Problem with porting

[Tanja]

I am trying to port my machine, but I have problems running "scripts_regression_tests.py".
I am on Ubuntu VirtualBox.
Below is my "config_machines.xml" file. When running "scripts_regression_tests.py" I get the error message saying "inputdata root is not a directory".
Best regards
Tanja



<?xml version="1.0"?>
<!-- This is an ordered list, not all fields are required, optional fields are noted below. -->
<config_machines version="2.0">
<!-- MACH is the name that you will use in machine options -->
<machine MACH="tanja-VirtualBox">

<!-- DESC: a text description of the machine, this field is current not used in code-->
<DESC></DESC>

<!-- NODENAME_REGEX: a regular expression used to identify this machine
it must work on compute nodes as well as login nodes, use machine option
to create_test or create_newcase if this flag is not available -->
<NODENAME_REGEX>tanja-VirtualBox</NODENAME_REGEX>

<!-- OS: the operating system of this machine. Passed to cppflags for
compiled programs as -DVALUE recognized are LINUX, AIX, Darwin, CNL -->
<OS>LINUX</OS>

<!-- PROXY: optional http proxy for access to the internet-->
<PROXY> https://howto.get.out </PROXY>
<!-- COMPILERS: compilers supported on this machine, comma seperated list, first is default -->

<COMPILERS>intel,gnu</COMPILERS>

<!-- MPILIBS: mpilibs supported on this machine, comma seperated list,
first is default, mpi-serial is assumed and not required in this list-->
<MPILIBS>mpt,openmpi,impi</MPILIBS>

<!-- PROJECT: A project or account number used for batch jobs
This value is used for directory names. If different from
actual accounting project id, use CHARGE_ACCOUNT
can be overridden in environment or $HOME/.cime/config -->
<PROJECT>tanja_clm</PROJECT>

<!-- CHARGE_ACCOUNT: A project or account number used for batch jobs
This is the actual project used for cost accounting set in
the batch script (ex. #PBS -A charge_account). Will default
to PROJECT if not set.
can be overridden in environment or $HOME/.cime/config -->
<CHARGE_ACCOUNT>tanja-clm</CHARGE_ACCOUNT>

<!-- SAVE_TIMING_DIR: (Acme only) directory for archiving timing output -->
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>

<!-- SAVE_TIMING_DIR_PROJECTS: (Acme only) projects whose jobs archive timing output -->
<SAVE_TIMING_DIR_PROJECTS> </SAVE_TIMING_DIR_PROJECTS>

<!-- CIME_OUTPUT_ROOT: Base directory for case output,
the case/bld and case/run directories are written below here -->
<CIME_OUTPUT_ROOT>clm_output</CIME_OUTPUT_ROOT>

<!-- DIN_LOC_ROOT: location of the inputdata data directory
inputdata is downloaded automatically on a case by case basis as
long as the user has write access to this directory. We recommend that
all cime model users on a system share an inputdata directory
as it can be quite large -->
<DIN_LOC_ROOT>clm_input</DIN_LOC_ROOT>

<!-- DIN_LOC_ROOT_CLMFORC: override of DIN_LOC_ROOT specific to CLM
forcing data -->
<DIN_LOC_ROOT_CLMFORC>clm_input</DIN_LOC_ROOT_CLMFORC>

<!-- DOUT_S_ROOT: root directory of short term archive files, short term
archiving moves model output data out of the run directory, but
keeps it on disk-->
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>

<!-- BASELINE_ROOT: Root directory for system test baseline files -->
<BASELINE_ROOT>$ENV{CESMDATAROOT}/cesm_baselines</BASELINE_ROOT>

<!-- CCSM_CPRNC: location of the cprnc tool, compares model output in testing-->
<CCSM_CPRNC>$ENV{CESMDATAROOT}/tools/cime/tools/cprnc/cprnc.cheyenne</CCSM_CPRNC>

<!-- GMAKE: gnu compatible make tool, default is 'gmake' -->
<GMAKE>gcc</GMAKE>

<!-- GMAKE_J: optional number of threads to pass to the gmake flag -->
<GMAKE_J>8</GMAKE_J>

<!-- BATCH_SYSTEM: batch system used on this machine,
supported values are: none, cobalt, lsf, pbs, slurm -->
<BATCH_SYSTEM>none</BATCH_SYSTEM>

<!-- SUPPORTED_BY: contact information for support for this system
this field is not used in code -->
<SUPPORTED_BY>cseg</SUPPORTED_BY>

<!-- MAX_TASKS_PER_NODE: maximum number of threads*tasks per
shared memory node on this machine,
should always be >= MAX_MPITASKS_PER_NODE -->
<MAX_TASKS_PER_NODE>36</MAX_TASKS_PER_NODE>

<!-- MAX_MPITASKS_PER_NODE: number of physical PES per shared node on
this machine, in practice the MPI tasks per node will not exceed this value -->
<MAX_MPITASKS_PER_NODE>36</MAX_MPITASKS_PER_NODE>

<!-- PROJECT_REQUIRED: Does this machine require a project to be specified to
the batch system? See PROJECT above -->
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>

<!-- mpirun: The mpi exec to start a job on this machine, supported values
are values listed in MPILIBS above, default and mpi-serial -->
<mpirun mpilib="default">
<!-- name of the exectuable used to launch mpi jobs -->
<executable>mpif90</executable>
<!-- arguments to the mpiexec command, the name attribute here is ignored-->
<arguments>
<arg name="labelstdout">-p "%g:"</arg>
<arg name="threadplacement"> omplace </arg>
</arguments>
</mpirun>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<!-- module system: allowed module_system type values are:
module http://www.tacc.utexas.edu/tacc-projects/mclay/lmod
soft softenv-intro - An introduction to the SoftEnv system and how to use it
none
-->
<module_system type="module">
<init_path lang="perl">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/perl</init_path>
<init_path lang="python">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/env_modules_python.py</init_path>
<init_path lang="csh">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/csh</init_path>
<init_path lang="sh">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/sh</init_path>
<cmd_path lang="perl">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/libexec/lmod perl</cmd_path>
<cmd_path lang="python">/glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/libexec/lmod python</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<modules>
<command name="purge"/>
<command name="load">ncarenv/1.0</command>
</modules>
<modules compiler="intel">
<command name="load">intel/16.0.3</command>
<command name="load">mkl</command>
</modules>
<modules compiler="gnu">
<command name="load">gnu/6.3.0</command>
</modules>
<modules>
<command name="load">mpt/2.15</command>
<command name="load">ncarcompilers/0.3.5</command>
</modules>
<modules mpilib="mpi-serial">
<command name="load">netcdf/4.4.1</command>
</modules>
<modules mpilib="mpt">
<command name="load">netcdf/4.4.1</command>
<!-- <command name="load">netcdf-mpi/4.4.1</command> -->
<command name="load">pnetcdf/1.8.0</command>
</modules>
</module_system>
<!-- environment variables, a blank entry will unset a variable -->
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
<env name="MPI_TYPE_DEPTH">16</env>
</environment_variables>
<!-- resource settings as defined in 36.13. resource — Resource usage information — Python 2.7.17 documentation -->
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
</config_machines>

 

[jedwards]

You need to create the inputdata directory in your file system:

<!-- DIN_LOC_ROOT: location of the inputdata data directory
inputdata is downloaded automatically on a case by case basis as
long as the user has write access to this directory. We recommend that
all cime model users on a system share an inputdata directory
as it can be quite large -->
<DIN_LOC_ROOT>clm_input</DIN_LOC_ROOT>

It should be a full path and you need to create it before you can create a case.

 

[mluongo]

You need to create the inputdata directory in your file system:

<!-- DIN_LOC_ROOT: location of the inputdata data directory
inputdata is downloaded automatically on a case by case basis as
long as the user has write access to this directory. We recommend that
all cime model users on a system share an inputdata directory
as it can be quite large -->
<DIN_LOC_ROOT>clm_input</DIN_LOC_ROOT>

It should be a full path and you need to create it before you can create a case.

Hi jedwards,
I seem to be having a similar problem. To reproduce results created using CESM1.1.2 I am trying to run the model on Cheyenne. When I try to configure the case using ./cesm_setup -clean I ran into an issue regarding changing the perl syntax (which you answered here: https://bb.cgd.ucar.edu/cesm/threads/error-in-producing-namelist.4981/) and it seems like I am running into a similar issue here with the build-namelist file which is read-only.

Should I be creating an inputdata directory of the CESM1.1.2 model so that I can create a case directly from there rather than /glade/p/cesmdata/cseg/releases/cesm1_1_2 and then I can edit the code block to account for that perl syntactical issue? If so, how do I go about doing that?

Thanks for you help! Errors below.

Matt

mluongo@cheyenne2:~/CESM1_runs/yellow> ./cesm_setup
Macros script already created ...skipping
Creating batch script yellow.run
env: ‘./Tools/mkbatch.cheyenne’: No such file or directory
env: ‘./Tools/mkbatch.cheyenne’: No such file or directory
Locking file env_mach_pes.xml
Running preview_namelist script
syntax error at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 790, near "$model qw(cpl atm lnd ice ocn glc rof)"
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 793.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 798.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 799.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 800.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 801.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 802.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 803.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 804.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 818.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 820.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 826.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 828.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 834.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 840.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 846.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 852.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 858.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 864.
Global symbol "$model" requires explicit package name at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 870.
syntax error at /glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist line 880, near "}"
/glade/p/cesmdata/cseg/releases/cesm1_1_2/models/drv/bld/build-namelist has too many errors.
ERROR: cpl.buildnml.csh failed
ERROR: /glade/u/home/mluongo/CESM1_runs/yellow/preview_namelists failed: 25344