MCT( supposed to be nuopc) Error with cesm3_0_beta01

[Jbuzan]

Hello CESM Users:

I have downloaded cesm3_0_beta01 (ccs_config at tag ccs_config_cesm0.0.109). I recompiled my NCAR PIO and ESMF for intel, and I am trying to build a case:
./create_newcase --case /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/Intel_cesm3_0_beta01_B1850_T_02 --compiler intel --compset B1850 --res f09_g17 --mach eiger --driver nuopc --run-unsupported



I get the following error:

configure: error: in `/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_B1850_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/mct':
configure: error: C compiler cannot create executables
See `config.log' for more details
gmake: *** [/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/Intel_cesm3_0_beta01_B1850_T_02/Tools/Makefile:650: /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_B1850_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/mct/Makefile.conf] Error 77

I am not sure what to make of this error because I do pass c compilers in the compiler cmake file. I attach the mct.log and the config.log, below. I also attach my machine configure, compilers, and batch scripts.

Cheers,
-Jonathan

 

[jedwards]

I think that this issue is that you are trying to build a compset that is no longer supported but which hasn't yet been fully removed.
The compset and resolution for a 1 degree B1850 in cesm3_0_beta01 is --res ne30pg3_t232. --compset BLT1850_v0c
But that name is only going to be valid for beta01 and we will be changing again in beta02. We hope that this transition settles out soon and we
arrive at the new long term compset names for cesm3.

 

[Jbuzan]

Thanks for the quick reply, Jim.
I'lll switch to that combination. Ultimately, the goal is to get benchmarking on Eiger (computational proposals are due next week). We'll be mentioning that the intent is to upgrade to the release version of CESM3 in the future, but for now, we need to demonstrate the performance of fully coupled (and fixed-SST simulations) on Eiger to get estimates of node hours and scalings.

I'll try out that combination of resolution and model that you suggested. Does Derecho have a comparable simulation? Since the computer architecture is similar between Derecho and Eiger, it could be useful to see if they have similar performance.

 

[jedwards]

Yes, we are running this configuration regularly on derecho. You may also consider backing up to the
last cesm2.3 tag, cesm2_3_beta17, which is capable of running the B1850 f09_g17.

 

[Jbuzan]

Great! I'll try the current (cesm3) tag first with the suggested compset, since it is in use on Derecho.

 

[Jbuzan]

Hi Jim,
I have created a new case.
./create_newcase --case /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/Intel_cesm3_0_beta01_BLT1850_v0c_T_02 --compiler intel --compset BLT1850_v0c --res ne30pg3_t232 --mach eiger --driver nuopc --run-unsupported

and reached the the ./case.build step, but I am encountering what looks to be the same mct error as before and I am not sure how to approach a solution. I am attaching the ./case.build, mct log, and the config log.

ERROR: configure: error: in `/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/mct':
configure: error: C compiler cannot create executables
See `config.log' for more details

 

[jedwards]

Here is the error from your config.log - it means that you are trying to use an inproper configuration of the cray mpich compiler - you are probably missing a module load step. Contact your system administrators for help.


configure:2827: cc -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -debug minimal -no-fma -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -no-fma -DLINUX -DCESMCOUPLED -DFORTRANUNDERSCORE -DCPRINTEL -DFORTRANUNDERSCORE -DCPRINTEL -DNDEBUG -DUSE_ESMF_LIB -DHAVE_MPI -DNUOPC_INTERFACE -DPIO2 -DHAVE_SLASHPROC -D_PNETCDF -DESMF_VERSION_MAJOR=8 -DESMF_VERSION_MINOR=6 -DATM_PRESENT -DICE_PRESENT -DLND_PRESENT -DOCN_PRESENT -DROF_PRESENT -DGLC_PRESENT -DWAV_PRESENT -DESP_PRESENT -DMED_PRESENT -DPIO2 -I.. -I. -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/CDEPS/fox/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/CDEPS/dshr -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/nuopc/esmf/c1a1l1i1o1r1g1/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/finclude -I/opt/cray/pe/netcdf-hdf5parallel/4.9.0.9/intel/2023.2/include -I/opt/cray/pe/parallel-netcdf/1.12.3.9/intel/2023.2/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/include conftest.c >&5
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: warning: libfabric.so.1, needed by /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpichf90.so, not found (try using -rpath or -rpath-link)
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_getinfo@FABRIC_1.3'
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_version@FABRIC_1.0'
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_freeinfo@FABRIC_1.3'
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_strerror@FABRIC_1.0'
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_fabric@FABRIC_1.1'
/usr/lib64/gcc/x86_64-suse-linux/12/../../../../x86_64-suse-linux/bin/ld: /opt/cray/pe/mpich/8.1.28/ofi/intel/2022.1/lib/libmpi_intel.so: undefined reference to `fi_dupinfo@FABRIC_1.3'
icx: error: linker command failed with exit code 1 (use -v to see invocation)
configure:2831: $? = 1
configure:2871: result: no
configure: failed program was:

 

[Jbuzan]

Hi Jim,

CSCS staff had me load my environment, then execute the specific command at that failure.
I can execute the command via the command line and it does not blow up. Which means that my loaded environment works.
However, when the ./case.build is executed I have the same error. Could CESM be dropping an environment?

/* confdefs.h */
#define PACKAGE_NAME "MCT"
#define PACKAGE_TARNAME "mct"
#define PACKAGE_VERSION "2.10"
#define PACKAGE_STRING "MCT 2.10"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
/* end confdefs.h. */
int
main (void)
{
;
return 0;
}

cc -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -debug minimal -no-fma -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -no-fma -DLINUX -DCESMCOUPLED -DFORTRANUNDERSCORE -DCPRINTEL -DFORTRANUNDERSCORE -DCPRINTEL -DNDEBUG -DUSE_ESMF_LIB -DHAVE_MPI -DNUOPC_INTERFACE -DPIO2 -DHAVE_SLASHPROC -D_PNETCDF -DESMF_VERSION_MAJOR=8 -DESMF_VERSION_MINOR=6 -DATM_PRESENT -DICE_PRESENT -DLND_PRESENT -DOCN_PRESENT -DROF_PRESENT -DGLC_PRESENT -DWAV_PRESENT -DESP_PRESENT -DMED_PRESENT -DPIO2 -I.. -I. -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/CDEPS/fox/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/CDEPS/dshr -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/nuopc/esmf/c1a1l1i1o1r1g1/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/finclude -I/opt/cray/pe/netcdf-hdf5parallel/4.9.0.9/intel/2023.2/include -I/opt/cray/pe/parallel-netcdf/1.12.3.9/intel/2023.2/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/Intel_cesm3_0_beta01_BLT1850_v0c_T_02/bld/intel/mpich/nodebug/nothreads/nuopc/include conftest.c

 

[jedwards]

You can check what the cesm environment is by running

source .env_mach_specific.sh

from the case directory.
This environment represents what you are loading in config_machines.xml

 

[Jbuzan]

Hi Jim,

I think this explains a lot. I think I am incorrectly calling the modules in the machines xml.

source .env_mach_specific.sh
CMake/3.26.5(12):ERROR:102: Tcl command execution failed: help([==[
Description
===========
CMake, the cross-platform, open-source build system. CMake is

a family of tools designed to build, test and package software.
More information
================
- Homepage: CMake - Upgrade Your Software Build System
]==])
cray-python/3.11.5(7):ERROR:102: Tcl command execution failed: --[[
file cray-python module
Copyright 2020-2023 Hewlett Packard Enterprise Development LP
]]--
cray-netcdf-hdf5parallel/4.9.0.9(4):ERROR:102: Tcl command execution failed: --[[
Module cray-netcdf-hdf5parallel
Copyright 2020 Cray Inc. All Rights Reserved.
]]--
cray-hdf5-parallel/1.12.2.9(4):ERROR:102: Tcl command execution failed: --[[
Module cray-hdf5-parallel
Copyright 2020 Cray Inc. All Rights Reserved.
]]--
...
cray-hdf5-parallel/1.12.2.9(12):ERROR:150: Module 'cray-hdf5-parallel/1.12.2.9' conflicts with the currently loaded module(s) 'cray-parallel-netcdf/1.12.3.9'
cray-hdf5-parallel/1.12.2.9(12):ERROR:102: Tcl command execution failed: conflict cray-parallel-netcdf

 

[Jbuzan]

I removed the module calls from the config_machines.xml and it made it past that error. Something related to gettid being not static.

ERROR: /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/buildlib FAILED, cat /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/FMS.bldlog.240710-210429
jbuzan@eiger-ln001:/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03 [21:10:10] $ cat /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/FMS.bldlog.240710-210429
fms bldroot is /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS installpath is /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc
gmake -f /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm  -C /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS CASEROOT=/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03 USER_INCLDIR="-I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS/FMS " COMPLIB=libfms.a CIME_MODEL=cesm  SMP=FALSE CASEROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03" CASETOOLS="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03/Tools" CIMEROOT="/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/cime" SRCROOT="/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01" COMP_INTERFACE="nuopc" COMPILER="intel" DEBUG="FALSE" EXEROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld" RUNDIR="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/run" INCROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/lib/include" LIBROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/lib" MACH="eiger" MPILIB="mpich" NINST_VALUE="c1a1l1i1o1r1g1" OS="LINUX" PIO_VERSION=2 SHAREDLIBROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld" BUILD_THREADED="FALSE" USE_ESMF_LIB="TRUE" USE_MOAB="FALSE" CAM_CONFIG_OPTS="-phys cam_dev -chem ghg_mam4 -nlev 58 -model_top lt" COMP_ATM="cam" COMP_ICE="cice" COMP_GLC="cism" COMP_LND="clm" COMP_OCN="mom" COMP_ROF="mosart" COMP_WAV="swav" USE_TRILINOS="FALSE" USE_ALBANY="FALSE" USE_PETSC="FALSE"
gmake: Entering directory '/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS'
/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03/Tools/mkSrcfiles
cp -f Filepath Deppath
/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/intel_cesm3_0_beta01_BLT1850_v0c_T_03/Tools/mkDepends  Deppath Srcfiles > Depends
cc -c -I. -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS/FMS  -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/nuopc/esmf/c1a1l1i1o1r1g1/include -I. -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/time_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/m4 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/axis_utils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/sat_vapor_pres -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/docs -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/platform -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/tridiagonal -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_integral -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/interpolator -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/memutils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/random_numbers -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/libFMS -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/exchange -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/cmake -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/constants4 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/block_control -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/tracer_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/monin_obukhov -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/field_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/topography -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mosaic -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/drifters -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/horiz_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/amip_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/time_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/data_override -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/constants -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/test_fms -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/coupler -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mosaic2 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/parser -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/column_diagnostics -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/astronomy -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/lib/include -qno-opt-dynamic-align -fp-model precise -std=gnu99 -O2 -debug minimal -no-fma -O2 -no-fma -I/opt/cray/pe/netcdf-hdf5parallel/4.9.0.9/intel/2023.2/include  -DLINUX -Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DSPMD -D__IFC -DNDEBUG -DHAVE_MPI  -DCESMCOUPLED -DFORTRANUNDERSCORE -DCPRINTEL -DFORTRANUNDERSCORE -DCPRINTEL -DHAVE_SLASHPROC /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c
gmake: Leaving directory '/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/intel_cesm3_0_beta01_BLT1850_v0c_T_03/bld/intel/mpich/nodebug/nothreads/nuopc/FMS'
cat: Srcfiles: No such file or directory
/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:51:14: error: static declaration of 'gettid' follows non-static declaration
static pid_t gettid(void)
             ^
/usr/include/bits/unistd_ext.h:34:16: note: previous declaration is here
extern __pid_t gettid (void) __THROW;
               ^
1 error generated.
gmake: *** [/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm:359: affinity.o] Error 1
ERROR: cat: Srcfiles: No such file or directory
/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:51:14: error: static declaration of 'gettid' follows non-static declaration
static pid_t gettid(void)
             ^
/usr/include/bits/unistd_ext.h:34:16: note: previous declaration is here
extern __pid_t gettid (void) __THROW;
               ^
1 error generated.
gmake: *** [/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm:359: affinity.o] Error 1

 

[Jbuzan]

An update: applying the same thing to GNU, I get past the module error, but also die on the gettid error.

jbuzan@eiger-ln001:/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07 [07:45:53] $ cat /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/FMS.bldlog.240711-074339


fms bldroot is /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS installpath is /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc


gmake -f /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm -C /capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS CASEROOT=/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07 USER_INCLDIR="-I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS/FMS " COMPLIB=libfms.a CIME_MODEL=cesm SMP=FALSE CASEROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07" CASETOOLS="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/Tools" CIMEROOT="/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/cime" SRCROOT="/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01" COMP_INTERFACE="nuopc" COMPILER="gnu" DEBUG="FALSE" EXEROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld" RUNDIR="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/run" INCROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/lib/include" LIBROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/lib" MACH="eiger" MPILIB="mpich" NINST_VALUE="c1a1l1i1o1r1g1" OS="LINUX" PIO_VERSION=2 SHAREDLIBROOT="/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld" BUILD_THREADED="FALSE" USE_ESMF_LIB="TRUE" USE_MOAB="FALSE" CAM_CONFIG_OPTS="-phys cam_dev -chem ghg_mam4 -nlev 58 -model_top lt" COMP_ATM="cam" COMP_ICE="cice" COMP_GLC="cism" COMP_LND="clm" COMP_OCN="mom" COMP_ROF="mosart" COMP_WAV="swav" USE_TRILINOS="FALSE" USE_ALBANY="FALSE" USE_PETSC="FALSE"
gmake: Entering directory '/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS'
/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/Tools/mkSrcfiles
cp -f Filepath Deppath
/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/cases/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/Tools/mkDepends Deppath Srcfiles > Depends


cc -c -I. -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils/include -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS/FMS -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/nuopc/esmf/c1a1l1i1o1r1g1/include -I. -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/time_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/include -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/m4 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/axis_utils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/sat_vapor_pres -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/docs -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/platform -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/tridiagonal -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_integral -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/string_utils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/interpolator -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/memutils -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/random_numbers -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/libFMS -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/exchange -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/cmake -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/constants4 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/block_control -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/tracer_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/monin_obukhov -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/field_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/fms2_io -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/topography -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mosaic -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/drifters -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/horiz_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/amip_interp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/time_manager -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/data_override -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/constants -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mpp -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/test_fms -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/coupler -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/mosaic2 -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/parser -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/column_diagnostics -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/astronomy -I/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/diag_manager -I/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/lib/include -std=gnu99 -O -std=gnu99 -O -w -I/opt/cray/pe/netcdf-hdf5parallel/4.9.0.9/gnu/12.3/include -DLINUX -Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DSPMD -D__IFC -DNDEBUG -DHAVE_MPI -DCESMCOUPLED -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU -DHAVE_SLASHPROC /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c
gmake: Leaving directory '/capstor/scratch/cscs/jbuzan/cesm3_0_beta01/output/gnu_cesm3_0_beta01_BLT1850_v0c_T_07/bld/gnu/mpich/nodebug/nothreads/nuopc/FMS'
cat: Srcfiles: No such file or directory
/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:51:14: error: static declaration of ‘gettid’ follows non-static declaration
51 | static pid_t gettid(void)
| ^~~~~~
In file included from /usr/include/unistd.h:1170,
from /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:30:
/usr/include/bits/unistd_ext.h:34:16: note: previous declaration of ‘gettid’ with type ‘__pid_t(void)’ {aka ‘int(void)’}
34 | extern __pid_t gettid (void) __THROW;
| ^~~~~~
gmake: *** [/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm:359: affinity.o] Error 1
ERROR: cat: Srcfiles: No such file or directory
/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:51:14: error: static declaration of gettid follows non-static declaration
51 | static pid_t gettid(void)
| ^~~~~~
In file included from /usr/include/unistd.h:1170,
from /users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/src/affinity/affinity.c:30:
/usr/include/bits/unistd_ext.h:34:16: note: previous declaration of gettid with type __pid_t(void) {aka int(void) }
34 | extern __pid_t gettid (void) __THROW;
| ^~~~~~
gmake: *** [/users/jbuzan/cesm3_0_beta01/cesm3_0_beta01/libraries/FMS/Makefile.cesm:359: affinity.o] Error 1

 

[Jbuzan]

Hello Jim,

Working with my department IT, we commented out the 'gettid' section. There's some sort of conflict where the configure does not see the gettid, but the compiler does and then has a conflict.

Cheers,
-Jonathan