LANL IC overview and search

DST Calendar (within LANL network)

Information about Slurm:

Machine specifications: chicoma turquoise network

login: ssh -t <username> ssh ch-fe

File locations:

  • small home directory, for start-up scripts only: /users/<username>

  • home directory, backed up: /usr/projects/climate/<username>

  • scratch space, not backed up: /lustre/scratch4/turquoise/<username> or scratch5

Check compute time:

  • sacctmgr list assoc user=<username> format=Cluster,Account%18,Partition,QOS%45

  • Which is my default account? sacctmgr list user <username>

  • sshare -a | head -2; sshare -a | grep $ACCOUNT | head -1

  • sreport -t Hours cluster AccountUtilizationByUser start=2019-12-02 | grep $ACCOUNT

  • check job priority: sshare -a | head -2; sshare -a | grep $ACCOUNT

  • LANL Cluster Usage Overview (within LANL yellow)

Check disk usage:

  • your home space: chkhome

  • total disk usage in Petabytes: df -BP |head -n 1; df -BP|grep climate; df -BP |grep scratch


  • turquoise HPSS archive

  • archive front end: ssh -t <username> ssh ar-tn

  • storage available at: cd /archive/<project_name>

  • you can just copy files directly into here for a particular project.

LANL uses slurm. To obtain an interactive node:

salloc -N 1 -t 2:0:0 --qos=interactive

Use --account=ACCOUNT_NAME to change to a particular account.


There has not yet been a release with Chicoma-CPU, so the following applies to the release of compass v1.2.0, when it happens.

Chicoma’s CPU and GPU nodes have different configuration options and compilers. We only support Chicoma-CPU at this time.

config options

Here are the default config options added when you choose -m chicoma-cpu when setting up test cases or a test suite:

# The paths section describes paths that are used within the ocean core test
# cases.

# A shared root directory where MPAS standalone data can be found
database_root = /usr/projects/regionalclimate/COMMON_MPAS/mpas_standalonedata/

# the path to the base conda environment where compass environments have
# been created
compass_envs = /usr/projects/climate/SHARED_CLIMATE/compass/chicoma-cpu/base

# Options related to deploying a compass conda environment on supported
# machines

# the compiler set to use for system libraries and MPAS builds
compiler = gnu

# the system MPI library to use for gnu compiler
mpi_gnu = mpich

# the base path for spack environments used by compass
spack = /usr/projects/climate/SHARED_CLIMATE/compass/chicoma-cpu/spack

# whether to use the same modules for hdf5, netcdf-c, netcdf-fortran and
# pnetcdf as E3SM (spack modules are used otherwise)
use_e3sm_hdf5_netcdf = True

# The parallel section describes options related to running jobs in parallel

# account for running diagnostics jobs
account =

# cores per node on the machine
cores_per_node = 128

# threads per core (set to 1 because trying to hyperthread seems to be causing
# hanging on chicoma)
threads_per_core = 1

# Config options related to creating a job script

# The job partition to use
partition = standard

# The job quality of service (QOS) to use
qos = standard

Additionally, some relevant config options come from the mache package:

# The parallel section describes options related to running jobs in parallel

# parallel system of execution: slurm, cobalt or single_node
system = slurm

# whether to use mpirun or srun to run a task
parallel_executable = srun

# cores per node on the machine
cores_per_node = 256

# available partition(s) (default is the first)
partitions = standard, gpu

# quality of service (default is the first)
qos = standard, debug

# Config options related to spack environments

# whether to load modules from the spack yaml file before loading the spack
# environment
modules_before = False

# whether to load modules from the spack yaml file after loading the spack
# environment
modules_after = False


By default, hyperthreading has been disable on Chicoma. We had found some some issues with runs hanging in early testing that seemed to be mitigated by disabling hyperthreading. We disable hyperthreading by setting threads_per_core = 1 and reducing cores_per_node to not include the 2 hyperthreads. You can re-enable hyperthreading on Chicoma by providing a user config file where you set threads_per_core and cores_per_node as follows:

# The parallel section describes options related to running jobs in parallel

# cores per node on the machine (including hyperthreading)
cores_per_node = 256

# threads per core with hyperthreading
threads_per_core = 2

Gnu on Chicoma-CPU

To load the compass environment and modules, and set appropriate environment variables:

source /usr/projects/climate/SHARED_CLIMATE/compass/chicoma-cpu/

To build the MPAS model with

make [DEBUG=true] [OPENMP=true] [ALBANY=true] gnu-cray