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ERROR About /CESM2.2/cime/src/build_scripts/buildlib.pio FAILED

xnnzka

xnnzka
New Member
Hi, everyone, I need your help.

I am a green hand and when I begin my first simulation about FHIST, I meet some errors.

Specifically, when I ./case.build, there is an error in Building pio.

The screen shows:
"
Building case in directory /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest
sharedlib_only is False
model_only is False
Setting Environment BASH_ENV=/public/apps/lmod/lmod/init/bash
Setting Environment NETCDF_C_PATH=/public/apps/netcdf-c-4.9.2
Setting Environment NETCDF_FORTRAN_PATH=/public/apps/netcdf-fortran-4.6.1
Setting Environment OMP_STACKSIZE=256M
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
2024-11-27 15:19:54 atm
Calling /public/home/zhenliu/CESM/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/camconf/atm_in file2 /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/atm_in
2024-11-27 15:19:55 lnd
Calling /public/home/zhenliu/CESM/components/clm//cime_config/buildnml
2024-11-27 15:19:56 ice
Calling /public/home/zhenliu/CESM/components/cice//cime_config/buildnml
...buildnml calling cice buildcpp to set build time options
2024-11-27 15:19:56 ocn
Calling /public/home/zhenliu/CESM/cime/src/components/data_comps_mct/docn/cime_config/buildnml
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/docnconf/docn_in -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/docnconf/docn.streams.txt.prescribed -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
2024-11-27 15:19:57 rof
Calling /public/home/zhenliu/CESM/components/mosart//cime_config/buildnml
2024-11-27 15:19:57 glc
Running /public/home/zhenliu/CESM/components/cism//cime_config/buildnml
2024-11-27 15:20:01 wav
Calling /public/home/zhenliu/CESM/cime/src/components/stub_comps_mct/swav/cime_config/buildnml
2024-11-27 15:20:01 iac
Running /public/home/zhenliu/CESM/cime/src/components/stub_comps_mct/siac/cime_config/buildnml
2024-11-27 15:20:01 esp
Calling /public/home/zhenliu/CESM/cime/src/components/stub_comps_mct/sesp/cime_config/buildnml
2024-11-27 15:20:01 cpl
Calling /public/home/zhenliu/CESM/cime/src/drivers/mct/cime_config/buildnml
NOTE: ignoring setting of rof2ocn_fmapname=idmap in seq_maps.rc
NOTE: ignoring setting of rof2ocn_ice_rmapname=idmap in seq_maps.rc
NOTE: ignoring setting of rof2ocn_liq_rmapname=idmap in seq_maps.rc
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/drv_in -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs/drv_flds_in -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/seq_maps.rc -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/cpl_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/ice_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/rof_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/atm_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/esp_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/wav_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/iac_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/ocn_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/glc_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/cplconf/lnd_modelio.nml -> /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/cpl_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/ice_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/rof_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/atm_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/esp_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/wav_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/iac_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/ocn_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/glc_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/lnd_modelio.nml -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/docn_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/atm_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/ice_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/mosart_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/drv_flds_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/cism_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/lnd_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/drv_in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/docn.streams.txt.prescribed -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/seq_maps.rc -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/run/cism.config -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/camconf/chem_mech.doc -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
copying /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Buildconf/camconf/chem_mech.in -> /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/CaseDocs
Building gptl with output to file /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gptl.bldlog.241127-151953
Calling /public/home/zhenliu/CESM/cime/src/build_scripts/buildlib.gptl
Building mct with output to file /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/mct.bldlog.241127-151953
Calling /public/home/zhenliu/CESM/cime/src/build_scripts/buildlib.mct
Building pio with output to file /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/pio.bldlog.241127-151953
Calling /public/home/zhenliu/CESM/cime/src/build_scripts/buildlib.pio
ERROR: /public/home/zhenliu/CESM/cime/src/build_scripts/buildlib.pio FAILED, cat /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/pio.bldlog.241127-151953
"
And I will attach my .csh file and pio.bldlog.241127-151953
 

xnnzka

xnnzka
New Member
I have just found my attachments can not be seen so I copy the pio.bldlog here:

pio_version_major = None pio_version = 1
make /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1/Makefile -C /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1 CASEROOT=/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest MODEL=pio1 COMP_NAME=pio1 USER_CMAKE_OPTS="-D GENF90_PATH=$CIMEROOT/src/externals/genf90 " PIO_LIBDIR=/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1 CASETOOLS=/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Tools USER_CPPDEFS=-DTIMING CIME_MODEL=cesm SMP=FALSE CASEROOT="/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest" CASETOOLS="/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Tools" CIMEROOT="/public/home/zhenliu/CESM/cime" COMP_INTERFACE="mct" COMPILER="gnu" DEBUG="FALSE" EXEROOT="/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld" INCROOT="/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/lib/include" LIBROOT="/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/lib" MACH="eesrf" MPILIB="openmpi" NINST_VALUE="c1a1l1i1o1r1g1w1i1e1" OS="LINUX" PIO_VERSION="1" SHAREDLIBROOT="/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld" SMP_PRESENT="FALSE" USE_ESMF_LIB="FALSE" USE_MOAB="FALSE" CAM_CONFIG_OPTS="-phys cam6" COMP_LND="clm" COMPARE_TO_NUOPC="FALSE" CISM_USE_TRILINOS="FALSE" USE_TRILINOS="FALSE" USE_ALBANY="FALSE" USE_PETSC="FALSE" -f /public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Tools/Makefile
make: Entering directory '/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1'
cd /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1; \
CC=mpicc CXX=mpicxx FC=mpif90 LDFLAGS="" cmake -D CMAKE_Fortran_FLAGS:STRING="-fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none -fallow-argument-mismatch -fallow-invalid-boz -O -DTIMING -DLINUX -DCESMCOUPLED -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU -DNDEBUG -DHAVE_MPI -DMCT_INTERFACE -DPIO1 -DHAVE_SLASHPROC -DATM_PRESENT -DICE_PRESENT -DLND_PRESENT -DOCN_PRESENT -DROF_PRESENT -DGLC_PRESENT -DWAV_PRESENT -DESP_PRESENT -DMED_PRESENT -I. -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/finclude -I/public/apps/netcdf-c-4.9.2/include -I/public/apps/netcdf-fortran-4.6.1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include" -D CMAKE_C_FLAGS:STRING="-std=gnu99 -O -DTIMING -DLINUX -DCESMCOUPLED -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU -DNDEBUG -DHAVE_MPI -DMCT_INTERFACE -DPIO1 -DHAVE_SLASHPROC -DATM_PRESENT -DICE_PRESENT -DLND_PRESENT -DOCN_PRESENT -DROF_PRESENT -DGLC_PRESENT -DWAV_PRESENT -DESP_PRESENT -DMED_PRESENT -I. -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/finclude -I/public/apps/netcdf-c-4.9.2/include -I/public/apps/netcdf-fortran-4.6.1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include" -D CMAKE_CXX_FLAGS:STRING="-DTIMING -DLINUX -DCESMCOUPLED -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU -DNDEBUG -DHAVE_MPI -DMCT_INTERFACE -DPIO1 -DHAVE_SLASHPROC -DATM_PRESENT -DICE_PRESENT -DLND_PRESENT -DOCN_PRESENT -DROF_PRESENT -DGLC_PRESENT -DWAV_PRESENT -DESP_PRESENT -DMED_PRESENT -I. -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/finclude -I/public/apps/netcdf-c-4.9.2/include -I/public/apps/netcdf-fortran-4.6.1/include -I/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/include" -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON -D GPTL_PATH:STRING=/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct -D PIO_ENABLE_TESTS:BOOL=OFF -D PIO_USE_MALLOC:BOOL=ON -D USER_CMAKE_MODULE_PATH:LIST="/public/home/zhenliu/CESM/cime/src/CMake;/public/home/zhenliu/CESM/cime/src/externals/pio2/cmake" -D NetCDF_C_PATH:PATH=/public/apps/netcdf-c-4.9.2 -D NetCDF_Fortran_PATH:PATH=/public/apps/netcdf-fortran-4.6.1 -D WITH_PNETCDF:LOGICAL=FALSE -D PIO_USE_MPIIO:LOGICAL=FALSE -D GENF90_PATH=/public/home/zhenliu/CESM/cime/scripts/Tools/../../src/externals/genf90 /public/home/zhenliu/CESM/cime/src/externals/pio1
make: Leaving directory '/public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1'
/bin/sh: line 2: cmake: command not found
make: *** [/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Tools/Makefile:798: /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1/Makefile] Error 127
ERROR: /bin/sh: line 2: cmake: command not found
make: *** [/public/home/zhenliu/CESM/cesmrun/mingming/FHISTtest/Tools/Makefile:798: /public/home/zhenliu/scratch/cesm/mingming/FHISTtest/bld/gnu/openmpi/nodebug/nothreads/mct/pio/pio1/Makefile] Error 127
 

xnnzka

xnnzka
New Member
These are txt-format files. FHIST_TEST is originally *csh file and the pio.bldlog is the log file.
 

Attachments

  • FHIST_TEST.txt
    5.5 KB · Views: 0
  • pio.bldlog.241127-151953.txt
    5.5 KB · Views: 2

xnnzka

xnnzka
New Member
And this is the location that occured in log. I found there is no relavant files about cmake and others here.
 

Attachments

  • 1732695631274.png
    1732695631274.png
    15.9 KB · Views: 4

xnnzka

xnnzka
New Member
Hi, everyone.
I found if I set the STOP_N=2; STOP_OPTION ='nyears' (i.e., modify the simulation time to be shorter), it can work.
So a new question arises from it: Can I simulate 10 years or longer at once? Or only simulate longer via resubmit?
I think I need your help, very thanks!
 

fischer

CSEG and Liaisons
Staff member
So I'm confused. You're able to successfully build cesm with STOP_N=2; STOP_OPTION='nyears'. But if you try 10 years, you can't build cesm. This doesn't make sense, the length of the run shouldn't affect the ability to build cesml. If you're able to build cesm, to get a 10 year run you would just need to set STOP_N=10, and provide a wallclock that's sufficient to be able to complete the 10 year run.

Chris
 

xnnzka

xnnzka
New Member
So I'm confused. You're able to successfully build cesm with STOP_N=2; STOP_OPTION='nyears'. But if you try 10 years, you can't build cesm. This doesn't make sense, the length of the run shouldn't affect the ability to build cesml. If you're able to build cesm, to get a 10 year run you would just need to set STOP_N=10, and provide a wallclock that's sufficient to be able to complete the 10 year run.

Chris
Very thanks for your reply! Your reply is very useful!
This error occured last week. I found this might be because I have not modified JOB_WALLCLOCK_TIME and the default value is 2 hours, which could not can't run for ten simulated years. So I am trying to modify the JOB_WALLCLOCK_TIME to make the experiment could run for 10 years.
 
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