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./case.build error

Jasper

New Member
When I build the case B1850 on CentOS7, some error occur when build the exe file.

There are many liines like this,

matrix_operations.F90:(.text+0xd9): undefined reference to `dsyev_'

matrix_operations.F90:(.text+0x6b2): undefined reference to `dlaqsy_'

and the final result is,
ERROR: BUILD FAIL: buildexe failed, cat /home/yhj/cesm/scratch/case1/bld/cesm.bldlog.210323-063012

I suppose it's caused by lapack library. But I have installed the latest LAPACK and BLAS in my system and export them to ~/.bashrc. I even copy the library file *.a to the path '/usr/local/lib' to prevent the link can't be find, but the error still exist. Attached is the bldlog file.

What can I do to solve the problem?

Thanks.
 

Attachments

  • cesm.bldlog.210323-063012.txt
    7.9 KB · Views: 11

jedwards

CSEG and Liaisons
Staff member
From your cesm bldlog you are not linking these libraries. You need to add them in config_compilers.xml to the SLIB argument.
It should look something like
-L/path/to/lapack/lib -llapack -L/path/to/blas/lib -lblas
 

Jasper

New Member
Thank you, jewards. I add those SLIB argument like this

<SLIBS>
<append>-L/home/yhj/program/netcdf/lib -lnetcdf -lnetcdff -L/home/yhj/program/lapack/lib -llapack -L/home/yhj/program/blas -lblas</append>
</SLIBS>

In path/to/lapack/lib, there are 4 files named as liblapack.a, liblapacke.a, librefblas.a, libtmglib.a. In path/to/blas , I can find the libblas.a and many .f and .o files.

But cesm bldlog still show I don't linking these library. I don't know why the link is not effective.
 

Attachments

  • cesm.bldlog.210324-053221.txt
    7.9 KB · Views: 6

jedwards

CSEG and Liaisons
Staff member
If you had added the SLIBS correctly you would see that code added to line 7 of the cesm bldlog. Review what you have done and look for other examples in the file.
 

Jasper

New Member
Thank you for your help, I check find my config_compiler and finally make the executable file successfully.

But when I run the model, I meet error about inputdata.

Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
- Prestaging REFCASE (/home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01) to /home/yhj/cesm/scratch/case1/run
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.atm
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.drv
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.glc
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ice
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.lnd
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.ovf
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.restart
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.ocn.tavg.5
Copy rpointer /home/yhj/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/rpointer.rof
Creating component namelists
Calling /home/yhj/cesm/components/cam//cime_config/buildnml
CAM namelist copy: file1 /home/yhj/cesm/cime/scripts/case1/Buildconf/camconf/atm_in file2 /home/yhj/cesm/scratch/case1/run/atm_in
Calling /home/yhj/cesm/components/clm//cime_config/buildnml
Calling /home/yhj/cesm/components/cice//cime_config/buildnml
Calling /home/yhj/cesm/components/pop//cime_config/buildnml
Calling /home/yhj/cesm/components/mosart//cime_config/buildnml
Running /home/yhj/cesm/components/cism//cime_config/buildnml
Calling /home/yhj/cesm/components/ww3//cime_config/buildnml
Calling /home/yhj/cesm/cime/src/components/stub_comps/sesp/cime_config/buildnml
Calling /home/yhj/cesm/cime/src/drivers/mct/cime_config/buildnml
Finished creating component namelists
Checking that inputdata is available as part of case submission
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Loading input file list: 'Buildconf/refcase.input_data_list'
Model refcase missing file refdir = '/root/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/'
Loading input file list: 'Buildconf/cam.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Loading input file list: 'Buildconf/cice.input_data_list'
Loading input file list: 'Buildconf/pop.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/ww3.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 '/home/yhj/cesm/scratch/case1/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
Trying to download file: '../inputdata_checksum.dat' to path '/home/yhj/cesm/scratch/case1/run/inputdata_checksum.dat.raw' using FTP protocol.
Using protocol svn with user and passwd
Trying to download file: 'None' to path '/home/yhj/cesm/scratch/case1/run/inputdata_checksum.dat.raw' using SVN protocol.
Could not automatically download file /home/yhj/cesm/scratch/case1/run/inputdata_checksum.dat Restoring existing version.
Client protocol None not enabled
Checking server ftp://gridanon.cgd.ucar.edu:2811/cesm/inputdata/ with protocol gftp
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 resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol wget with user anonymous and passwd user@example.edu
Loading input file list: 'Buildconf/refcase.input_data_list'
Model refcase missing file refdir = '/root/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/'
Cannot download file since it lives outside of the input_data_root '/home/yhj/cesm/inputdata'
Loading input file list: 'Buildconf/cam.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Loading input file list: 'Buildconf/cice.input_data_list'
Loading input file list: 'Buildconf/pop.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/ww3.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server ftp.cgd.ucar.edu/cesm/inputdata with protocol ftp
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
Loading input file list: 'Buildconf/refcase.input_data_list'
Model refcase missing file refdir = '/root/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/'
Cannot download file since it lives outside of the input_data_root '/home/yhj/cesm/inputdata'
Loading input file list: 'Buildconf/cam.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Loading input file list: 'Buildconf/cice.input_data_list'
Loading input file list: 'Buildconf/pop.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/ww3.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata with protocol svn
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Using protocol svn with user and passwd
Loading input file list: 'Buildconf/refcase.input_data_list'
Model refcase missing file refdir = '/root/cesm/inputdata/cesm2_init/b.e20.B1850.f19_g17.release_cesm2_1_0.020/0301-01-01/'
Cannot download file since it lives outside of the input_data_root '/home/yhj/cesm/inputdata'
Loading input file list: 'Buildconf/cam.input_data_list'
Loading input file list: 'Buildconf/clm.input_data_list'
Loading input file list: 'Buildconf/cice.input_data_list'
Loading input file list: 'Buildconf/pop.input_data_list'
Loading input file list: 'Buildconf/mosart.input_data_list'
Loading input file list: 'Buildconf/cism.input_data_list'
Loading input file list: 'Buildconf/ww3.input_data_list'
Loading input file list: 'Buildconf/cpl.input_data_list'
Checking server None with protocol None
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Client protocol None not enabled
ERROR: Could not find all inputdata on any server

How can I solve the mistake?
Thank you very much.
 

jedwards

CSEG and Liaisons
Staff member
It looks like you've got a conflict in the definition of DIN_LOC_ROOT in config_machines.xml
In one case it's /root/cesm/inputdata/ and in another it's /home/yhj/cesm/inputdata

It looks like the refcase path is wrong.
 

Jasper

New Member
Sorry for the late response,
With your kindly help, the case starts to run, but I meet another mistake during the process

===================================================================================
BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 53124 RUNNING AT localhost.localdomain
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

I wonder what's that exit code mean and is there any reference to lookup.

How can I solve this mistake?
 

jedwards

CSEG and Liaisons
Staff member
This is a generic message from the system about the job failure. You need to scan further up in the cesm.log to find the actual error.
 

Jasper

New Member
Well, I check cesm.log and cpl.log, I think the error occured when initialized component ocn

But I can't find the exact error in ocn.log, maybe the 'Overflow' is related to error? I have no idea about that.

Any suggestion?
 

Attachments

  • cesm.log.txt
    77 KB · Views: 5
  • cpl.log.txt
    41 KB · Views: 0
  • ocn.log.txt
    29.6 KB · Views: 1

jedwards

CSEG and Liaisons
Staff member
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)

This indicates that your application was killed by an external process. Often HPC machines run code that
will kick out your application if you are approaching maximum allowed memory. Check the queueing system logs and
check with your system administrators.
 

xliu

Jon
Member
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)

This indicates that your application was killed by an external process. Often HPC machines run code that
will kick out your application if you are approaching maximum allowed memory. Check the queueing system logs and
check with your system administrators.

Is there a way to load GPU to run the cesm.exe? . thx.
 

jedwards

CSEG and Liaisons
Staff member
No there are no gpu capabilities in the current cesm version. Perhaps you should get something basic running first.
 
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