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Clm5.0 case running error

sunxupeng

hoperu/2016
New Member
I have successfully created the case:./create_newcase --case case1 --compset I2000Clm50SpGs --res f09_g17 --mach homebrew --run-unsupported
But my computer can't be used ./case.submit
I choose to use instructions:miexec -n 2 ./cesm.exe
But I encountered the following errors:
[root@localhost cesm_build]# mpiexec -n 6 ./cesm.exe
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 5 1 ( npes = 6) ( 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 6 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

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f6405db616a
#1 0x7f6405db52d3
#2 0x7f6403e9f78f
#3 0x7f640680cee3
#4 0xb2c684
#5 0xb3527a
#6 0xb141ca
#7 0x4b0d75
#8 0x4a59a0
#9 0x423315
#10 0x412c03
#11 0x420ac1
#12 0x7f6403e8b6a2
#13 0x405cdd
#14 0xffffffffffffffff

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 3722 RUNNING AT localhost.localdomain
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

How can I solve this mistake?
thank you very much indeed
 

jedwards

CSEG and Liaisons
Staff member
Why can't your computer use case.submit? This is the only supported way to submit a cesm job.
 

sunxupeng

hoperu/2016
New Member
Why can't your computer use case.submit? This is the only supported way to submit a cesm job.
[/引用]
Because when I started using commands/ case.submit
发生以下错误:


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 .
Trying to download file: '../inputdata_checksum.dat' to path '/home/sxp/Library/cesm_build/inputdata_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/sxp/clm5.0/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 157, in submit
custom_success_msg_functor=verbatim_success_msg)
File "/home/sxp/clm5.0/cime/scripts/Tools/../../scripts/lib/CIME/utils.py", line 1683, in run_and_log_case_status
rv = func()
File "/home/sxp/clm5.0/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 155, in <lambda>
batch_args=batch_args)
File "/home/sxp/clm5.0/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 85, in _submit
case.check_case()
File "/home/sxp/clm5.0/cime/scripts/Tools/../../scripts/lib/CIME/case/case_submit.py", line 171, in check_case
self.check_all_input_data()
File "/home/sxp/clm5.0/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/sxp/clm5.0/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 don't know how to solve it
 

Attachments

  • error.txt
    10.9 KB · Views: 3

jedwards

CSEG and Liaisons
Staff member
You need to solve this problem in order to download input data.
Please try anonymous ftp to ftp.cgd.ucar.edu/cesm/inputdata
if it doesn't work, engage your local support staff to help figure out why.
 

sunxupeng

hoperu/2016
New Member
You need to solve this problem in order to download input data.
Please try anonymous ftp to ftp.cgd.ucar.edu/cesm/inputdata
if it doesn't work, engage your local support staff to help figure out why.
Do you mean that I can submit my homework only after I download the missing data through this connection? I'm new to CLM and I'm not familiar with it
 

dayon

Member
I encountered the same problem, I used the 80 pes to run the cesm2.1.3 and the case.build couyld work, but the case.submit always failed.
 
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