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ERROR: Could not initialize machine object from /mnt/sdb3/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml

Gemstone

Wonseok Lee
New Member
I just downloaded the CESM2 code on my labtop.
And to run the FHIST compset, and create a case called fhist, run the following commands

cd cime/scripts/
./create_newcase --case fhist --compset FHIST --res f09_f09_mg17

and the results show

Compset longname is HIST_CAM60_CLM50%BGC-CROP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /mnt/sdb3/my_cesm_sandbox/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:BGC (vert. resol. CN and methane) with prognostic crop:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /mnt/sdb3/my_cesm_sandbox/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1979-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_0.9x1.25_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/share/domains/domain.ocn.fv0.9x1.25_gx1v7.151020.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Compset specific settings: name is RUN_TYPE and value is hybrid
Compset specific settings: name is RUN_REFCASE and value is b.e20.BHIST.f09_g17.20thC.297_01_v2
Compset specific settings: name is RUN_REFDATE and value is 1979-01-01
Compset specific settings: name is RUN_REFDIR and value is cesm2_init
Could not find machine match for 'localhost' or 'sslab-server'
ERROR: Could not initialize machine object from /mnt/sdb3/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml or /home/waccm/.cime/config_machines.xml

how can I figure out this problem ?
 

mlevy

Michael Levy
CSEG and Liaisons
Staff member
You need to define config_machines.xml and place it in either $CESMROOT/cime/config/cesm/machines/ or $HOME/.cime/. I would recommend the former if you expect other users to create cases from your CESM sandbox and the latter if you plan on running cases from multiple versions of CESM on the machine. If neither of those apply, I recommend using $HOME/.cime/ in case you decide to delete CESM at some point in the future and then later want to re-download it and run some more.

To learn more about what is required in the file, see the CIME documentation.
 

Gemstone

Wonseok Lee
New Member
Thanks for reply.
Then should I change the bolded directories in the file of config_machines.xml ?
I'm not familiar with this work....

For example, line 195 to line 242 shows

195 <machine MACH="centos7-linux">
196 <DESC>
197 Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
198 using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
199 </DESC>
200 <NODENAME_REGEX>regex.expression.matching.your.machine</NODENAME_REGEX>
201 <OS>LINUX</OS>
202 <PROXY> https://howto.get.out </PROXY>
203 <COMPILERS>gnu</COMPILERS>
204 <MPILIBS>mpich</MPILIBS>
205 <PROJECT>none</PROJECT>
206 <SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
207 <CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
208 <DIN_LOC_ROOT>$ENV{HOME}/cesm/inputdata</DIN_LOC_ROOT>
209 <DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
210 <DOUT_S_ROOT>$ENV{HOME}/cesm/archive/$CASE</DOUT_S_ROOT>
211 <BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
212 <CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
213 <GMAKE>gmake</GMAKE>
214 <GMAKE_J>8</GMAKE_J>
215 <BATCH_SYSTEM>none</BATCH_SYSTEM>
216 <SUPPORTED_BY>me@my.address</SUPPORTED_BY>
217 <MAX_TASKS_PER_NODE>8</MAX_TASKS_PER_NODE>
218 <MAX_MPITASKS_PER_NODE>8</MAX_MPITASKS_PER_NODE>
219 <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
220 <mpirun mpilib="default">
221 <executable>mpiexec</executable>
222 <arguments>
223 <arg name="ntasks"> -np {{ total_tasks }} </arg>
224 </arguments>
225 </mpirun>
226 <module_system type="module">
227 <init_path lang="perl">/usr/share/Modules/init/perl.pm</init_path>
228 <init_path lang="python">/usr/share/Modules/init/python.py</init_path>
229 <init_path lang="csh">/usr/share/Modules/init/csh</init_path>
230 <init_path lang="sh">/usr/share/Modules/init/sh</init_path>
231 <cmd_path lang="perl">/usr/bin/modulecmd perl</cmd_path>
232 <cmd_path lang="python">/usr/bin/modulecmd python</cmd_path>
233 <cmd_path lang="sh">module</cmd_path>
234 <cmd_path lang="csh">module</cmd_path>
235 <modules>
236 <command name="purge"/>
237 </modules>
238 <modules compiler="gnu">
239 <command name="load">compiler/gnu/7.2.0</command>
240 <command name="load">mpi/gcc/mpich-3.2</command>
241 <command name="load">tool/netcdf/4.4.1.1/gcc</command>
242 <command name="load">tool/parallel-netcdf/mpich</command>
 

Gemstone

Wonseok Lee
New Member
I changed this part using "uname -n"

200 <NODENAME_REGEX>regex.expression.matching.your.machine</NODENAME_REGEX>

to

200 <NODENAME_REGEX>my.machine</NODENAME_REGEX>

then It works

afterthat I executed the ./check_input_data
but another ERRORs come up..

ERROR: module command /usr/bin/modulecmd python load compiler/gnu/7.2.0 mpi/gcc/mpich-3.2 tool/netcdf/4.4.1.1/gcc tool/parallel-netcdf/mpich failed with message:
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'compiler/gnu/7.2.0'
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'mpi/gcc/mpich-3.2'
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'tool/netcdf/4.4.1.1/gcc'
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'tool/parallel-netcdf/mpich'
 

mlevy

Michael Levy
CSEG and Liaisons
Staff member
Do you use modules to maintain different libraries? If so, lines 239 - 242 should include module load statements used to make sure the gnu fortran compiler, an mpi library, netcdf, and pnetcdf are installed (pnetcdf is not strictly necessary)
 

mlevy

Michael Levy
CSEG and Liaisons
Staff member
Hi, is your problem solved? I have the same problem now, can you help me?

I also meet the same problem,and it says Could not find machine match for 'log03.hpc.com' or 'log03'

@ziyucheng and @lvxin -- what version of CESM are you each running? The first response in this thread should fix Could not find machine match errors in CESM 2.0

You need to define config_machines.xml and place it in either $CESMROOT/cime/config/cesm/machines/ or $HOME/.cime/. I would recommend the former if you expect other users to create cases from your CESM sandbox and the latter if you plan on running cases from multiple versions of CESM on the machine. If neither of those apply, I recommend using $HOME/.cime/ in case you decide to delete CESM at some point in the future and then later want to re-download it and run some more.

To learn more about what is required in the file, see the CIME documentation.
 

ella

ellawang
New Member
Hi, I met the same problem. I saw your reply above. But as a beginner here, I don't know how to define the config_machines.xml. It is many lines of code in it. Can anyone tell me how to do that or suggest a link on how to do it?Thanks so much!
 

lvxin

lvxin
New Member
Hi, I met the same problem. I saw your reply above. But as a beginner here, I don't know how to define the config_machines.xml. It is many lines of code in it. Can anyone tell me how to do that or suggest a link on how to do it?Thanks so much!
This site has many tutorials
 
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