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case.build coupling_period error

A

abdulla_sakalli@iste_edu_tr

New Member
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:       Linux 64bit                                     none    LINUX                                                         gnu                                         mpich                                           $ENV{HOME}/projects/scratch    $ENV{HOME}/projects/cesm-inputdata    $ENV{HOME}/projects/ptclm-data    $ENV{HOME}/projects/scratch/archive/$CASE    $ENV{HOME}/projects/baselines    $CIMEROOT/tools/cprnc/build/cprnc    2    none    abdulla.sakalli@iste.edu.tr    12    12          mpirun          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/buildnmlInvalid 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 
 
J

jedwards

CSEG and Liaisons
Staff member
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.
 
A

abdulla_sakalli@iste_edu_tr

New Member
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
 
A

abdulla_sakalli@iste_edu_tr

New Member
Dear All,after building the case, I try to run it. I got following errormpirun -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
 
J

jedwards

CSEG and Liaisons
Staff member
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).
 
A

abdulla_sakalli@iste_edu_tr

New Member
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_runCASE 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.  
 
J

jedwards

CSEG and Liaisons
Staff member
It looks like you are using 20 tasks for the cpl but only 12 for the other components.  In config machines you havempirun -np 20
That should bempirun -np {{ total_tasks }}
 
A

abdulla_sakalli@iste_edu_tr

New Member
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 -aLinux 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 lscpuArchitecture:          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

 
 
J

jedwards

CSEG and Liaisons
Staff member
You need to recreate the case after editing the config_machines.xml file in order for the change to take effect.
 
L

liyongkang

liyongkang
New Member
Hi jedwards and abdulla, I Met the same mistake with you that displays "ERROR: (seq_timemgr_alarmInit): nday invalid opt_n". I want to know some specific steps and some changed about "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".Your reply will be appreciated, thanks.

Invalid PIO rearranger comm max pend req (comp2io), 0
Resetting PIO rearranger comm max pend req (comp2io) to 64
PIO rearranger options:
comm type =
p2p

comm fcd =
2denable

max pend req (comp2io) = 0
enable_hs (comp2io) = T
enable_isend (comp2io) = F
max pend req (io2comp) = 64
enable_hs (io2comp) = F
enable_isend (io2comp) = T
(seq_comm_setcomm) init ID ( 1 GLOBAL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_setcomm) init ID ( 2 CPL ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_setcomm) init ID ( 5 ATM ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 6 CPLATM ) join IDs = 2 5 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 3 ALLATMID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 4 CPLALLATMID ) join IDs = 2 3 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 9 LND ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 10 CPLLND ) join IDs = 2 9 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 7 ALLLNDID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 8 CPLALLLNDID ) join IDs = 2 7 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 13 ICE ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 14 CPLICE ) join IDs = 2 13 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 11 ALLICEID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 12 CPLALLICEID ) join IDs = 2 11 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 17 OCN ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 18 CPLOCN ) join IDs = 2 17 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 15 ALLOCNID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 16 CPLALLOCNID ) join IDs = 2 15 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 21 ROF ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 22 CPLROF ) join IDs = 2 21 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 19 ALLROFID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 20 CPLALLROFID ) join IDs = 2 19 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 25 GLC ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 26 CPLGLC ) join IDs = 2 25 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 23 ALLGLCID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 24 CPLALLGLCID ) join IDs = 2 23 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 29 WAV ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 30 CPLWAV ) join IDs = 2 29 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 27 ALLWAVID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 28 CPLALLWAVID ) join IDs = 2 27 ( npes = 1) ( nthreads = 1)
(seq_comm_setcomm) init ID ( 33 ESP ) pelist = 0 0 1 ( npes = 1) ( nthreads = 1)( suffix =)
(seq_comm_joincomm) init ID ( 34 CPLESP ) join IDs = 2 33 ( npes = 1) ( nthreads = 1)
(seq_comm_jcommarr) init ID ( 31 ALLESPID ) join multiple comp IDs ( npes = 1) ( nthreads = 1)
(seq_comm_joincomm) init ID ( 32 CPLALLESPID ) join IDs = 2 31 ( npes = 1) ( nthreads = 1)
(seq_comm_printcomms) 1 0 1 1 GLOBAL:
(seq_comm_printcomms) 2 0 1 1 CPL:
(seq_comm_printcomms) 3 0 1 1 ALLATMID:
(seq_comm_printcomms) 4 0 1 1 CPLALLATMID:
(seq_comm_printcomms) 5 0 1 1 ATM:
(seq_comm_printcomms) 6 0 1 1 CPLATM:
(seq_comm_printcomms) 7 0 1 1 ALLLNDID:
(seq_comm_printcomms) 8 0 1 1 CPLALLLNDID:
(seq_comm_printcomms) 9 0 1 1 LND:
(seq_comm_printcomms) 10 0 1 1 CPLLND:
(seq_comm_printcomms) 11 0 1 1 ALLICEID:
(seq_comm_printcomms) 12 0 1 1 CPLALLICEID:
(seq_comm_printcomms) 13 0 1 1 ICE:
(seq_comm_printcomms) 14 0 1 1 CPLICE:
(seq_comm_printcomms) 15 0 1 1 ALLOCNID:
(seq_comm_printcomms) 16 0 1 1 CPLALLOCNID:
(seq_comm_printcomms) 17 0 1 1 OCN:
(seq_comm_printcomms) 18 0 1 1 CPLOCN:
(seq_comm_printcomms) 19 0 1 1 ALLROFID:
(seq_comm_printcomms) 20 0 1 1 CPLALLROFID:
(seq_comm_printcomms) 21 0 1 1 ROF:
(seq_comm_printcomms) 22 0 1 1 CPLROF:
(seq_comm_printcomms) 23 0 1 1 ALLGLCID:
(seq_comm_printcomms) 24 0 1 1 CPLALLGLCID:
(seq_comm_printcomms) 25 0 1 1 GLC:
(seq_comm_printcomms) 26 0 1 1 CPLGLC:
(seq_comm_printcomms) 27 0 1 1 ALLWAVID:
(seq_comm_printcomms) 28 0 1 1 CPLALLWAVID:
(seq_comm_printcomms) 29 0 1 1 WAV:
(seq_comm_printcomms) 30 0 1 1 CPLWAV:
(seq_comm_printcomms) 31 0 1 1 ALLESPID:
(seq_comm_printcomms) 32 0 1 1 CPLALLESPID:
(seq_comm_printcomms) 33 0 1 1 ESP:
(seq_comm_printcomms) 34 0 1 1 CPLESP:
(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= 4
(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): nday invalid opt_n
Image PC Routine Line Source
cesm.exe 0000000001075746 Unknown Unknown Unknown
cesm.exe 0000000000D25AAE shr_abort_mod_mp_ 114 shr_abort_mod.F90
cesm.exe 0000000000D1CD1E seq_timemgr_mod_m 1601 seq_timemgr_mod.F90
cesm.exe 0000000000D23658 seq_timemgr_mod_m 916 seq_timemgr_mod.F90
cesm.exe 000000000042BB7C cime_comp_mod_mp_ 1010 cime_comp_mod.F90
cesm.exe 0000000000430968 MAIN__ 76 cime_driver.F90
cesm.exe 000000000041443E Unknown Unknown Unknown
libc-2.27.so 000014AE84454BF7 __libc_start_main Unknown Unknown
cesm.exe 000000000041432A Unknown Unknown Unknown
application called MPI_Abort(MPI_COMM_WORLD, 1001) - process 0
Click to expand...
 
I

icetea

Yue Cheng
New Member
liyongkang said:
Hi jedwards and abdulla, I Met the same mistake with you that displays "ERROR: (seq_timemgr_alarmInit): nday invalid opt_n". I want to know some specific steps and some changed about "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".Your reply will be appreciated, thanks.
Click to expand...
I have same problem, "ERROR: (seq_timemgr_alarmInit): nday invalid opt_n". Could you please give me some help?
 
C

CaliFornia

CF
New Member
icetea said:
I have same problem, "ERROR: (seq_timemgr_alarmInit): nday invalid opt_n". Could you please give me some help?
Click to expand...
I met the same issue but probably this post is too late for your question.

The 'ERROR: (seq_timemgr_alarmInit): nday invalid opt_n' issue is probably due to the start_date settings for the simulation you plan to run. I have a script in which compset is FC2010climo (or FCnudged), setenv run_startdate 2010-01-01. Both cases show the same error message. After commenting the commands where there is 'run_startate', the simulation can run smoothly.

Now my confusion become how to select a proper run_type (like startup, hybrid, branch) with a starting date that I chose.
For example, I want to run a 20-year case, starting at 2010-01-01 with daily output of serial variables. How to pick the proper initial/ boundary condition files and select the run_type and run_start_date.

I hope this post could help some people, and also someone could solve my confusion.
 
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