_aq
#set Mechanism = saprc07tc_ae6_aq
 set Tracer = trac0 # default: no tracer species

#> user choices: set process analysis linkages
 set PABase = $GlobInc
 set PAOpt = pa_noop

#> user choices: computing system configuration:
#> compiler name and location/link flags
#> library paths

#> Set full path of Fortran 90 and C compilers
 set FC = ${myFC}
 set FP = $FC
 set CC = ${myCC}

#> Set location of M3Bld executable
 set Blder = $M3LIB/bldmake

#> Set location of libraries/include files
 set LIOAPI = "${M3LIB}/ioapi/Linux2_x86_64pg_pgcc_nomp -lioapi"
 set IOAPIMOD = "${M3LIB}/ioapi/fixed_src"

 set NETCDF = "${M3LIB}/netcdf/lib -lnetcdf"

 if ( $?ParOpt ) then # Multiprocessor system configuration
set PARIO = ${M3LIB}/pario
set STENEX = ${M3LIB}/se_snl
 else
set PARIO = "."
set STENEX = "${M3LIB}/se_noop"
set MPI_INC = "."
 endif

#> Set compiler flags
 set F_FLAGS = "${myFFLAGS} -I ${IOAPIMOD} -I ${PARIO} -I ${STENEX} -I ${MPI_INC} -I."
 set F90_FLAGS = "${myFRFLAGS} -I ${IOAPIMOD} -I ${PARIO} -I ${STENEX} -I ${MPI_INC} -I."
 set CPP_FLAGS = ""
 set C_FLAGS = "${myCFLAGS} -DFLDMN -I ${MPI_INC}"
 set LINK_FLAGS = "${myLINK_FLAG}"

#:#:#:#:#:#:#:#:#:#:#:# End of User Input Section :#:#:#:#:#:#:#:#:#:#:#:#:#

 if ( $?ParOpt ) then # Multiprocessor system configuration
set seL = se_snl
set LIB2 = "-L${M3LIB}/pario -lpario"
set LIB3 = 
set LIB4 = "-L${M3LIB}/mpich/lib ${mpi} ${extra_lib}"
set Str1 = (// Parallel / Include message passing definitions)
set Str2 = (include SUBST_MPI ${MPI_INC}/mpif.h;)
 else
set seL = sef90_noop
set LIB2 =
set LIB3 =
set LIB4 =
set Str1 =
set Str2 =
 endif

 set LIB1 = "-L${STENEX} -l${seL}"
 set LIB5 = "-L${LIOAPI}"
 set LIB6 = "-L${NETCDF}"
 set LIBS = "$LIB1 $LIB2 $LIB3 $LIB4 $LIB5 $LIB6"
 
 source $Base/relinc.cctm

 set ICL_PAR = $Bld
 set ICL_CONST = $Bld
 set ICL_FILES = $Bld
 set ICL_EMCTL = $Bld
 set ICL_MECH = $Bld
 set ICL_PA = $Bld

 if ( $?ParOpt ) then # split to avoid line > 256 char
set PAR = ( -Dparallel )

set Popt = SE
 else
echo " Not Parallel; set Serial (no-op) flags"
set PAR = ""
set Popt = NOOP
 endif
 
 if ( $build_twoway ) then # split to avoid line > 256 char
set TWOWAY = ( -Dtwoway )
 else
echo " Not twoway"
set TWOWAY = ""
 endif

 set STX1 = ( -DSUBST_MODULES=${Popt}_MODULES\
          -DSUBST_BARRIER=${Popt}_BARRIER )
 set STX2 = ( -DSUBST_GLOBAL_MAX=${Popt}_GLOBAL_MAX\
          -DSUBST_GLOBAL_MIN=${Popt}_GLOBAL_MIN\
          -DSUBST_GLOBAL_MIN_DATA=${Popt}_GLOBAL_MIN_DATA\
          -DSUBST_GLOBAL_TO_LOCAL_COORD=${Popt}_GLOBAL_TO_LOCAL_COORD\
          -DSUBST_GLOBAL_SUM=${Popt}_GLOBAL_SUM\
          -DSUBST_GLOBAL_LOGICAL=${Popt}_GLOBAL_LOGICAL\
          -DSUBST_LOOP_INDEX=${Popt}_LOOP_INDEX\
          -DSUBST_SUBGRID_INDEX=${Popt}_SUBGRID_INDEX )
 set STX3 = ( -DSUBST_HI_LO_BND_PE=${Popt}_HI_LO_BND_PE\
          -DSUBST_SUM_CHK=${Popt}_SUM_CHK\
          -DSUBST_INIT_ARRAY=${Popt}_INIT_ARRAY\
          -DSUBST_COMM=${Popt}_COMM\
          -DSUBST_MY_REGION=${Popt}_MY_REGION\
          -DSUBST_SLICE=${Popt}_SLICE\
          -DSUBST_GATHER=${Popt}_GATHER\
          -DSUBST_DATA_COPY=${Popt}_DATA_COPY\
          -DSUBST_IN_SYN=${Popt}_IN_SYN )

#> make the config file

 set Cfile = ${CFG}.bld
 set quote = '"'

 echo > $Cfile
 echo "model $MODEL;" >> $Cfile
 echo >> $Cfile
 echo "FPP $FP;" >> $Cfile
 echo >> $Cfile
 set text = "$quote$CPP_FLAGS $PAR $sens $STX1 $STX2 $STX3$quote;"
 echo "cpp_flags $text" >> $Cfile
 echo >> $Cfile
 echo "f_compiler $FC;" >> $Cfile
 echo >> $Cfile
 echo "f_flags $quote$F_FLAGS$quote;" >> $Cfile
 echo >> $Cfile
 echo "f90_flags $quote$F90_FLAGS$quote;" >> $Cfile
 echo >> $Cfile
 echo "c_compiler $CC;" >> $Cfile
 echo >> $Cfile
 echo "c_flags $quote$C_FLAGS$quote;" >> $Cfile
 echo >> $Cfile
 echo "link_flags $quote$LINK_FLAGS$quote;" >> $Cfile
 echo >> $Cfile
 echo "libraries $quote$LIBS$quote;" >> $Cfile
 echo >> $Cfile

 set text="// mechanism:"
 echo "$text ${Mechanism}" >> $Cfile
 echo "// model repository: ${M3MODEL}" >> $Cfile
 echo >> $Cfile
#if ( $compiler == gfort ) then
# set ICL_PAR = '.'
# set ICL_CONST = '.'
# set ICL_FILES = '.'
# set ICL_EMCTL = '.'
# set ICL_MECH = '.'
# set ICL_PA = '.'
#endif
 echo "include SUBST_PE_COMM $ICL_PAR/PE_COMM.EXT;" >> $Cfile
 echo "include SUBST_CONST $ICL_CONST/CONST.EXT;" >> $Cfile
 echo "include SUBST_FILES_ID $ICL_FILES/FILES_CTM.EXT;" >> $Cfile
 echo "include SUBST_EMISPRM $ICL_EMCTL/EMISPRM.EXT;" >> $Cfile
 echo "include SUBST_RXCMMN $ICL_MECH/RXCM.EXT;" >> $Cfile
 echo "include SUBST_RXDATA $ICL_MECH/RXDT.EXT;" >> $Cfile
 echo >> $Cfile

 set text = "// Process Analysis / Integrated Reaction Rates processing"
 echo $text >> $Cfile
 echo "include SUBST_PACTL_ID $ICL_PA/PA_CTL.EXT;" >> $Cfile
 echo "include SUBST_PACMN_ID $ICL_PA/PA_CMN.EXT;" >> $Cfile
 echo "include SUBST_PADAT_ID $ICL_PA/PA_DAT.EXT;" >> $Cfile
 echo >> $Cfile

 echo "$Str1" >> $Cfile
 if ( $compiler == gfort ) then
  echo "include SUBST_MPI ${MPI_INC}/mpif.h;" >> $Cfile
 else
  echo "$Str2" >> $Cfile
 endif
 echo >> $Cfile

 if ( $build_twoway ) then
set text = "twoway"
echo "// options are" $text >> $Cfile
echo "Module ${Twoway};" >> $Cfile
echo >> $Cfile
 endif

 set text = "ctm_wrf and ctm_yamo"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModDriver};" >> $Cfile
 echo >> $Cfile

 set text = "cartesian"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModGrid};" >> $Cfile
 echo >> $Cfile

 set text = "par, par_nodistr and par_noop"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModPar};" >> $Cfile
 echo >> $Cfile

 set text = "init_yamo"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModInit};" >> $Cfile
 echo >> $Cfile

#set text = ""
#echo "// options are" $text >> $Cfile
#echo "Module ${ModAdjc};" >> $Cfile
#echo >> $Cfile

 set text = "gencoor_wrf and gencoor"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModCpl};" >> $Cfile
 echo >> $Cfile

 set text = "hyamo"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModHadv};" >> $Cfile
 echo >> $Cfile

 set text = "vwrf and vyamo"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModVadv};" >> $Cfile
 echo >> $Cfile

 set text = "multiscale"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModHdiff};" >> $Cfile
 echo >> $Cfile

 set text = "acm2 and acm2_mp"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModVdiff};" >> $Cfile
 echo >> $Cfile

 set text = "m3dry and m3dry_mp"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModDepv};" >> $Cfile
 echo >> $Cfile

 set text = "emis"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModEmis};" >> $Cfile
 echo >> $Cfile

 set text = "beis3"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModBiog};" >> $Cfile
 echo >> $Cfile

 set text = "smoke"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModPlmrs};" >> $Cfile
 echo >> $Cfile

 set text = "cgrid_spcs_nml and cgrid_spcs_icl"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModCgrds};" >> $Cfile
 echo >> $Cfile

 set text = "phot_inline and phot_table"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModPhot};" >> $Cfile
 echo >> $Cfile

 set text = "smvgear, ros3, ebi_cb05cl, ebi_cb05tucl, ebi_cb05tump, ebi_saprc99, ebi_saprc07tb, and ebi_saprc07tc"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModGas};" >> $Cfile
 echo >> $Cfile

 set text = "aero5, aero6, and aero6_mp"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModAero};" >> $Cfile
 echo >> $Cfile

 set text = "cloud_acm_ae5, cloud_acm_ae6, and cloud_acm_ae6_mp"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModCloud};" >> $Cfile
 echo >> $Cfile

 set text = "pa, which requires the"
 echo "// options are" $text "replacement of the three" >> $Cfile
 set text = "// global include files with their pa_noop counterparts"
 echo $text >> $Cfile
 echo "Module ${ModPa};" >> $Cfile
 echo >> $Cfile

 set text = "util"
 echo "// options are" $text >> $Cfile
 echo "Module ${ModUtil};" >> $Cfile
 echo >> $Cfile
 
 set text = "isam"
 echo "// options are" $text >> $Cfile
 echo "Module ${ISAM};" >> $Cfile
 echo >> $Cfile

 if ( $?ModMisc ) then
echo "Module ${ModMisc};" >> $Cfile
echo >> $Cfile
 endif

#> make the Makefile or the model executable

 unalias mv rm
 set cfg_options =
 if ( $?MakeFileOnly ) then
set cfg_options = "-makefo"
 endif
 if ( $?Local ) then
set cfg_options = "$cfg_options -git_local"
 endif
 if ( $build_twoway ) then
set cfg_options = "$cfg_options -twoway"
 endif

 $Blder $cfg_options $Cfile

 mv Makefile Makefile.$COMPILER
 if ( -e Makefile.$COMPILER && -e Makefile ) rm Makefile
 ln -s Makefile.$COMPILER Makefile

 if ( $status != 0 ) then
echo " ***failure in $Blder***"
exit 1
 endif
 if ( -e "$Base/${CFG}" ) then
echo " >>> previous ${CFG} exists, re-naming to ${CFG}.old <<<"
mv $Base/${CFG} $Base/${CFG}.old
 endif
 mv ${CFG}.bld ${CFG}

 set is_using_git = `ls -alog $M3MODEL | grep git | wc -l`

 if ( $is_using_git[1] ) then
#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#
cd $M3MODEL
set brnch = `git branch`
@ i = 0
while ( $i < $#brnch )
   @ i++
   if ( "$brnch[$i]" == "*" ) @ l = $i + 1
end
set rep = `echo $cwd | tr "/" "#"`
set rln = "repo:${rep},branch:${brnch[$l]},compiler:${COMPILER}"
set ref = $Bld/$rln
/bin/touch $ref
if ( -d $M3MODEL/branch ) /bin/cp $M3MODEL/branch/branch.* $Bld
 endif

 exit

```

2021-04-20T16:00:00Z