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Porting with NUOPC errors.

J

jedwards

CSEG and Liaisons
Staff member
In config_machines.xml replace ESMF_LIB with
<env name="ESMFMKFILE">/APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/esmf.mk</env>
 
P

pengzhou

peng zhou
New Member
jedwards said:
In config_machines.xml replace ESMF_LIB with
<env name="ESMFMKFILE">/APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/esmf.mk</env>
Click to expand...
Thank you very, very much for your answer, this answer solves a problem that has been bothering me for a long time. I continue to try to compile, but the following error occurs, can you continue to guide me, thank you very much! The error message is as follows:


/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:119: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:130: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(pionfget_mod.F90.o): in function `pionfget_mod_mp_get_var1_id_double_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:119: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:130: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(pionfget_mod.F90.o): in function `pionfget_mod_mp_get_var1_id_int_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:119: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:130: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(pionfget_mod.F90.o): in function `pionfget_mod_mp_get_var1_id_short_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:119: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/pionfget_mod.F90.in:130: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(piodarray.F90.o): in function `piodarray_mp_write_darray_1d_cinterface_real_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(piodarray.F90.o): in function `piodarray_mp_write_darray_1d_cinterface_int_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(piodarray.F90.o): in function `piodarray_mp_write_darray_1d_cinterface_double_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpiof.a(piodarray.F90.o): in function `piodarray_mp_write_darray_1d_cinterface_short_':
/XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/pio/pio2/src/flib//XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `inq_var_bzip2_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:1244: undefined reference to `PIOc_inq_var_bzip2'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `inq_filter_avail_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:2986: undefined reference to `PIOc_inq_filter_avail'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `inq_var_filter_info_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:1301: undefined reference to `PIOc_inq_var_filter_info'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `inq_var_filter_ids_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:1193: undefined reference to `PIOc_inq_var_filter_ids'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `def_var_filter_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:3032: undefined reference to `PIOc_def_var_filter'
ld: /XYFS01/sysu_atmos_choujm_1/zhoup/CTSMoutput/I20008/bld/intel/mpich/nodebug/nothreads/lib//libpioc.a(pio_msg.c.o): in function `inq_var_zstandard_handler':
/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/libraries/parallelio/src/clib/pio_msg.c:1445: undefined reference to `PIOc_inq_var_zstandard'
gmake: *** [/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/cime/scripts/I20008/Tools/Makefile:935: ../../cesm.exe] Error 1
[sysu_atmos_choujm_1@ln202%TianheXY-CN I20008]$


[sysu_atmos_choujm_1@ln202%TianheXY-CN I20008]$ module list
Currently Loaded Modulefiles:
1) szip/2025 7) libxml/2.9.14-icc-2023
2) bzip2/1.0.8 8) netcdf/4.9.3-icc-oneapi2023.2-mpich-4.1.2-ch4
3) intel/oneapi2023.2_noimpi 9) python/python3/3.9.7
4) mpi/mpich/4.1.2-icc-oneapi2023.2-ch4 10) perl/5.41.8-gcc-11.4.0
5) pnetcdf/1.12.3-icc-oneapi2023.2-mpich-4.1.2-ch4 11) pio/ParallelIO-pio2.6.2-icc-2023
6) hdf5/1.14.3-icc-oneapi2023.2-mpich-4.1.2-ch4 12) esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4

Key:
auto-loaded
[sysu_atmos_choujm_1@ln202%TianheXY-CN I20008]$
 
J

jedwards

CSEG and Liaisons
Staff member
It looks like you are using a pio module in pio/ParallelIO-pio2.6.2-icc-2023 but the model isnt
recognizing that module and is trying to build pio again. The pio module is expected to define
the following environment variables to avoid the cesm build of pio:
PIO_VERSION_MAJOR
PIO_TYPENAME_VALID_VALUES
PIO
 
P

pengzhou

peng zhou
New Member
jedwards said:
It looks like you are using a pio module in pio/ParallelIO-pio2.6.2-icc-2023 but the model isnt
recognizing that module and is trying to build pio again. The pio module is expected to define
the following environment variables to avoid the cesm build of pio:
PIO_VERSION_MAJOR
PIO_TYPENAME_VALID_VALUES
PIO
Click to expand...
Thank you once again for your prompt and generous guidance. I have carefully attempted the steps you recommended, but I fear I may not have fully applied your advice. Before running ./case.setup, I exported the environment variables as discussed, yet I still encounter the same PIO-related error. I would be immensely grateful if you could kindly clarify or point out any misstep in my approach. Your expertise and assistance are deeply appreciated—thank you for your time and for sharing your invaluable knowledge.

export PIO=/APP/u22/x86/modulepath/application/pio/ParallelIO-pio2.6.2-icc-2023
export PIO_VERSION_MAJOR=2
export PIO_TYPENAME_VALID_VALUES="netcdf4,pnetcdf"

[sysu_atmos_choujm_1@ln202%TianheXY-CN I200013]$ module show pio/ParallelIO-pio2.6.2-icc-2023
-------------------------------------------------------------------
/APP/u22/x86/modulepath/application/pio/ParallelIO-pio2.6.2-icc-2023:

module-whatis {SQLite3 is an SQL database engine in a C library. Programs that link the SQLite3 library can have SQL database access without running a separate RDBMS process. }
conflict pio
prepend-path LD_LIBRARY_PATH /APP/u22/x86/pio/ParallelIO-pio2_6_2/lib
prepend-path LIBRARY_PATH /APP/u22/x86/pio/ParallelIO-pio2_6_2/lib
prepend-path INCLUDE /APP/u22/x86/pio/ParallelIO-pio2_6_2/include
prepend-path CPATH /APP/u22/x86/pio/ParallelIO-pio2_6_2/include
prepend-path CMAKE_PREFIX_PATH /APP/u22/x86/pio/ParallelIO-pio2_6_2/
-------------------------------------------------------------------
[sysu_atmos_choujm_1@ln202%TianheXY-CN I200013]$

/GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/build/src/flib//GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/build/src/flib//GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /APP/u22/x86/pio/ParallelIO-pio2_6_2/lib/libpiof.a(piodarray.F90.o): in function `piodarray_mp_write_darray_1d_cinterface_short_':
/GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/build/src/flib//GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/src/flib/piodarray.F90.in:131: undefined reference to `perf_mod_mp_t_startf_'
ld: /GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/build/src/flib//GLOBALFS/nscc_ts_7/xzx/ParallelIO-pio2_6_2/src/flib/piodarray.F90.in:139: undefined reference to `perf_mod_mp_t_stopf_'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `inq_var_bzip2_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:1244: undefined reference to `PIOc_inq_var_bzip2'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `inq_filter_avail_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:2986: undefined reference to `PIOc_inq_filter_avail'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `inq_var_filter_info_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:1301: undefined reference to `PIOc_inq_var_filter_info'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `inq_var_filter_ids_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:1193: undefined reference to `PIOc_inq_var_filter_ids'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `def_var_filter_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:3032: undefined reference to `PIOc_def_var_filter'
ld: /APP/u22/x86/esmf/8.8.0-icc-oneapi2023.2-mpich-4.1.2-ch4/lib/libO/Linux.intel.64.mpich.default/libpioc.a(pio_msg.c.o): in function `inq_var_zstandard_handler':
/GLOBALFS/nscc_ts_7/huangchx/esmf-8.8.0/src/Infrastructure/IO/PIO/ParallelIO/src/clib/pio_msg.c:1445: undefined reference to `PIOc_inq_var_zstandard'
gmake: *** [/XYFS01/sysu_atmos_choujm_1/zhoup/ctsm5.3.030/cime/scripts/I200014/Tools/Makefile:935: ../../cesm.exe] Error 1
 
J

jedwards

CSEG and Liaisons
Staff member
Now it looks like you are using the installed pio module but perhaps that module was built with the timing library?
You should rebuild pio using the option PIO_ENABLE_TIMING=OFF
 
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