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Modules required

  1. lang/Perl/5.28.1-GCCcore-6.3.0
  2. data/netCDF-Fortran/4.4.5-intel-2018.5.274
  3. data/netCDF/4.6.2-intel-2018.5.274
  4. toolchain/intel/2018.5.274
  5. devel/CMake/3.12.1-intel-2018.5.274
  6. data/XML-LibXML/2.0206-GCCcore-6.3.0

Prerequisite steps

Alternate setup for XML-LibXML

This step can be skipped if you use the data/XML-LibXML/2.0206-GCCcore-6.3.0 module .  These instructions are provided in the case the default module does not work or you have another reason to install your own version of the perl library.

Install Required Perl Module 

These steps will create a interactive session and install the XML::LibXML package into a local directory for Perl 5.28.1.  One might notice we have two extra steps where we create a directory and create a symbolic link to where perl5 will typically place libraries.  The reason for this, is due to how the home file system on Mana acts and will work around these oddities.  All that we are doing is utilize a different mount that points to your home directory, but access your home space in a slightly different manner.

[user@login001 ~]$ srun -p sandbox --mem=6G -c 2 -t 60 --pty /bin/bash
[user@node-0005 ~]$ module load lang/Perl/5.28.1-GCCcore-6.3.0
[user@node-0005 ~]$ mkdir .perl5
[user@node-0005 ~]$ ln -s /mnt/home/noac/${USER}/.perl5 perl5  
[user@node-0005 ~]$ cpan install  XML::LibXML

Add Personal Perl Library Paths to .bash_profile

These steps above are needed once you have installed the XML::LibXML for perl 5.  As we are depending on a local library, the above steps will make it so that perl knows where to look for your local libraries.  We add it to the .bash_profile so these variables are added to your environment on connecting to Mana.  If you did not want to have this added to your environment every time, these variables could potentially be added to the job submission script itself, prior to utilize perl.

#!/bin/bash
echo -e "\nPATH=\"${HOME}/perl5/bin/"\${PATH:+:\${PATH}}"\"" >> ~/.bash_profile
echo -e "\nPERL5LIB=\"${HOME}/perl5/lib/perl5"\${PERL5LIB:+:\${PERL5LIB}}"\"" >> ~/.bash_profile
echo -e "\nPERL_LOCAL_LIB_ROOT=\"${HOME}/perl5"\${PERL_LOCAL_LIB_ROOT:+:\${PERL_LOCAL_LIB_ROOT}}"\"" >> ~/.bash_profile
echo -e "\nPERL_MB_OPT=\"--install_base \"${HOME}/perl5\"\"" >> ~/.bash_profile
echo -e "\nPERL_MM_OPT=\"INSTALL_BASE=${HOME}/perl5\"" >> ~/.bash_profile
echo -e "\n" >> ~/.bash_profile
echo -e '\nexport ${PATH}' >> ~/.bash_profile
echo -e '\nexport ${PERL5LIB}' >> ~/.bash_profile
echo -e '\nexport ${PERL_LOCAL_LIB_ROOT}' >> ~/.bash_profile
echo -e '\nexport ${PERL_MB_OPT}' >> ~/.bash_profile
echo -e '\nexport ${PERL_MM_OPT}' >> ~/.bash_profile

Setup a joined directory of a specific version of NetCDF

Older models, such as CESM 1.x, require that all parts of NetCDF be in a single directory.  Unfortunately, the modules on the cluster do not provide this, so we need to create our own joined directory on the version of NetCDF we want to use. 


The script below will; create a  directory called netcdf4 in your home directory that will then be populated with symlinks to the NetCDF libraries.  This script should be run in an interactive session, or it will not find the directories in which the components of netCDF live in. 

netcdf4_single_dir.sh 
#!/bin/bash

mkdir -p ~/netcdf4/bin ~/netcdf4/include ~/netcdf4/lib ~/netcdf4/lib/pkgconfig

cd ~/netcdf4/bin
find /opt/apps/software/data/PnetCDF/1.9.0-intel-2018.5.274/bin/ -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF-Fortran/4.4.5-intel-2018.5.274/bin -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF/4.6.2-intel-2018.5.274/bin/ -maxdepth 1 -type f -exec ln -s {} . \;

cd ~/netcdf4/include
find /opt/apps/software/data/PnetCDF/1.9.0-intel-2018.5.274/include -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF-Fortran/4.4.5-intel-2018.5.274/include -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF/4.6.2-intel-2018.5.274/include -maxdepth 1 -type f -exec ln -s {} . \;

cd ~/netcdf4/lib
find /opt/apps/software/data/PnetCDF/1.9.0-intel-2018.5.274/lib -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF-Fortran/4.4.5-intel-2018.5.274/lib -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF/4.6.2-intel-2018.5.274/lib64 -maxdepth 1 -type f -exec ln -s {} . \;

ln -s libnetcdff.so.* libnetcdff.so
ln -s libnetcdf.so.* libnetcdf.so

cd ~/netcdf4/lib/pkgconfig
find /opt/apps/software/data/PnetCDF/1.9.0-intel-2018.5.274/lib/pkgconfig -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF-Fortran/4.4.5-intel-2018.5.274/lib/pkgconfig -maxdepth 1 -type f -exec ln -s {} . \;
find /opt/apps/software/data/netCDF/4.6.2-intel-2018.5.274/lib64/pkgconfig -maxdepth 1 -type f -exec ln -s {} . \;


Additions to the config_machines.xml

 

As Mana has two different Infiniband networks (QDR and HDR), two different machine entries are created.  This also means that subsequent files will also come in duplicate, with only changes in selecting the right network to use.


config_machines.xml 
<machine MACH="uhhpc_qdr">
<DESC>User Defined Machine</DESC> <!-- can be anything -->
<OS>LINUX</OS> <!-- LINUX,Darwin,CNL,AIX,BGL,BGP -->
<COMPILERS>intel</COMPILERS> <!-- intel,ibm,pgi,pathscale,gnu,cray,lahey -->
<MPILIBS>impi</MPILIBS> <!-- openmpi, mpich, ibm, mpi-serial -->
<CESMSCRATCHROOT>~/lus_scratch/cesm/case</CESMSCRATCHROOT> <!-- complete path to the 'scratch' directory -->
<RUNDIR>$CASEROOT/run</RUNDIR> <!-- complete path to the run directory -->
<EXEROOT>$CASEROOT/bld</EXEROOT> <!-- complete path to the build directory -->
<DIN_LOC_ROOT>~/cesm/input</DIN_LOC_ROOT> <!-- complete path to the inputdata directory -->
<DIN_LOC_ROOT_CLMFORC>USERDEFINED_optional_build</DIN_LOC_ROOT_CLMFORC> <!-- path to the optional forcing data for CLM (for CRUNCEP forcing) -->
<DOUT_S>TRUE</DOUT_S> <!-- logical for short term archiving -->
<DOUT_S_ROOT>$CASEROOT/output</DOUT_S_ROOT> <!-- complete path to a short term archiving directory -->
<DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT> <!-- complete path to a long term archiving directory -->
<CCSM_BASELINE>USERDEFINED_optional_run</CCSM_BASELINE> <!-- where the cesm testing scripts write and read baseline results -->
<CCSM_CPRNC>USERDEFINED_optional_test</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<BATCHQUERY>squeue -a</BATCHQUERY>
<BATCHSUBMIT>sbatch</BATCHSUBMIT>
<SUPPORTED_BY>uh</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
<MAX_TASKS_PER_NODE>19</MAX_TASKS_PER_NODE>
</machine>


<machine MACH="uhhpc_hdr"> 
<DESC>User Defined Machine</DESC> <!-- can be anything --> 
<OS>LINUX</OS> <!-- LINUX,Darwin,CNL,AIX,BGL,BGP --> 
<COMPILERS>intel</COMPILERS> <!-- intel,ibm,pgi,pathscale,gnu,cray,lahey --> 
<MPILIBS>impi</MPILIBS> <!-- openmpi, mpich, ibm, mpi-serial -->
<CESMSCRATCHROOT>~/lus_scratch/cesm/case</CESMSCRATCHROOT> <!-- complete path to the 'scratch' directory -->
<RUNDIR>$CASEROOT/run</RUNDIR> <!-- complete path to the run directory --> 
<EXEROOT>$CASEROOT/bld</EXEROOT> <!-- complete path to the build directory --> 
<DIN_LOC_ROOT>~/cesm/input</DIN_LOC_ROOT> <!-- complete path to the inputdata directory --> 
<DIN_LOC_ROOT_CLMFORC>USERDEFINED_optional_build</DIN_LOC_ROOT_CLMFORC> <!-- path to the optional forcing data for CLM (for CRUNCEP forcing) -->
<DOUT_S>TRUE</DOUT_S> <!-- logical for short term archiving --> 
<DOUT_S_ROOT>$CASEROOT/output</DOUT_S_ROOT> <!-- complete path to a short term archiving directory -->
<DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT> <!-- complete path to a long term archiving directory -->
<CCSM_BASELINE>USERDEFINED_optional_run</CCSM_BASELINE> <!-- where the cesm testing scripts write and read baseline results -->
<CCSM_CPRNC>USERDEFINED_optional_test</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<BATCHQUERY>squeue -a</BATCHQUERY>
<BATCHSUBMIT>sbatch</BATCHSUBMIT>
<SUPPORTED_BY>uh</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
<MAX_TASKS_PER_NODE>39</MAX_TASKS_PER_NODE> 
</machine>

Create env_mach_specific files

A files for the uhhpc_qdr and the uhhpc_hdr machines needs to be made to define the build environment.  These two files should be identical as building for the QDR or the HDR network are identical on Mana.


env_mach_specific.uhhpc_qdr 
#! /bin/csh -f

# -------------------------------------------------------------------------
# UHHPC_QDR build specific settings
# -------------------------------------------------------------------------


source /etc/profile.d/lmod.csh
module purge

module load devel/CMake/3.12.1-intel-2018.5.274
module load lang/Perl/5.28.1-GCCcore-6.3.0
module load data/netCDF-Fortran/4.4.5-intel-2018.5.274
module load data/netCDF/4.6.2-intel-2018.5.274
module load toolchain/intel/2018.5.274

setenv NETCDF ${HOME}/netcdf4
setenv LD_LIBRARY_PATH ${HOME}/netcdf4/lib/:$LD_LIBRARY_PATH
setenv LIBRARY_PATH ${HOME}/netcdf4/lib/:$LIBRARY_PATH
setenv PATH ${HOME}/netcdf4/bin/:$PATH
setenv CPATH ${HOME}/netcdf4/include/:$CPATH

# -------------------------------------------------------------------------
# Build and runtime environment variables - edit before the initial build
# -------------------------------------------------------------------------
limit stacksize unlimited
limit datasize unlimited


env_mach_specific.uhhpc_hdr 
#! /bin/csh -f

# -------------------------------------------------------------------------
# UHHPC_QDR build specific settings
# -------------------------------------------------------------------------


source /etc/profile.d/lmod.csh
module purge

module load devel/CMake/3.12.1-intel-2018.5.274
module load lang/Perl/5.28.1-GCCcore-6.3.0
module load data/netCDF-Fortran/4.4.5-intel-2018.5.274
module load data/netCDF/4.6.2-intel-2018.5.274
module load toolchain/intel/2018.5.274

setenv NETCDF ${HOME}/netcdf4
setenv LD_LIBRARY_PATH ${HOME}/netcdf4/lib/:$LD_LIBRARY_PATH
setenv LIBRARY_PATH ${HOME}/netcdf4/lib/:$LIBRARY_PATH
setenv PATH ${HOME}/netcdf4/bin/:$PATH
setenv CPATH ${HOME}/netcdf4/include/:$CPATH

# -------------------------------------------------------------------------
# Build and runtime environment variables - edit before the initial build
# -------------------------------------------------------------------------
limit stacksize unlimited
limit datasize unlimited


Create the mkbatch files

mkbatch.uhhpc_qdr 
#! /bin/csh -f

#################################################################################
if ($PHASE == set_batch) then
#################################################################################

source ./Tools/ccsm_getenv || exit -1

module load lang/Perl/5.28.1-GCCcore-6.3.0
set ntasks = `${CASEROOT}/Tools/taskmaker.pl -sumonly`
set maxthrds = `${CASEROOT}/Tools/taskmaker.pl -maxthrds`
module purge
@ nodes = $ntasks / ${MAX_TASKS_PER_NODE}
if ( $ntasks % ${MAX_TASKS_PER_NODE} > 0) then
@ nodes = $nodes + 1
@ ntasks = $nodes * ${MAX_TASKS_PER_NODE}
endif
@ taskpernode = ${MAX_TASKS_PER_NODE} / ${maxthrds}
set qname = batch
set tlimit = "3-00:00:00"

if ($?TESTMODE) then
set file = $CASEROOT/${CASE}.test
else
set file = $CASEROOT/${CASE}.run
endif

cat >! $file << EOF1
#!/bin/csh
#SBATCH --job-name=${CASE}
#SBATCH --constraint="ib_qdr"
#SBATCH --distribution="*:*:*"
#SBATCH --partition=exclusive
#SBATCH --time=$tlimit
#SBATCH --job-name=${CASE}
#SBATCH --ntasks=$ntasks
#SBATCH --cpus-per-task=$maxthrds
#SBATCH --output=${CASE}.%A.out


# Configure the Intel MPI parameters
setenv I_MPI_FABRICS "shm:ofi"
setenv I_MPI_PMI_LIBRARY "/lib64/libpmi.so"
# ### FOR QDR NETWORK #####
setenv FI_PROVIDER "psm"
setenv FI_PSM_TAGGED_RMA 0
setenv FI_PSM_AM_MSG 1
setenv FI_PSM_UUID \`uuidgen\`
# # ###### ######## ###### ##
module purge

EOF1

#################################################################################
else if ($PHASE == set_exe) then
#################################################################################
module load lang/Perl/5.28.1-GCCcore-6.3.0
set maxthrds = `${CASEROOT}/Tools/taskmaker.pl -maxthrds`
set maxtasks = `${CASEROOT}/Tools/taskmaker.pl -sumtasks`
module purge


cat >> ${CASEROOT}/${CASE}.run << EOF1
# -------------------------------------------------------------------------
# Run the model
# -------------------------------------------------------------------------

sleep 25
cd \$RUNDIR
echo "\`date\` -- CSM EXECUTION BEGINS HERE"
setenv OMP_NUM_THREADS ${maxthrds}
module load data/netCDF-Fortran/4.4.5-intel-2018.5.274
module load data/netCDF/4.6.2-intel-2018.5.274
module load toolchain/intel/2018.5.274
srun --ntasks=${maxtasks} --cpu_bind=sockets --cpu_bind=verbose --kill-on-bad-exit \$EXEROOT/cesm.exe >&! cesm.log.\$LID
wait
echo "\`date\` -- CSM EXECUTION HAS FINISHED"

EOF1


#################################################################################
else if ($PHASE == set_larch) then
#################################################################################

#This is a place holder for a long-term archiving script

#################################################################################
else
#################################################################################

echo " PHASE setting of $PHASE is not an accepted value"
echo " accepted values are set_batch, set_exe and set_larch"
exit 1

#################################################################################
endif
#################################################################################


mkbatch.uhhpc_hdr 
#! /bin/csh -f

#################################################################################
if ($PHASE == set_batch) then
#################################################################################

source ./Tools/ccsm_getenv || exit -1
maxtasks
module load lang/Perl/5.28.1-GCCcore-6.3.0
set ntasks = `${CASEROOT}/Tools/taskmaker.pl -sumonly`
set maxthrds = `${CASEROOT}/Tools/taskmaker.pl -maxthrds`
module purge
@ nodes = $ntasks / ${MAX_TASKS_PER_NODE}
if ( $ntasks % ${MAX_TASKS_PER_NODE} > 0) then
@ nodes = $nodes + 1
@ ntasks = $nodes * ${MAX_TASKS_PER_NODE}
endif
@ taskpernode = ${MAX_TASKS_PER_NODE} / ${maxthrds}
set qname = batch
set tlimit = "3-00:00:00"

if ($?TESTMODE) then
set file = $CASEROOT/${CASE}.test
else
set file = $CASEROOT/${CASE}.run
endif

cat >! $file << EOF1
#!/bin/csh
#SBATCH --job-name=${CASE}
#SBATCH --constraint="ib_hdr"
#SBATCH --distribution="*:*:*"
#SBATCH --partition=exclusive
#SBATCH --time=$tlimit
#SBATCH --job-name=${CASE}
#SBATCH --ntasks=$ntasks
#SBATCH --cpus-per-task=$maxthrds
#SBATCH --output=${CASE}.%A.out


###### ######## ###### ##
# Libfabric method
###### ######## ###### ##
# Configure the Intel MPI parameters
setenv I_MPI_FABRICS "shm:ofi"
setenv I_MPI_PMI_LIBRARY "/lib64/libpmi.so"
 setenv I_MPI_HYDRA_TOPOLIB "ipl" # May be required if newer libfabric and intel MPI is used
### FOR HDR NETWORK #####
# https://ofiwg.github.io/libfabric/master/man/
# https://ofiwg.github.io/libfabric/v1.9.1/man/
setenv FI_PROVIDER "shm,verbs;ofi_rxm"
setenv FI_MR_CACHE_MONITOR "disabled" # currently a bug exists that a segfault could happen
setenv FI_VERBS_MR_CACHE_ENABLE "0" # currently a bug exists that a segfault could happen
setenv  FI_VERBS_INLINE_SIZE "256"
setenv FI_UNIVERSE_SIZE "${maxtasks}" # should equal at least the max number of tasks one task will communicate with
setenv FI_VERBS_IFACE "i"
###### ######## ###### ##

###### ######## ###### ##
# DAPL method (deprecated but not gone in Intel 2018)
###### ######## ###### ##
# Configure the Intel MPI parameters

#setenv I_MPI_FABRICS "shm:dapl"
#setenv I_MPI_PMI_LIBRARY "/lib64/libpmi.so"

###### ######## ###### ##

module purge

EOF1

#################################################################################
else if ($PHASE == set_exe) then
#################################################################################
module load lang/Perl/5.28.1-GCCcore-6.3.0
set maxthrds = `${CASEROOT}/Tools/taskmaker.pl -maxthrds`
set maxtasks = `${CASEROOT}/Tools/taskmaker.pl -sumtasks`
module purge


cat >> ${CASEROOT}/${CASE}.run << EOF1
# -------------------------------------------------------------------------
# Run the model
# -------------------------------------------------------------------------

sleep 25
cd \$RUNDIR
setenv OMP_NUM_THREADS ${maxthrds}
module load data/netCDF-Fortran/4.4.5-intel-2018.5.274
module load data/netCDF/4.6.2-intel-2018.5.274
module load toolchain/intel/2018.5.274
echo "\`date\` -- CSM EXECUTION BEGINS HERE" 
srun --ntasks=${maxtasks} --cpu_bind=sockets --cpu_bind=verbose --kill-on-bad-exit \$EXEROOT/cesm.exe >&! cesm.log.\$LID
wait
echo "\`date\` -- CSM EXECUTION HAS FINISHED"

EOF1


#################################################################################
else if ($PHASE == set_larch) then
#################################################################################

#This is a place holder for a long-term archiving script

#################################################################################
else
#################################################################################

echo " PHASE setting of $PHASE is not an accepted value"
echo " accepted values are set_batch, set_exe and set_larch"
exit 1

#################################################################################
endif
#################################################################################


Build  & Run

Once the above files are made and added to the  "/scripts/ccsm_utils/Machines/" of the CESM directory, we should now be able to build and then even run our model.


submission.slurm 
#!/bin/bash
#SBATCH --job-name=submit
#SBATCH --partition=sandbox
#SBATCH --time=00-04:00:00 ## time format is DD-HH:MM:SS
#SBATCH --cpus-per-task=8
#SBATCH --mem=64G
#SBATCH --output=submit.%A.out


MODELDIR=${HOME}/cesm1_2_2
CASEDIR=${HOME}/lus_scratch/cesm_output/
EXPNAME=ood.I5
CASEROOT=$CASEDIR/$EXPNAME

module purge
module load lang/Perl/5.28.1-GCCcore-6.3.0

#================================================================;
#===================== 1. CREATE CASE ===========================;
#================================================================;
cd $MODELDIR/scripts
./create_newcase -case $CASEDIR/$EXPNAME -compset FC5 -res f19_f19 -mach uhhpc_qdr

#=================== PE LAYOUT CONTROL ====================#
cd $CASEDIR/$EXPNAME

./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_ROF -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_WAV -val "24"
./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val "24"

./cesm_setup
#================================================================;
#========================== 2. BUILD ============================;
#================================================================;
cd $CASEDIR/$EXPNAME

#==================== RUN START CONTROL ==================#
./xmlchange -file env_run.xml -id RUN_TYPE -val "startup"

#==================== RUN TIME CONTROL =====================#
./xmlchange -file env_run.xml -id STOP_OPTION -val "nyears"
./xmlchange -file env_run.xml -id STOP_N -val "50"

#===================== RESTART CONTROL ==============#
./xmlchange -file env_run.xml -id REST_OPTION -val "nyears"
./xmlchange -file env_run.xml -id REST_N -val "1"

#================= OUTPUT CONTROL ================#
./xmlchange -file env_run.xml -id DOUT_S -val "TRUE"
./xmlchange -file env_run.xml -id DOUT_S_ROOT -val '$CASEROOT/output'


./xmlchange -file env_build.xml -id DEBUG -val "TRUE"

#========================= BUILD ===========================#
./$EXPNAME.build

#================================================================;
#========================== 3. RUN ============================;
#================================================================;
./$EXPNAME.submit



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