Unable to build the case

csp · Sep 13, 2022

Hello again,
I tried to follow the steps given in Quick Start: CESM Model Workflow (CESM2.2) — CESM CESM2.2 documentation . When I am building the case using

Code:

./case.build

I am getting the following error:

Code:

ERROR: /home/csp/my_cesm_sandbox/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gptl.bldlog.220913-143935

When I tried to cat the error file, I am getting this error:

Code:

gcc: error: precise: No such file or directory
gcc: error: minimal: No such file or directory
gcc: error: unrecognized command line option ‘-qno-opt-dynamic-align’
gcc: error: unrecognized command line option ‘-fp-model’
gmake: *** [/home/csp/my_cesm_sandbox/cime/src/share/timing/Makefile:81: gptl.o] Error 1
ERROR: gcc: error: precise: No such file or directory
gcc: error: minimal: No such file or directory
gcc: error: unrecognized command line option    -qno-opt-dynamic-align   
gcc: error: unrecognized command line option    -fp-model   
gmake: *** [/home/csp/my_cesm_sandbox/cime/src/share/timing/Makefile:81: gptl.o] Error 1

Could any one please help, how to rectify this issue?

jedwards · Sep 13, 2022

It looks like you are specifying the intel compiler but finding the gcc compiler. If you want intel make sure that compiler is found first in your path,
if you want the gcc compiler change the default compiler in config_machines.xml

csp · Sep 13, 2022

Many thanks @jedwards for your kind help, I am not sure how to check and what to do next, the config_machines.xml in the /home/csp/.cime looks like:

Code:

<?xml version="1.0"?>
<config_machines>
   <machine MACH="CSP">
      <!-- customize these fields as appropriate for your system (max tasks) and
           desired layout (change '${HOME}/projects' to your
           prefered location). -->
      <DESC>__USEFUL_DESCRIPTION__</DESC>
      <NODENAME_REGEX>CSP</NODENAME_REGEX>
      <OS>Ubuntu</OS>
      <COMPILERS>intel</COMPILERS>
      <MPILIBS>impi</MPILIBS>
      <CIME_OUTPUT_ROOT>/home/csp/OUTPUT/CESM/scratch</CIME_OUTPUT_ROOT>
      <DIN_LOC_ROOT>/home/csp/OUTPUT/CESM/cesm-inputdata</DIN_LOC_ROOT>
      <DIN_LOC_ROOT_CLMFORC>/home/csp/my_cesm_sandbox/cesm-inputdataptclm-data</DIN_LOC_ROOT_CLMFORC>
      <DOUT_S_ROOT>/home/csp/OUTPUT/CESM/scratch/archive/$CASE</DOUT_S_ROOT>
      <BASELINE_ROOT>/home/csp/OUTPUT/CESM/baselines</BASELINE_ROOT>
      <CCSM_CPRNC>$CIMEROOT/tools/cprnc/build/cprnc</CCSM_CPRNC>
      <GMAKE_J>8</GMAKE_J>
      <BATCH_SYSTEM>none</BATCH_SYSTEM>
      <SUPPORTED_BY>csp</SUPPORTED_BY>
      <MAX_TASKS_PER_NODE>4</MAX_TASKS_PER_NODE>
      <MAX_MPITASKS_PER_NODE>4</MAX_MPITASKS_PER_NODE>
      <mpirun mpilib="default">
    <executable>mpirun</executable>
    <arguments>
      <arg name="anum_tasks"> -np $TOTALPES</arg>
      <arg name="labelstdout">--prepend-rank</arg>
    </arguments>
      </mpirun>
      <module_system type="none"/>
   </machine>

</config_machines>

In the terminal if I check

Code:

gfortran --version

it gives me:

Code:

GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

and if I check

Code:

ifort --version

, I get the following output:

Code:

ifort (IFORT) 2021.4.0 20210910
Copyright (C) 1985-2021 Intel Corporation.  All rights reserved.

Any further comment/suggestion would be a great help, thanks in advance.

jedwards · Sep 13, 2022

If you want to use the gnu compiler change your config_machines.xml file and replace
<COMPILERS>intel</COMPILERS>
with
<COMPILERS>gnu</COMPILERS>

If you want to use the intel compiler you need to make sure that it is found in your path BEFORE the
gnu compilers are. If you don't know how to do this please talk to your local system administrator.

csp · Sep 13, 2022

Thanks a lot @jedwards but unfortunately nothing working out for me as of now. Could you please suggest/comment something?

csp · Sep 14, 2022

Hi again,
Don't know really if this problem was sorted out, I tried changing as per your guidelines and now trapped into another error, which says:

Code:

ERROR: /home/csp/my_cesm_sandbox/cime/src/build_scripts/buildlib.pio FAILED, cat /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/pio.bldlog.220914-151624

digging furthermore, it is giving the following error:

Code:

- Check for working Fortran compiler: /opt/intel/oneapi/mpi/2021.4.0/bin/mpiifort - broken
-- Configuring incomplete, errors occurred!
See also "/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/pio/pio1/CMakeFiles/CMakeOutput.log".
See also "/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/pio/pio1/CMakeFiles/CMakeError.log".
gmake: Leaving directory '/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/pio/pio1'
CMake Error at /usr/share/cmake-3.24/Modules/CMakeTestFortranCompiler.cmake:61 (message):
  The Fortran compiler

    "/opt/intel/oneapi/mpi/2021.4.0/bin/mpiifort"

  is not able to compile a simple test program.

  It fails with the following output:

    Change Dir: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/pio/pio1/CMakeFiles/CMakeTmp

Seems like intel fortran compiler issue, but unable to figure out, any comment would be appreciated, thanks in advance.

csp · Sep 15, 2022

Managed to figure out this issue by directing towards gnu instead of intel, but now no clue about this problem:

Code:

Building cesm from /home/csp/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildexe with output to /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.bldlog.220915-154911 
lapack_interfaces.F90:(.text+0x13): undefined reference to `strmv_'

lapack_interfaces.F90:(.text+0x2f): undefined reference to `dtrmv_'

lapack_interfaces.F90:(.text+0x4d): undefined reference to `ssyev_'

lapack_interfaces.F90:(.text+0x6b): undefined reference to `dsyev_'

lapack_interfaces.F90:(.text+0x85): undefined reference to `slaqsy_'

lapack_interfaces.F90:(.text+0x9f): undefined reference to `dlaqsy_'

lapack_interfaces.F90:(.text+0xb1): undefined reference to `spoequ_'

lapack_interfaces.F90:(.text+0xc3): undefined reference to `dpoequ_'

lapack_interfaces.F90:(.text+0xd7): undefined reference to `spotrf_'

lapack_interfaces.F90:(.text+0xeb): undefined reference to `dpotrf_'

lapack_interfaces.F90:(.text+0x262): undefined reference to `sgtsvx_'

lapack_interfaces.F90:(.text+0x2e7): undefined reference to `dgtsvx_'

lapack_interfaces.F90:(.text+0x300): undefined reference to `sgtsv_'

lapack_interfaces.F90:(.text+0x316): undefined reference to `dgtsv_'

lapack_interfaces.F90:(.text+0x3a8): undefined reference to `sgbsvx_'

lapack_interfaces.F90:(.text+0x43d): undefined reference to `dgbsvx_'

lapack_interfaces.F90:(.text+0x45e): undefined reference to `sgbsv_'

lapack_interfaces.F90:(.text+0x47c): undefined reference to `dgbsv_'

SoilWaterMovementMod.F90:(.text+0x25f7): undefined reference to `dgtsv_'

UrbBuildTempOleson2015Mod.F90:(.text+0x2b83): undefined reference to `dgesv_'

BandDiagonalMod.F90:(.text+0xb31): undefined reference to `dgbsv_'

dcgs.f:(.text+0x105): undefined reference to `dnrm2_'

/usr/bin/ld: dcgs.f:(.text+0x1f9): undefined reference to `dnrm2_'

/usr/bin/ld: dcgs.f:(.text+0x260): undefined reference to `dnrm2_'

/usr/bin/ld: dcgs.f:(.text+0x283): undefined reference to `dnrm2_'

/usr/bin/ld: dcgs.f:(.text+0x2cd): undefined reference to `dnrm2_'

dcgs.f:(.text+0x712): undefined reference to `ddot_'

/usr/bin/ld: dcgs.f:(.text+0x7bd): undefined reference to `daxpy_'

/usr/bin/ld: dcgs.f:(.text+0x85a): undefined reference to `daxpy_'

/usr/bin/ld: dcgs.f:(.text+0x96f): undefined reference to `ddot_'

dcg.f:(.text+0x8a): undefined reference to `dnrm2_'

/usr/bin/ld: dcg.f:(.text+0x17a): undefined reference to `dnrm2_'

/usr/bin/ld: dcg.f:(.text+0x1e5): undefined reference to `dnrm2_'

/usr/bin/ld: dcg.f:(.text+0x208): undefined reference to `dnrm2_'

/usr/bin/ld: dcg.f:(.text+0x25b): undefined reference to `dnrm2_'

dcg.f:(.text+0x579): undefined reference to `dcopy_'

/usr/bin/ld: dcg.f:(.text+0x5c3): undefined reference to `ddot_'

/usr/bin/ld: dcg.f:(.text+0x604): undefined reference to `daxpy_'

/usr/bin/ld: dcg.f:(.text+0x635): undefined reference to `daxpy_'

/usr/bin/ld: dcg.f:(.text+0x75e): undefined reference to `ddot_'

dgmres.f:(.text+0xfd): undefined reference to `daxpy_'

dgmres.f:(.text+0x165): undefined reference to `dscal_'

/usr/bin/ld: dgmres.f:(.text+0x1a4): undefined reference to `dcopy_'

dgmres.f:(.text+0x692): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0x71b): undefined reference to `ddot_'

/usr/bin/ld: dgmres.f:(.text+0x76b): undefined reference to `daxpy_'

/usr/bin/ld: dgmres.f:(.text+0x794): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0x847): undefined reference to `daxpy_'

/usr/bin/ld: dgmres.f:(.text+0x88b): undefined reference to `ddot_'

dgmres.f:(.text+0xa16): undefined reference to `daxpy_'

/usr/bin/ld: dgmres.f:(.text+0xab0): undefined reference to `dcopy_'

dgmres.f:(.text+0xd3a): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0xd97): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0xe13): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0xea8): undefined reference to `dscal_'

/usr/bin/ld: dgmres.f:(.text+0x100a): undefined reference to `dscal_'

/usr/bin/ld: dgmres.f:(.text+0x11de): undefined reference to `dnrm2_'

dgmres.f:(.text+0x143c): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0x15ac): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x16ac): undefined reference to `dscal_'

/usr/bin/ld: dgmres.f:(.text+0x1888): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x1951): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x1a1c): undefined reference to `dnrm2_'

/usr/bin/ld: dgmres.f:(.text+0x1bc4): undefined reference to `dscal_'

/usr/bin/ld: dgmres.f:(.text+0x1c1c): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x1fa0): undefined reference to `daxpy_'

/usr/bin/ld: dgmres.f:(.text+0x202b): undefined reference to `dcopy_'

dgmres.f:(.text+0x263c): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x26c4): undefined reference to `dcopy_'

/usr/bin/ld: dgmres.f:(.text+0x26f9): undefined reference to `dnrm2_'

ERROR: BUILD FAIL: buildexe failed

jedwards · Sep 15, 2022

It does seem like something is missing in lapack - intel has the mkl library that provides lapack, have you tried that?

csp · Sep 15, 2022

Thanks a lot @jedwards for your prompt reply and help. Now I am compiling everything using gnu, because as in the previous post, intel and gnu were messing up each other. I indepently installed LAPACK using

Code:

sudo apt-get install libblas-dev liblapack-dev

Furthermore if I cat the complete error, it says:

Code:

Warning: Nonexistent include directory ‘/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/finclude’ [-Wmissing-include-dirs]
/usr/bin/mpif90  -o /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_iac_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -latm  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lice  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/lib/ -lclm  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -locn  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lrof  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lglc  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lwav  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lesp  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -liac  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib/ -lglimmercismfortran -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib -lcsm_share -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/lib -lpio -lgptl -lmct -lmpeu  -L/usr/local/netcdf/lib -lnetcdff -L/usr/local/netcdf/lib -lnetcdf -lnetcdf  
cime_comp_mod.o: in function `__cime_comp_mod_MOD_cime_run_atmocn_setup':
cime_comp_mod.F90:(.text+0x285): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_xao' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x47f): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_xao' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x2e77): additional relocation overflows omitted from the output
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_strmv_wrap':
lapack_interfaces.F90:(.text+0x13): undefined reference to `strmv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dtrmv_wrap':
lapack_interfaces.F90:(.text+0x2f): undefined reference to `dtrmv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_ssyev_wrap':
lapack_interfaces.F90:(.text+0x4d): undefined reference to `ssyev_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dsyev_wrap':
lapack_interfaces.F90:(.text+0x6b): undefined reference to `dsyev_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_slaqsy_wrap':
lapack_interfaces.F90:(.text+0x85): undefined reference to `slaqsy_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dlaqsy_wrap':
lapack_interfaces.F90:(.text+0x9f): undefined reference to `dlaqsy_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_spoequ_wrap':
lapack_interfaces.F90:(.text+0xb1): undefined reference to `spoequ_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dpoequ_wrap':
lapack_interfaces.F90:(.text+0xc3): undefined reference to `dpoequ_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_spotrf_wrap':
lapack_interfaces.F90:(.text+0xd7): undefined reference to `spotrf_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dpotrf_wrap':
lapack_interfaces.F90:(.text+0xeb): undefined reference to `dpotrf_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_sgtsvx_wrap':
lapack_interfaces.F90:(.text+0x262): undefined reference to `sgtsvx_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dgtsvx_wrap':
lapack_interfaces.F90:(.text+0x2e7): undefined reference to `dgtsvx_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_sgtsv_wrap':
lapack_interfaces.F90:(.text+0x300): undefined reference to `sgtsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dgtsv_wrap':
lapack_interfaces.F90:(.text+0x316): undefined reference to `dgtsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_sgbsvx_wrap':
lapack_interfaces.F90:(.text+0x3a8): undefined reference to `sgbsvx_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dgbsvx_wrap':
lapack_interfaces.F90:(.text+0x43d): undefined reference to `dgbsvx_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_sgbsv_wrap':
lapack_interfaces.F90:(.text+0x45e): undefined reference to `sgbsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib//libatm.a(lapack_interfaces.o): in function `__lapack_interfaces_MOD_dgbsv_wrap':
lapack_interfaces.F90:(.text+0x47c): undefined reference to `dgbsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/lib//libclm.a(SoilWaterMovementMod.o): in function `__soilwatermovementmod_MOD_soilwater_moisture_form':
SoilWaterMovementMod.F90:(.text+0x25f7): undefined reference to `dgtsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/lib//libclm.a(UrbBuildTempOleson2015Mod.o): in function `__urbbuildtempoleson2015mod_MOD_buildingtemperature':
UrbBuildTempOleson2015Mod.F90:(.text+0x2b83): undefined reference to `dgesv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/lib//libclm.a(BandDiagonalMod.o): in function `__banddiagonalmod_MOD_banddiagonal':
BandDiagonalMod.F90:(.text+0xb31): undefined reference to `dgbsv_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o): in function `isdcgs_':
dcgs.f:(.text+0x105): undefined reference to `dnrm2_'
/usr/bin/ld: dcgs.f:(.text+0x1f9): undefined reference to `dnrm2_'
/usr/bin/ld: dcgs.f:(.text+0x260): undefined reference to `dnrm2_'
/usr/bin/ld: dcgs.f:(.text+0x283): undefined reference to `dnrm2_'
/usr/bin/ld: dcgs.f:(.text+0x2cd): undefined reference to `dnrm2_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o):dcgs.f:(.text+0x2f7): more undefined references to `dnrm2_' follow
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o): in function `dcgs_':
dcgs.f:(.text+0x712): undefined reference to `ddot_'
/usr/bin/ld: dcgs.f:(.text+0x7bd): undefined reference to `daxpy_'
/usr/bin/ld: dcgs.f:(.text+0x85a): undefined reference to `daxpy_'
/usr/bin/ld: dcgs.f:(.text+0x96f): undefined reference to `ddot_'
/usr/bin/ld: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib//libglimmercismfortran.a(dcg.f.o): in function `isdcg_':
dcg.f:(.text+0x8a): undefined reference to `dnrm2_'
collect2: error: ld returned 1 exit status

csp · Sep 16, 2022

I managed to resolve this issue (hopefully), by adding

Code:

<LAPACK_LIBDIR> /usr/lib/x86_64-linux-gnu/lapack </LAPACK_LIBDIR>

in the config_compilers.xml file as:

Code:

<NETCDF_PATH>/usr/local/netcdf</NETCDF_PATH>
<LAPACK_LIBDIR> /usr/lib/x86_64-linux-gnu/lapack </LAPACK_LIBDIR>
<SLIBS>

But now I am getting the following error:

Code:

f951: Warning: Nonexistent include directory ‘/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/finclude’ [-Wmissing-include-dirs]
/usr/bin/mpif90  -o /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_iac_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -latm  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lice  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/lib/ -lclm  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -locn  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lrof  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lglc  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lwav  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -lesp  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/lib/ -liac  -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/glc/lib/ -lglimmercismfortran -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib -lcsm_share -L/home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/lib -lpio -lgptl -lmct -lmpeu  -L/usr/local/netcdf/lib -lnetcdff -L/usr/local/netcdf/lib -lnetcdf -lnetcdf -L/usr/lib/x86_64-linux-gnu/lapack  -llapack -lblas  
cime_comp_mod.o: in function `__cime_comp_mod_MOD_cime_run_atmocn_setup':
cime_comp_mod.F90:(.text+0x285): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_xao' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x2d2): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_frc' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x47f): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_xao' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x4bf): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_frc' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x72c): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_xao' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x779): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_num_inst_frc' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.o: in function `__cime_comp_mod_MOD_cime_final':
cime_comp_mod.F90:(.text+0x1811): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_cpl_inst_tag' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x1ffb): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_cpl_inst_tag' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.o: in function `__cime_comp_mod_MOD_cime_run':
cime_comp_mod.F90:(.text+0x2643): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_cpl_inst_tag' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x2670): relocation truncated to fit: R_X86_64_PC32 against symbol `__seq_comm_mct_MOD_cpl_inst_tag' defined in .bss section in /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/gnu/mpich/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
cime_comp_mod.F90:(.text+0x2e77): additional relocation overflows omitted from the output
collect2: error: ld returned 1 exit status
gmake: *** [/home/csp/my_cesm_sandbox/cime/scripts/csp/cases/b.e20.B1850.f19_g17.test/Tools/Makefile:985: /home/csp/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.exe] Error 1

Could @jedwards or anyone else comment/suggest something, it would be very kind help, thanks in advance.

jedwards · Sep 16, 2022

These errors are due to the static data size exceeding that allowed for the memory model. Sometimes it works to set NTASKS larger, but for an f19 case you shouldn't need to do that. This also occurs with some older versions of the netcdf library. You might try netcdf-c 4.9.0

csp · Sep 19, 2022

Hello @jedwards , I am now trying with different machine, but again some weird kind of error is been flashing, unable to figure out, what it is and what needs to be done to rectify it, please help and advice:

Code:

ifort: command line remark #10412: option '-mkl=cluster' is deprecated and will be removed in a future release. Please use the replacement option '-qmkl=cluster'
cime_comp_mod.o: In function `cime_comp_mod_mp_cime_run_':
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2602:(.text+0x1ed4): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_iac_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2614:(.text+0x1fc3): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_ice_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2626:(.text+0x20b2): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_lnd_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2638:(.text+0x21a1): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_rof_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2650:(.text+0x2290): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_wav_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2823:(.text+0x257b): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_atm_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:2835:(.text+0x266a): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_glc_layout_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:3083:(.text+0x27ed): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_atmid_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:3088:(.text+0x287e): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_lndid_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:3093:(.text+0x290f): relocation truncated to fit: R_X86_64_32S against symbol `seq_comm_mct_mp_ocnid_' defined in COMMON section in /home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/intel/impi/nodebug/nothreads/mct/mct/noesmf/c1a1l1i1o1r1g1w1i1e1/lib/libcsm_share.a(seq_comm_mct.o)
/home/chandra/SOURCE/my_cesm_sandbox/cime/src/drivers/mct/main/cime_comp_mod.F90:3098:(.text+0x29a0): additional relocation overflows omitted from the output
/home/chandra/SOURCE/my_cesm_sandbox/cime/scripts/chandra/cases/b.e20.B1850.f19_g17.test/Tools/Makefile:985: recipe for target '/home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.exe' failed
gmake: *** [/home/chandra/OUTPUT/CESM/scratch/b.e20.B1850.f19_g17.test/bld/cesm.exe] Error 1

jedwards · Sep 19, 2022

It's the same error you last asked about.

csp · Sep 19, 2022

Thanks a lot @jedwards for your feedback, but from where could I install netcdf-c 4.9.0? I understand that it's not really a related question but would be very kind if you could help. It may be trivial but since I am new to this area, thus would be very helpful, thanks in advance.

jedwards · Sep 19, 2022

Unidata | NetCDF

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

www.unidata.ucar.edu

csp · Sep 19, 2022

Thanks a lot @jedwards for your consistent help and support. But I was surprised that the previous case that was there as a tutorial case for CESM 2.1 (not remember exactly) created as:

Code:

./create_newcase --case aqua_case --compset QPC6 --res f09_f09_mg17

ran successfully with the current/installed netcdf libraries of 4.6.1, thus not sure what to make out of it. At this moment, I am even not sure if I have compiled and installed CESM 2 correctly or not. Could you please advice and suggest some other case to be sure. And as I said I am very naive to the subject, kindly give some detailed description. Many thanks in advance.

Unable to build the case

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