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./case.submit error

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H

huo

huo
New Member
When I submit the case I1PtClm50SpRsGs,some error occur whensubmit the file.

There are many liines like this,
env_batch.xml appears to have changed, regenerating batch scripts
manual edits to these file will be lost!

Creating batch scripts
Writing case.run script from input template /public1/home/sca0755/my_cesm_sandbox/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /public1/home/sca0755/my_cesm_sandbox/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Creating component namelists
2021-06-15 19:28:37 atm
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/data_comps_mct/datm/cime_config/buildnml
2021-06-15 19:28:38 lnd
Calling /public1/home/sca0755/my_cesm_sandbox/components/clm//cime_config/buildnml
2021-06-15 19:28:38 ice
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sice/cime_config/buildnml
2021-06-15 19:28:38 ocn
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/socn/cime_config/buildnml
2021-06-15 19:28:38 rof
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/srof/cime_config/buildnml
2021-06-15 19:28:38 glc
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml
2021-06-15 19:28:38 wav
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/swav/cime_config/buildnml
2021-06-15 19:28:38 iac
Running /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/siac/cime_config/buildnml
2021-06-15 19:28:39 esp
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml
2021-06-15 19:28:39 cpl
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildnml
Checking that inputdata is available as part of case submission
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Client protocol gftp not enabled
Using protocol wget with user anonymous and passwd user@example.edu
Trying to download file: '../inputdata_checksum.dat' to path '/public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/run/inputdata_checksum.dat.raw' using WGET protocol.
SUCCESS

Using protocol ftp with user anonymous and passwd user@example.edu
server address ftp.cgd.ucar.edu root path cesm/inputdata
ftp login timeout! [Errno -2] Name or service not known
Using protocol svn with user and passwd

Could not connect to svn repo 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata'
This is most likely either a credential, proxy, or network issue .
To check connection and store your credential run 'svn ls https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata' and permanently store your password
Client protocol None not enabled
Checking server ftp://gridanon.cgd.ucar.edu:2811/cesm/inputdata/ with protocol gftp
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol gftp not enabled
Checking server ftp://ftp.cgd.ucar.edu/cesm/inputdata/ with protocol wget
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol wget with user anonymous and passwd user@example.edu
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Trying to download file: 'share/domains/UNSET' to path '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET' using WGET protocol.
wget failed with output: and errput --2021-06-15 19:34:04-- ftp://ftp.cgd.ucar.edu/cesm/inputdata/share/domains/UNSET
Connecting to 172.16.58.14:8888... connected.
Proxy request sent, awaiting response... 404 Not Found
2021-06-15 19:34:09 ERROR 404: Not Found.

Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server ftp.cgd.ucar.edu/cesm/inputdata with protocol ftp
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol ftp with user anonymous and passwd user@example.edu
server address ftp.cgd.ucar.edu root path cesm/inputdata
ftp login timeout! [Errno -2] Name or service not known
Checking server https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata with protocol svn
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol svn with user and passwd

Could not connect to svn repo 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata'
This is most likely either a credential, proxy, or network issue .
To check connection and store your credential run 'svn ls https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata' and permanently store your password
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Trying to download file: 'share/domains/UNSET' to path '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET' using SVN protocol.
svn export failed with output: and errput svn: E175002: Unable to connect to a repository at URL 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/share/domains/UNSET'
svn: E175002: OPTIONS of 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/share/domains/UNSET': Could not resolve hostname `svn-ccsm-inputdata.cgd.ucar.edu': Host not found (https://svn-ccsm-inputdata.cgd.ucar.edu)

Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server None with protocol None
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol None not enabled
ERROR: Could not find all inputdata on any server

What can I do to solve the problem?

Thanks.
 
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member
It's not finding all of the inpudata needed for your case.

In your case directory run the check_input_data script and see what it says. One problem I see is that you haven't set the domain file needed for your case. The I1PtClm50SpRsGs compset is only setup to work out of the box for a couple single point resolutions. If you want to run it for your own grid, there's a bunch of things you have to do to get it to work. See the CLM User's Guide for more information on how to do this.
 
H

huo

huo
New Member
erik said:
It's not finding all of the inpudata needed for your case.

In your case directory run the check_input_data script and see what it says. One problem I see is that you haven't set the domain file needed for your case. The I1PtClm50SpRsGs compset is only setup to work out of the box for a couple single point resolutions. If you want to run it for your own grid, there's a bunch of things you have to do to get it to work. See the CLM User's Guide for more information on how to do this.
Click to expand...
thanks! I solved the problem.But there is anothere problem.When I ./case.submit:
the CaseStatus file:
model execution error
ERROR: Command: 'mpirun -n 1 /public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed with error '' from dir '/public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/run'
---------------------------------------------------
case.run error
ERROR: RUN FAIL: Command 'mpirun -n 1 /public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed
See log file for details: /public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/run/cesm.log.272516.210616-160453
I want to run a single point.I do not know how to solve this problem.Thanks for your reply!
 

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  • cesm.log.272516.txt
    9.8 KB · Views: 12
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member
The stack trace that the cesm.log tells you is that it's dying in the datm model reading in one of the streams. To debug this you should also look at the atm.log file and figure out which stream text file it's choking on, and then look at that file to figure out why. There is something wrong in how it's configured. Another thing that can be helpful is to setup a simple out of the box case that works and then compare how it's different to your case that you want to work. Get it to work in another simple case, and then work through what you need to change in your case to get it to go.
 
Z

zqzq

zqzqzqzq
Member
huo said:
When I submit the case I1PtClm50SpRsGs,some error occur whensubmit the file.

There are many liines like this,
env_batch.xml appears to have changed, regenerating batch scripts
manual edits to these file will be lost!

Creating batch scripts
Writing case.run script from input template /public1/home/sca0755/my_cesm_sandbox/cime/config/cesm/machines/template.case.run
Creating file .case.run
Writing case.st_archive script from input template /public1/home/sca0755/my_cesm_sandbox/cime/config/cesm/machines/template.st_archive
Creating file case.st_archive
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Creating component namelists
2021-06-15 19:28:37 atm
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/data_comps_mct/datm/cime_config/buildnml
2021-06-15 19:28:38 lnd
Calling /public1/home/sca0755/my_cesm_sandbox/components/clm//cime_config/buildnml
2021-06-15 19:28:38 ice
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sice/cime_config/buildnml
2021-06-15 19:28:38 ocn
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/socn/cime_config/buildnml
2021-06-15 19:28:38 rof
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/srof/cime_config/buildnml
2021-06-15 19:28:38 glc
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sglc/cime_config/buildnml
2021-06-15 19:28:38 wav
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/swav/cime_config/buildnml
2021-06-15 19:28:38 iac
Running /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/siac/cime_config/buildnml
2021-06-15 19:28:39 esp
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml
2021-06-15 19:28:39 cpl
Calling /public1/home/sca0755/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildnml
Checking that inputdata is available as part of case submission
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Client protocol gftp not enabled
Using protocol wget with user anonymous and passwd user@example.edu
Trying to download file: '../inputdata_checksum.dat' to path '/public1/home/sca0755/my_cesm_sandbox/cimecases/Tang1/run/inputdata_checksum.dat.raw' using WGET protocol.
SUCCESS

Using protocol ftp with user anonymous and passwd user@example.edu
server address ftp.cgd.ucar.edu root path cesm/inputdata
ftp login timeout! [Errno -2] Name or service not known
Using protocol svn with user and passwd

Could not connect to svn repo 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata'
This is most likely either a credential, proxy, or network issue .
To check connection and store your credential run 'svn ls https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata' and permanently store your password
Client protocol None not enabled
Checking server ftp://gridanon.cgd.ucar.edu:2811/cesm/inputdata/ with protocol gftp
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol gftp not enabled
Checking server ftp://ftp.cgd.ucar.edu/cesm/inputdata/ with protocol wget
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol wget with user anonymous and passwd user@example.edu
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Trying to download file: 'share/domains/UNSET' to path '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET' using WGET protocol.
wget failed with output: and errput --2021-06-15 19:34:04-- ftp://ftp.cgd.ucar.edu/cesm/inputdata/share/domains/UNSET
Connecting to 172.16.58.14:8888... connected.
Proxy request sent, awaiting response... 404 Not Found
2021-06-15 19:34:09 ERROR 404: Not Found.

Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server ftp.cgd.ucar.edu/cesm/inputdata with protocol ftp
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol ftp with user anonymous and passwd user@example.edu
server address ftp.cgd.ucar.edu root path cesm/inputdata
ftp login timeout! [Errno -2] Name or service not known
Checking server https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata with protocol svn
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol svn with user and passwd

Could not connect to svn repo 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata'
This is most likely either a credential, proxy, or network issue .
To check connection and store your credential run 'svn ls https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata' and permanently store your password
Loading input file list: 'Buildconf/clm.input_data_list'
Model clm missing file fatmlndfrc = '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET'
Trying to download file: 'share/domains/UNSET' to path '/public1/home/sca0755/my_cesm_sandbox/inputdata/share/domains/UNSET' using SVN protocol.
svn export failed with output: and errput svn: E175002: Unable to connect to a repository at URL 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/share/domains/UNSET'
svn: E175002: OPTIONS of 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/share/domains/UNSET': Could not resolve hostname `svn-ccsm-inputdata.cgd.ucar.edu': Host not found (https://svn-ccsm-inputdata.cgd.ucar.edu)

Loading input file list: 'Buildconf/datm.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server None with protocol None
Setting Environment NETCDF_PATH=/public1/soft/netcdf/4.6.3-intel20
Setting Environment PNETCDF_PATH=/public1/soft/pnetcdf/1.12.1
Setting Environment UCX_TLS=ud,sm,self
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol None not enabled
ERROR: Could not find all inputdata on any server

What can I do to solve the problem?

Thanks.
Click to expand...
Hello,i meet the same problem，when I submit the case，the model feedback Could not find all inputdata on any server，I do think it is as a result of Model clm missing file fatmlndfrc = '/es01/paratera/sce0489/cesm2.2/my_cesm_sandbox/inputdata/share/domains/UNSET'.
 
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member
zqzq said:
Hello,i meet the same problem，when I submit the case，the model feedback Could not find all inputdata on any server，I do think it is as a result of Model clm missing file fatmlndfrc = '/es01/paratera/sce0489/cesm2.2/my_cesm_sandbox/inputdata/share/domains/UNSET'.
Click to expand...

The domain file isn't set. Is this a case with NUOPC or the MCT driver (check COMP_INTERFACE). You need to set the domain file if it's a MCT case, and if it's a NUOPC case it doesn't need the domain file, so one way around it is to set it /dev/null so that it has a file that exists, but it won't actually use.
 
Z

zqzq

zqzqzqzq
Member
zqzq said:
Hello,i meet the same problem，when I submit the case，the model feedback Could not find all inputdata on any server，I do think it is as a result of Model clm missing file fatmlndfrc = '/es01/paratera/sce0489/cesm2.2/my_cesm_sandbox/inputdata/share/domains/UNSET'.
Click to expand...

erik said:
The domain file isn't set. Is this a case with NUOPC or the MCT driver (check COMP_INTERFACE). You need to set the domain file if it's a MCT case, and if it's a NUOPC case it doesn't need the domain file, so one way around it is to set it /dev/null so that it has a file that exists, but it won't actually use.
Click to expand...

Thank you very much for your reply，After my query found it is a MCT case,Can you tell me how to set the domain file?Thanks again.
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
From a post above: "The I1PtClm50SpRsGs compset is only setup to work out of the box for a couple single point resolutions. If you want to run it for your own grid, there's a bunch of things you have to do to get it to work. See the CLM User's Guide for more information on how to do this."

So, if you want to run a single point simulation of your own choosing, you'll need to create the domain file and the surface dataset. See the example in section 1.6.3.5 of the User's Guide:

1.6.3. Running Single Point Configurations — ctsm CTSM master documentation

For more details on the CLM tools:

 
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