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CESM runtime error - NetCDF: Invalid dimension ID or name - glibc detected

N

nitkbhat@gmail_com

Member
I have installed NetCDF. I am getting the following error when I run the model after a successful build.  [nitin@master case_B_f19_g16_userdefined_3]$ cat case_B_f19_g16_.o546    Warning: no access to tty (Bad file descriptor).Thus no job control in this shell.------------------------------------------------------------------------- CESM BUILDNML SCRIPT STARTING - To prestage restarts, untar a restart.tar file into /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/Run infile is /storage/home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/Buildconf/cplconf/cesm_namelistCAM writing dry deposition namelist to drv_flds_inCAM writing namelist to atm_inCLM configure done.CLM adding use_case 2000_control defaults for var sim_year with val 2000CLM adding use_case 2000_control defaults for var sim_year_range with val constantCLM adding use_case 2000_control defaults for var use_case_desc with val Conditions to simulate 2000 land-useCICE configure done.POP2 build-namelist: ocn_grid is gx1v6POP2 build-namelist: ocn_tracer_modules are  iage CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY-------------------------------------------------------------------------------------------------------------------------------------------------- CESM PRESTAGE SCRIPT STARTING - Case input data directory, DIN_LOC_ROOT, is /home/nitin/CESM/cesm1_2_2/input_data - Checking the existence of input datasets in DIN_LOC_ROOT CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY-------------------------------------------------------------------------Fri Dec 26 14:58:54 IST 2014 -- CSM EXECUTION BEGINS HEREFri Dec 26 14:58:56 IST 2014 -- CSM EXECUTION HAS FINISHEDModel did not complete - see /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/Run/cesm.log.141226-145822    Log File Content  60  node5 61  node5 62  node5 63  node5 Opened existing file /home/nitin/CESM/cesm1_2_2/input_data/atm/cam/inic/fv/cami_0000-01-01_1.9x2.5_L 26_c070408.nc       65536 Opened existing file /home/nitin/CESM/cesm1_2_2/input_data/atm/cam/topo/USGS-gtopo30_1.9x2.5_remap_c 050602.nc      131072 NetCDF: Invalid dimension ID or name*** glibc detected *** /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/cesm.exe: malloc(): memory corruption: 0x0000000012e80fb0 ****** glibc detected *** /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/cesm.exe: malloc(): memory corruption: 0x0000000011f68560 ****** glibc detected *** /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/cesm.exe: malloc(): memory corruption: 0x00000000119f3570 ****** glibc detected *** /home/nitin/CESM/cesm1_2_2/nitin_cases/case_B_f19_g16_userdefined_3/cesm.exe: malloc(): memory corruption: 0x0000000012e80fb0 ***.....     How do i resolve this error? Thanks
 
N

nitkbhat@gmail_com

Member
I am using the intel fortran compiler (ifort, mpiifort). I created a new case and built again. I don't get the memory corruption error anymore. During run time, the model doesn't complete and the NetCDF error still shows up. Opened existing file /home/nitin/CESM/NEW_CASES/INPUT_DATA/atm/cam/ozone/ozone_1.9x2.5_L26_2000clim_ c091112.nc      196608 NetCDF: Invalid dimension ID or name Opened existing file /home/nitin/CESM/NEW_CASES/INPUT_DATA/atm/cam/chem/trop_mozart_aero/aero/aero_1 .9x2.5_L26_2000clim_c091112.nc      262144 NetCDF: Invalid dimension ID or name Opened existing file /home/nitin/CESM/NEW_CASES/INPUT_DATA/atm/cam/chem/trop_mozart_aero/aero/aeroso ldep_monthly_1849-2006_1.9x2.5_c090803.nc      327680 NetCDF: Variable not found NetCDF: Variable not found NetCDF: Invalid dimension ID or name NetCDF: Invalid dimension ID or nameThanks.
 
N

nitkbhat@gmail_com

Member
Along with the intel compilers, I use the Luster file system. I want to run CESM 1.2.2. Should I just install Netcdf C and Netcdf fortran or should I also install zlib, hdf5 and other dependencies?Also, regarding pnetcdf, should this be installed? And should it be linked with netcdf at the time of installation? How do I ensure that Netcdf and all other dependencies do not cause errors during build/run.Thanks. 
 
S

santos

Member
Those netCDF messages are not errors, just warnings. We need to figure out how to suppress them to keep the log clean, but they are not a problem.The glibc error may have been due to using Intel 14 or Intel 15. These compiler versions have bugs that cause some CESM 1.2.2 configurations to fail, as mentioned here:https://bb.cgd.ucar.edu/fv-dycore-spmddynf90-and-intel-14x-compilerAlternatively, the glibc error may have been an error in an installed library, or an incompatibility between libraries used during compilation, and dynamic libraries loaded at run time. "Should I just install Netcdf C and Netcdf fortran or should I also install zlib, hdf5 and other dependencies?Also, regarding pnetcdf, should this be installed? And should it be linked with netcdf at the time of installation?" Deciding whether to install pnetcdf is up to you. CESM only requires netCDF itself, and the other libraries are only required to the extent that netCDF requires them. pnetcdf is likely to be faster, but whether this makes enough difference to matter depends on whether the types of runs that you usually perform tend to incur a large I/O cost on your particular system. CESM still links to netCDF directly whether pnetcdf is present or not.
 
N

nitkbhat@gmail_com

Member
I have reverted to cesm 1.0.4. And I am using netcdf 4.1.3. With hdf5 and zlib. Now, I am getting successful builds.  I will be trying to run cesm 1.2.2 once I get the 1.0.4 version running.  Thanks for all the supportNitin
 
S

santos

Member
I have added the file as a gzipped attachment here:https://bb.cgd.ucar.edu/fv-dycore-spmddynf90-and-intel-14x-compiler
 
C

chenjunwenchina@qq_com

New Member
Thanks. But when I replace the spmd_dyn.F file in cesm 1.2.2, I got some errors during cam building:/users/yangsong3/CESM/cesm1_2_2/models/atm/cam/src/dynamics/fv/spmd_dyn.F90(26): error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [CAM_ABORTUTILS]
   use cam_abortutils,     only: endrun
-------^
/users/yangsong3/CESM/cesm1_2_2/models/atm/cam/src/dynamics/fv/spmd_dyn.F90(26): error #6580: Name in only-list does not exist.   [ENDRUN]
   use cam_abortutils,     only: endrun
---------------------------------^
/users/yangsong3/CESM/cesm1_2_2/models/atm/cam/src/dynamics/fv/spmd_dyn.F90(638): error #6406: Conflicting attributes or multiple declaration of name.   [ENDRUN]
         call endrun ('SPMDINIT_DYN: less than 3 latitudes per subdomain')
--------------^
.....
compilation aborted for /users/yangsong3/CESM/cesm1_2_2/models/atm/cam/src/dynamics/fv/spmd_dyn.F90 (code 1)
gmake: *** [spmd_dyn.o] Error 1
gmake: *** Waiting for unfinished jobs...The whole log is in the attachment. My fortran complier is Intel 15.0.1, with netcdf 4.3.2 and netcdf-fortran 4.4.1.It seems that we still have to add or change some files? Thank you.
 
N

nitkbhat@gmail_com

Member
Yes. When the change is made from "cam_abortutils" to "abortutils", the run is successful with model completion. Verified for CESM 1.0.6 with Intel 14 compiler. Thanks a lot for all the help.  Nitin K Bhat,Indian Institute of Science
 
L

littledddna@gmail_com

Member
Hi, I am posting a comment because I had the same issue. I updated the spmd_dyn.F90 under /cesm1_2_2/models/atm/cam/src/dynamics/fv and build the model again. However, I still got the error  Opened existing file
cesm_inputdata/atm/cam/topo/USGS-gtopo30_0.9x1.25_remap_c051
 027.nc      131072
 NetCDF: Invalid dimension ID or name


Do you think it is still due to intel 14xxx compiler ?  Thanks very much
 
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