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Problems Porting CESM2.1.2 in my local cluster

A

adrianabossolasco

Member
Hi all
I am trying to port CESM2.1.2 in one local cluster (called artemis). For that I have create in my home a .cime/ directory to modify the config_machines.xml, config_batch.xml and config_compiles.xml
Then when I run the scripts_regression_tests.py I get a lot of error, I think should be something about my config_machines.xml file, I don't have to much knowledge on this, so probably I have a very basic error.
I attach here the .xml files and also the src.txt file with the results of run the script regression test.

Any help will be very useful

Thanks!
 

Attachments

  • srt.txt
    196.7 KB · Views: 8
  • config_compilers.txt
    41.2 KB · Views: 13
  • config_batch.txt
    23.1 KB · Views: 5
  • config_machines.txt
    108.8 KB · Views: 15
J

jedwards

CSEG and Liaisons
Staff member
The files in .cime are appended to the default files and as such should only contain the additions that you want to make and not be copies of the entire files.
 
A

adrianabossolasco

Member
Hi jedwards

Now I was able to create a new case and setup, but have problems when I build my case. Apparently there is a problem with the flags for NETCDF PATH
Here is the error that I have

gmake -f /home/abossolasco/cesm2.1.2/cime/scripts/mycase/Tools/Makefile -C /home/abossolasco/cesm2.1.2/cime/scripts/mycase/run/mycase/bld/intel/openmpi/nodebug/nothreads/mct CASEROOT=/home/abossolasco/cesm2.1.2/cime/scripts/mycase MODEL=mct /home/abossolasco/cesm2.1.2/cime/scripts/mycase/run/mycase/bld/intel/openmpi/nodebug/nothreads/mct/Makefile.conf
gmake: Entering directory `/home/abossolasco/cesm2.1.2/cime/scripts/mycase/run/mycase/bld/intel/openmpi/nodebug/nothreads/mct'
gmake: Leaving directory `/home/abossolasco/cesm2.1.2/cime/scripts/mycase/run/mycase/bld/intel/openmpi/nodebug/nothreads/mct'
cat: Filepath: No such file or directory
ERROR: Python 2, minor version 7 is required, you have 2.6
ERROR: Python 2, minor version 7 is required, you have 2.6
/home/abossolasco/cesm2.1.2/cime/scripts/mycase/Tools/Makefile:199: *** NETCDF not found: Define NETCDF_PATH or NETCDF_C_PATH and NETCDF_FORTRAN_PATH in config_machines.xml or config_compilers.xml. Stop.
ERROR: cat: Filepath: No such file or directory
ERROR: Python 2, minor version 7 is required, you have 2.6
ERROR: Python 2, minor version 7 is required, you have 2.6
/home/abossolasco/cesm2.1.2/cime/scripts/mycase/Tools/Makefile:199: *** NETCDF not found: Define NETCDF_PATH or NETCDF_C_PATH and NETCDF_FORTRAN_PATH in config_machines.xml or config_compilers.xml. Stop.


I attached my config_compilers.xml file

I also doesn't understand why the model took by default python 2.6 because in my .bashrc I have loaded python 2.7
module load python/2.7.8

I really apreciate your help

Best

Adriana
 

Attachments

  • config_compilers.txt
    41.2 KB · Views: 10
J

jedwards

CSEG and Liaisons
Staff member
First you really need to fix this issue: ERROR: Python 2, minor version 7 is required, you have 2.6
python 2 is end of life, you should install python3.

In config_compilers.xml you have

<compiler MACH="artemis">
<CONFIG_ARGS>
<base/>
</CONFIG_ARGS>
<CPPDEFS>
<append/>
</CPPDEFS>
<ESMF_LIBDIR/>
<MPI_LIB_NAME/>
<MPI_PATH/>/cm/shared/apps/openmpi/intel/64/1.8</MPI_PATH>
<NETCDF_PATH>/cm/shared/apps/tmp/netcdf/parallel/intel/4.3.2</NETCDF_PATH>
<PNETCDF_PATH/> /cm/shared/apps/tmp/pnetcdf/intel/1.5.0</PNETCDF_PATH>
<SLIBS>
<append></append>
</SLIBS>

</compiler>

The empty settings for CONFIG_ARGS, CPPDEFS, SLIBS cause the defaults set above in the file to be removed. The paths for NETCDF and PNETCDF should be set in config_machines.xml instead of here.
 
A

adrianabossolasco

Member
Hi jedwards

Thanks for the answer. I resolved the python problem. Next I have changed my config_compilers file and put the NETCDF and PNETCF paths in <environment_variables> in the configure_machines.
Now have other problems when I build my case, I think I still have problems with compiler configuration, I attach the pio.bldlog
Is something with the Pnetcdf I think.... but I check the path and is ok


Thanks for your help

Adriana
 

Attachments

  • pio.bldlog.200724-162516.txt
    7.5 KB · Views: 9
J

jedwards

CSEG and Liaisons
Staff member
You can try building without pnetcdf, check your directories in /cm/shared/apps/tmp/pnetcdf/intel/1.5.0 for file pnetcdf.mod
 
A

adrianabossolasco

Member
Hi jedwards!
Great! works now! :)
But as many people I have problems now with download the inputdata. When I submit the case (case.submit) says:

Client protocol gftp not enabled
Using protocol wget with user anonymous and passwd user@example.edu
Could not connect to repo 'ftp://ftp.cgd.ucar.edu/cesm/inputdata'
This is most likely either a proxy, or network issue .
checksum.dat.raw' using NoneType protocol.
Traceback (most recent call last):
File "./case.submit", line 107, in <module>
_main_func(__doc__)
File "./case.submit", line 104, in _main_func
mail_user=mail_user, mail_type=mail_type, batch_args=batch_args)
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 157, in submit
custom_success_msg_functor=verbatim_success_msg)
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/utils.py", line 1683, in run_and_log_case_status
rv = func()
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 155, in <lambda>
batch_args=batch_args)
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 85, in _submit
case.check_case()
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 171, in check_case
self.check_all_input_data()
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 163, in check_all_input_data
_download_checksum_file(self.get_value("RUNDIR"))
File "/home/abossolasco/cesm2.1.2/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 54, in _download_checksum_file
success = server.getfile(rel_path, new_file)
AttributeError: 'NoneType' object has no attribute 'getfile'


I have also tried this command
wget --no-check-certificate --user anonymous --password user@example.edu --spider ftp://ftp.cgd.ucar.edu/cesm/inputdata

and I get this:
--2020-07-27 17:26:52-- ftp://ftp.cgd.ucar.edu/cesm/inputdata
=> “inputdata”
Resolving ftp.cgd.ucar.edu... 128.117.23.220
Connecting to ftp.cgd.ucar.edu|128.117.23.220|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /cesm ... done.
==> SIZE inputdata ... done.
==> PASV ... couldn’t connect to 128.117.23.220 port 49167: Connection timed out
Retrying.

So it is suppose that there is a problem with my machine? How can I resolve this?


Thanks

Adriana
 
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