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case.build coupling_period error

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abdulla.sakalli@...
case.build coupling_period error

Dear All,

I'm installing cesm2 on my own server. I tried to run a simple case (I1850Clm50BgcCrop) to test the model and have a benchmark for the timing request. I run the model on a Linux Gnu machine. My machine xml code is:

   <machine MACH="nephentes2">

    <DESC>Linux 64bit</DESC>                                 <!-- can be anything -->

    <NODENAME_REGEX>none</NODENAME_REGEX>

    <OS>LINUX</OS>                                                     <!-- LINUX -->

    <COMPILERS>gnu</COMPILERS>                                     <!--gnu-->

    <MPILIBS>mpich</MPILIBS>                                       <!--mpich-->

    <CIME_OUTPUT_ROOT>$ENV{HOME}/projects/scratch</CIME_OUTPUT_ROOT>

    <DIN_LOC_ROOT>$ENV{HOME}/projects/cesm-inputdata</DIN_LOC_ROOT>

    <DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/projects/ptclm-data</DIN_LOC_ROOT_CLMFORC>

    <DOUT_S_ROOT>$ENV{HOME}/projects/scratch/archive/$CASE</DOUT_S_ROOT>

    <BASELINE_ROOT>$ENV{HOME}/projects/baselines</BASELINE_ROOT>

    <CCSM_CPRNC>$CIMEROOT/tools/cprnc/build/cprnc</CCSM_CPRNC>

    <GMAKE_J>2</GMAKE_J>

    <BATCH_SYSTEM>none</BATCH_SYSTEM>

    <SUPPORTED_BY>abdulla.sakalli@iste.edu.tr</SUPPORTED_BY>

    <MAX_TASKS_PER_NODE>12</MAX_TASKS_PER_NODE>

    <MAX_MPITASKS_PER_NODE>12</MAX_MPITASKS_PER_NODE>

    <mpirun mpilib="default">

      <executable>mpirun</executable>

    </mpirun>

    <module_system type="none"/>

  </machine>

The case was created and set up successfully. But when I try to build the case, I get the the follwing error:

   Calling /home/as2/CESM2/my_cesm_sandbox/components/mosart//cime_config/buildnml

Invalid values ['10800.0']

ERROR: Variable 'coupling_period' has invalid value ['10800.0'].

 

I looked for the error but I could find any information to solve it. Could you please help me with this issue. Many thanks in advance.

Kind regards,

Abdulla

 

jedwards

Hi Abdulla,

 

I think that this problem is due to using python version 3.   Although the cime code itself is fully compatible with python3 some of the components will only work with python 2.7.x.

CESM Software Engineer

abdulla.sakalli@...

Hi Jedwards,

Thank you very much for your support. That was the problem. I just changed the path from Python 3.5 to 2.7. And the problem was solved.

 

Many thanks again.

 

Best wishes,

Abdulla

abdulla.sakalli@...

Dear All,

after building the case, I try to run it. I got following error

mpirun -np 20 bld/cesm.exe
 ERROR: (cime_cpl_init) :: namelist read returns an end of file or end of record condition
#0  0x7F83C484AE08
#1  0xF50C02 in __shr_abort_mod_MOD_shr_abort_backtrace
#2  0xF50DEF in __shr_abort_mod_MOD_shr_abort_abort
#3  0x4068B0 in __cime_comp_mod_MOD_cime_cpl_init at cime_comp_mod.F90:?
#4  0x41F362 in __cime_comp_mod_MOD_cime_pre_init1
#5  0x421B92 in MAIN__ at cime_driver.F90:?
application called MPI_Abort(MPI_COMM_WORLD, 1001) - process 0

What could cause this problem? Thank you very much for your help in advance.

Best wishes,

Abdulla

jedwards

You are trying to run from the case directory instead of the run directory.  Use the case.submit script to start the job (even if you do not have a batch system).

CESM Software Engineer

abdulla.sakalli@...

Dear jedwards,

I changed it. I run the model via case.submit, and got following errors.

 (t_initf) Read in prof_inparm namelist from: drv_in
 (t_initf) Using profile_disable=          F
 (t_initf)       profile_timer=                      4
 (t_initf)       profile_depth_limit=                2
 (t_initf)       profile_detail_limit=               2
 (t_initf)       profile_barrier=          F
 (t_initf)       profile_outpe_num=                  1
 (t_initf)       profile_outpe_stride=               0
 (t_initf)       profile_single_file=      F
 (t_initf)       profile_global_stats=     T
 (t_initf)       profile_ovhd_measurement= F
 (t_initf)       profile_add_detail=       F
 (t_initf)       profile_papi_enable=      F
 ERROR: (seq_timemgr_alarmInit): ndays invalid opt_n
 ERROR: (seq_timemgr_alarmInit): ndays invalid opt_n
 ERROR: (seq_timemgr_alarmInit): ndays invalid opt_n
 ERROR: (seq_timemgr_alarmInit): ndays invalid opt_n
 ERROR: (seq_timemgr_alarmInit): ndays invalid opt_n

 

That is the results from preview_run

CASE INFO:
  nodes: 2
  total tasks: 12
  tasks per node: 6
  thread count: 1

BATCH INFO:
  FOR JOB: case.run
    ENV:
      Setting Environment NETCDF_HOME=/home/as2/local/netcdf461
      Setting Environment OMP_NUM_THREADS=1
    SUBMIT CMD:
      None

  FOR JOB: case.st_archive
    ENV:
      Setting Environment NETCDF_HOME=/home/as2/local/netcdf461
      Setting Environment OMP_NUM_THREADS=1
    SUBMIT CMD:
      None

MPIRUN:
  mpirun -np 20  /home/as2/projects/scratch/denemeI1850Clm50BgcCrop/bld/cesm.exe  >> cesm.log.$LID 2>&1

 

My xml files and cesm lof file are in attachment. Thank you very much for your help in advance.

 

 

jedwards

No log files attached.

CESM Software Engineer

abdulla.sakalli@...

Strange! I already uploaded it.

 

jedwards

It looks like you are using 20 tasks for the cpl but only 12 for the other components.  In config machines you have

<mpirun mpilib="default">
<executable>mpirun -np 20</executable>

That should be
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks"> -np {{ total_tasks }}</arg>
</arguments>

CESM Software Engineer

abdulla.sakalli@...

Thank you very much for quick response. I added the arguments to my machine file. But The problem is still there. Is ıt possible that I'm doing something wrong in my env_run.xml file?

 

uname -a

Linux nephentes2 4.15.0-34-generic #37~16.04.1-Ubuntu SMP Tue Aug 28 10:44:06 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

 

lscpu

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 44
Model name:            Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
Stepping:              2
CPU MHz:               2522.531
BogoMIPS:              5319.95
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              12288K
NUMA node0 CPU(s):     0,2,4,6,8,10,12,14,16,18,20,22
NUMA node1 CPU(s):     1,3,5,7,9,11,13,15,17,19,21,23
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm pti tpr_shadow vnmi flexpriority ept vpid dtherm arat

 

abdulla.sakalli@...

And this is the README.case file. Maybe it could be help to identify the problem

Attachment: 
jedwards

You need to recreate the case after editing the config_machines.xml file in order for the change to take effect.

CESM Software Engineer

abdulla.sakalli@...

Hi jedwards,

After each change in the config machine file, I recreate the case. It did not change anything in the error. Still get same error.

 

abdulla.sakalli@...

Hi jedwards,

the problem is solved. I had to add -lcurl in my config_compiler.xml file, and change some variable in my env_run.xml file. Than it was ok.

 

Kind regards,

Abdulla

jedwards

Oh good, I never would have got that from the description

CESM Software Engineer

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