CESM 1.2.2.1 cesm_setup module issue on Cheyenne

[swang54@uh_edu]

Hello,I had some issues with cesm_setup on Cheyenne (CESM 1.2.2.1). After creating my new case, I tried to do ./cesm_setup but I got the following error messages:

Please do not use this module, load 2.19 instead 2.19 is loaded effectively ... just to help old scriptsThis module will be deprecated soon!!!! Lmod has detected the following error:  These module(s) exist but cannot be loaded as requested: "netcdf-mpi/4.4.1.1"Try: "module spider netcdf-mpi/4.4.1.1" to see how to load the module(s).  Lmod has detected the following error:  These module(s) exist but cannot be loaded as requested: "pnetcdf/1.8.0"Try: "module spider pnetcdf/1.8.0" to see how to load the module(s). NETCDF: Undefined variable.ERROR: /gpfs/u/home/swang54/run_cheyenne/RCP_runs/RCP4.5run/preview_namelists failed: 65280 I think the issue is the mpt module. I checked the required modules for loading netcdf-mpi/4.4.1.1 and pnetcdf/1.8.0, and both require mpt/2.16. But the system didn't allow me to load mpt/2.16 (it will force me to load mpt/2.19 instead).Have anyone had this issue before? How can I fix that?

Thank you!!

Regards,
Sally

 

[jedwards]

Due to the cheyenne maintenance this week you need to update some modulesintel/17.0.1pnetcdf/1.11.0 If you are using cesm2 also update netcdf:netcdf/4.6.1netcdf-mpi/4.6.1 if you are using an older cesm version usenetcdf-mpi/4.4.1.1

 

[swang54@uh_edu]

Hello jedwards.

Thank you for your prompt reply!! I fixed it and setup the case sucessfully!!

These are the detailed processes to fix it for people who might have the same issue:1. Go to your code directory: ~/cesm1_2_2_1/scripts/ccsm_utils/Machines2. vi env_mach_specific.cheyenne3. update the listed modules to what jedwards suggested4. make sure recreate your cases using your modified code so that the changes would update to your new cases


Thanks again for your help!! I really appreciate it!

Regards,
Sally

 

[sungduk@uci_edu]

I modified env_mach_specific.cheyenne (for CESM1.2.2.1) as suggested: intel/17.0.1, mpt/2.19, netcdf/4.6.1, netcdf-mpi/4.6.1, pnetcdf/1.11.0, ncarenv/1.0, mkl, ncarcompilers/0.3.5.However, I still have an error during building stage. Would you let me know how to fix this problem?Thank you,Sungduk Yu In "cesm.bldlog",ccsm_comp_mod.o: In function `ccsm_comp_mod_mp_ccsm_run_':ccsm_comp_mod.F90:(.text+0x26): relocation truncated to fit: R_X86_64_32 against symbol `seq_avdata_mod_mp_infodata_' defined in COMMON section in seq_avdata_mod.occsm_comp_mod.F90:(.text+0x467): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_begstep_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x495): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4c8): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4e7): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_ncpl_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4ee): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4f5): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4fc): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x503): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x512): additional relocation overflows omitted from the output/glade/work/sungduk/ENSO/cases/_EXP/SungdukSST_STEP1_test1_env1/Tools/Makefile:629: recipe for target '/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env1/bld/cesm.exe' failedgmake: *** [/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env1/bld/cesm.exe] Error 1    

 

[swang54@uh_edu]

Actually I got the same error messages as you did when building the case. I was wondering whether it was a bug induced by different versions of software or I had something that didn't update correctly.

 

[jedwards]

Some older model versions - specifically older versions of pio (earlier than pio1.10.0) are not compatible with netcdf-mpi/4.6.2  cisl user support has now reinstalled netcdf-mpi/4.4.1.1 please try changing that module back and see if it solves the problem.  

 

[sungduk@uci_edu]

Thank you for suggestion.I tried building CESM1.2.2.1 with netcdf-mpi/4.4.1.1, but it failed with a same problem.

 

[swang54@uh_edu]

Same as here. I got the same error messages too. Here is the module list in the env_mach_specific.cheyenne file as a reference: source  /etc/profile.d/modules.csh module purge module load intel/17.0.1module load ncarenv/1.0module load mklmodule load ncarcompilers/0.3.5module load mpt/2.19if( $MPILIB == "mpi-serial" ) then  module load netcdf/4.6.1else  module load netcdf-mpi/4.4.1.1  module load pnetcdf/1.11.0 endif

 

[jedwards]

Please be clear about what error - this one? "relocation truncated to fit: R_X86_64_32"  if so make sure that you completly clean and rebuild after you make the suggested change.  

 

[jedwards]

For 1.2.2.1 you should have the following in env_mach_specific
module purge module load intel/17.0.1module load ncarenv/1.2module load mklmodule load ncarcompilers/0.4.1module load mpt/2.19if( $MPILIB == "mpi-serial" ) then  module load netcdf/4.4.1.1else  module load netcdf-mpi/4.4.1.1  module load pnetcdf/1.11.0endif

 

[swang54@uh_edu]

Hi jedwards,
Thank you for your reply. I did the following steps and still got the error messages when building the case: "ccsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.o".1. I changed the module list in the env_mach_specific.cheyenne as you suggested above2. create a new case3. ./cesm_setup4. ./case.build Did I miss any step?

Thank you!

Regards,
Sally

 

[swang54@uh_edu]

Hi jedwards,
Thank you for your reply. I did the following steps and still got the error messages when building the case: "ccsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.o".1. I changed the module list in the env_mach_specific.cheyenne as you suggested above2. create a new case3. ./cesm_setup4. ./case.build Did I miss any step?

Thank you!

Regards,
Sally

 

[sungduk@uci_edu]

I also have a same error, even after updated env_mach_specific and clean_build. At the end of cesm.bldlog:ccsm_comp_mod.o: In function `ccsm_comp_mod_mp_ccsm_run_':ccsm_comp_mod.F90:(.text+0x26): relocation truncated to fit: R_X86_64_32 against symbol `seq_avdata_mod_mp_infodata_' defined in COMMON section in seq_avdata_mod.occsm_comp_mod.F90:(.text+0x467): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_begstep_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x495): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4c8): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4e7): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_ncpl_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4ee): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4f5): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4fc): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x503): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x512): additional relocation overflows omitted from the output/glade/work/sungduk/ENSO/cases/_EXP/SungdukSST_STEP1_test1_env4/Tools/Makefile:629: recipe for target '/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env4/bld/cesm.exe' failedgmake: *** [/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env4/bld/cesm.exe] Error 1

 

[sungduk@uci_edu]

I also have a same error, even after updated env_mach_specific and clean_build. At the end of cesm.bldlog:ccsm_comp_mod.o: In function `ccsm_comp_mod_mp_ccsm_run_':ccsm_comp_mod.F90:(.text+0x26): relocation truncated to fit: R_X86_64_32 against symbol `seq_avdata_mod_mp_infodata_' defined in COMMON section in seq_avdata_mod.occsm_comp_mod.F90:(.text+0x467): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_begstep_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x495): relocation truncated to fit: R_X86_64_32S against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4c8): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_dtime_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4e7): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_ncpl_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4ee): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4f5): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x4fc): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x503): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.occsm_comp_mod.F90:(.text+0x512): additional relocation overflows omitted from the output/glade/work/sungduk/ENSO/cases/_EXP/SungdukSST_STEP1_test1_env4/Tools/Makefile:629: recipe for target '/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env4/bld/cesm.exe' failedgmake: *** [/glade/scratch/sungduk/ENSO/_EXP/SungdukSST_STEP1_test1_env4/bld/cesm.exe] Error 1

 

[jedwards]

So the next suggestion is a little more complicated.  In your source tree:cd models/utilsmv pio pio.old(sorry this was the wrong tag) [svn co https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio ] svn co https://github.com/NCAR/ParallelIO.git/tags/pio1_8_14/pio then clean and rebuild your case.  You should be able to use either netcdf version with this change, I recommend netcdf-mpi/4.6.1

 

[jedwards]

So the next suggestion is a little more complicated.  In your source tree:cd models/utilsmv pio pio.old(sorry this was the wrong tag) [svn co https://github.com/NCAR/ParallelIO.git/tags/pio1_8_12/pio ] svn co https://github.com/NCAR/ParallelIO.git/tags/pio1_8_14/pio then clean and rebuild your case.  You should be able to use either netcdf version with this change, I recommend netcdf-mpi/4.6.1

 

[swang54@uh_edu]

Hi Jedwards.

Thanks for keeping updating the solutions! I really appreciate your help.I tried the method you suggested (using new pio) but it still return the error: "ccsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.o".I tried both netcdf-mpi/4.6.1 and netcdf-mpi/4.4.1.1 but both didn't work and still returned the above error.

Regards,
Sally

 

[swang54@uh_edu]

Hi Jedwards.

Thanks for keeping updating the solutions! I really appreciate your help.I tried the method you suggested (using new pio) but it still return the error: "ccsm_comp_mod.F90:(.text+0x50a): relocation truncated to fit: R_X86_64_PC32 against symbol `ccsm_comp_mod_mp_cktime_acc_' defined in COMMON section in ccsm_comp_mod.o".I tried both netcdf-mpi/4.6.1 and netcdf-mpi/4.4.1.1 but both didn't work and still returned the above error.

Regards,
Sally

 

[jedwards]

This appears to be a different problem than the pio one.   The problem is in pop - I can run an F case without any issues - from the symptoms I think that pop is trying to declare some array to an unrealistically large size but I've not been able to pinpoint it.  

 

[jedwards]

This appears to be a different problem than the pio one.   The problem is in pop - I can run an F case without any issues - from the symptoms I think that pop is trying to declare some array to an unrealistically large size but I've not been able to pinpoint it.