./case.build error: CESM2.1.5 (CLM) on Niagara cluster -- undefined reference to '.......'

[MS_CLM]

I'm trying to build cesm2.1.5 (clm), it gives error in ./case.build

./create_newcase --case $SCRATCH/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop --res f09_g17 --compset I1850Clm50BgcCrop --mach niagara --> OK
./case.setup --> OK
./case.build --> gives multiple errors related to: undefined reference to '.......' -- please see below.

Any suggestions pleas?

=====================
./case.build
Building case in directory /gpfs/fs0/scratch/c/cgf/msol/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop
sharedlib_only is False
model_only is False
Generating component namelists as part of build
Creating component namelists
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/scratch/c/cgf/msol/cesm2.1.5_clm5/inputdata/share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc", will attempt to download in check_input_data phase
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/clm//cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/components/stub_comps/sice/cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/components/stub_comps/socn/cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/mosart//cime_config/buildnml
File not found: frivinp_rtm = "/scratch/c/cgf/msol/cesm2.1.5_clm5/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
Running /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism//cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/components/stub_comps/swav/cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/components/stub_comps/sesp/cime_config/buildnml
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/drivers/mct/cime_config/buildnml
File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/0.9x1.25/map_0.9x1.25_nomask_to_0.5x0.5_nomask_aave_da_c120522.nc", will attempt to download in check_input_data phase
File not found: rof2lnd_fmapname = "lnd/clm2/mappingdata/maps/0.9x1.25/map_0.5x0.5_nomask_to_0.9x1.25_nomask_aave_da_c121019.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv0.9x1.25/map_fv0.9x1.25_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv0.9x1.25/map_fv0.9x1.25_TO_gland4km_blin.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_fmapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv0.9x1.25_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv0.9x1.25_aave.170429.nc", will attempt to download in check_input_data phase
Finished creating component namelists
Building gptl with output to file /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/gptl.bldlog.240207-131557
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/build_scripts/buildlib.gptl
Building mct with output to file /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/mct.bldlog.240207-131557
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/build_scripts/buildlib.mct
Building pio with output to file /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/pio.bldlog.240207-131557
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/build_scripts/buildlib.pio
Component pio build complete with 5 warnings
Building csm_share with output to file /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/csm_share.bldlog.240207-131557
Calling /gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/cime/src/build_scripts/buildlib.csm_share
Component csm_share build complete with 20 warnings
- Building clm4_5/clm5_0 Library
Building lnd with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/lnd.bldlog.240207-131557
Component lnd build complete with 9 warnings
clm built in 146.385082 seconds
Building atm with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/atm.bldlog.240207-131557
Building ice with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/ice.bldlog.240207-131557
Building ocn with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/ocn.bldlog.240207-131557
Building rof with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/rof.bldlog.240207-131557
Building glc with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/glc.bldlog.240207-131557
Building wav with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/wav.bldlog.240207-131557
Building esp with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/esp.bldlog.240207-131557
socn built in 4.300654 seconds
sesp built in 4.313364 seconds
swav built in 4.315642 seconds
sice built in 4.317824 seconds
datm built in 6.327823 seconds
mosart built in 25.125156 seconds
Component glc build complete with 2 warnings
cism built in 155.976992 seconds
Building cesm with output to /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/cesm.bldlog.240207-131557
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/clm/src/biogeophys/SoilWaterMovementMod.F90:1278: undefined reference to `dgtsv_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/clm/src/biogeophys/UrbBuildTempOleson2015Mod.F90:653: undefined reference to `dgesv_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/clm/src/biogeophys/BandDiagonalMod.F90:198: undefined reference to `dgbsv_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:279: undefined reference to `ddot_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:300: undefined reference to `ddot_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:311: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:316: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:1098: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:1100: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:1103: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:1107: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dcgs.f:1087: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6210: undefined reference to `ddot_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6203: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6246: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6256: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6261: undefined reference to `ddot_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6263: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6265: undefined reference to `ddot_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglide/glam_strs2.F90:6320: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:1637: undefined reference to `dnrm2_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:1927: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:1863: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:1644: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:2147: undefined reference to `dscal_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:2124: undefined reference to `dcopy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:1366: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:2296: undefined reference to `daxpy_'
/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve/SLAP/dgmres.f:2304: undefined reference to `dcopy_'
ERROR: BUILD FAIL: buildexe failed, cat /scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_I1850Clm50BgcCrop/bld/cesm.bldlog.240207-131557

Please note that I needed to shorten the above message to be <10000.

 

[oleson]

Moving this to the porting/infrastructure Forum

 

[MS_CLM]

Moving this to the porting/infrastructure Forum

OK, thanks.

 

[oleson]

Maybe this post will help. It refers to not linking the blas and lapack libraries:

Problem while setting up a case

Whenever I try to setup the case using ./case.setup command. i get the following error on my Linux Ubuntu 16.0.4 machine. ERROR: module command /usr/bin/modulecmd python purge failed with message: /bin/sh: 1: /usr/bin/modulecmd: not found

bb.cgd.ucar.edu

 

[MS_CLM]

Maybe this post will help. It refers to not linking the blas and lapack libraries:

Problem while setting up a case

Whenever I try to setup the case using ./case.setup command. i get the following error on my Linux Ubuntu 16.0.4 machine. ERROR: module command /usr/bin/modulecmd python purge failed with message: /bin/sh: 1: /usr/bin/modulecmd: not found

bb.cgd.ucar.edu

Thank you, Keith.
I did check it...., in my case the following files are available in that directory:

msol@nia-login07:/gpfs/fs1/home/c/cgf/msol/cesm2.1.5_clm5/components/cism/source_cism/libglimmer-solve$ ll
drwxr-s--- 2 msol cgf 4096 Feb 5 15:33 blas
-rw-r----- 1 msol cgf 17946 Feb 5 15:33 glimmer_sparse.F90
-rw-r----- 1 msol cgf 19745 Feb 5 15:33 glimmer_sparse_slap.F90
-rw-r----- 1 msol cgf 16083 Feb 5 15:33 glimmer_sparse_type.F90
drwxr-s--- 2 msol cgf 4096 Feb 7 14:57 SLAP

Also, in other directory:
msol@nia-login07:/scratch/c/cgf/msol/cesm2.1.5_clm5/runs/RUN_cesm2.1.5_CLM5_IHistClm50Sp/bld$ ll
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 atm
-rw-r----- 1 msol cgf 4779 Feb 7 14:31 atm.bldlog.240207-142613
-rw-r----- 1 msol cgf 52 Feb 7 14:26 CASEROOT
-rw-r----- 1 msol cgf 60240 Feb 7 14:34 cesm.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 cpl
-rw-r----- 1 msol cgf 169074 Feb 7 14:28 csm_share.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 esp
-rw-r----- 1 msol cgf 2129 Feb 7 14:31 esp.bldlog.240207-142613
drwxr-s--- 7 msol cgf 4096 Feb 7 14:31 glc
-rw-r----- 1 msol cgf 296606 Feb 7 14:34 glc.bldlog.240207-142613
-rw-r----- 1 msol cgf 3970 Feb 7 14:26 gptl.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 ice
-rw-r----- 1 msol cgf 2129 Feb 7 14:31 ice.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 intel
drwxr-s--- 3 msol cgf 4096 Feb 7 14:34 lib
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 lnd
-rw-r----- 1 msol cgf 633086 Feb 7 14:30 lnd.bldlog.240207-142613
-rw-r----- 1 msol cgf 81995 Feb 7 14:27 mct.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 ocn
-rw-r----- 1 msol cgf 2129 Feb 7 14:31 ocn.bldlog.240207-142613
-rw-r----- 1 msol cgf 70646 Feb 7 14:27 pio.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 rof
-rw-r----- 1 msol cgf 18282 Feb 7 14:31 rof.bldlog.240207-142613
drwxr-s--- 3 msol cgf 4096 Feb 7 14:26 wav
-rw-r----- 1 msol cgf 2129 Feb 7 14:31 wav.bldlog.240207-142613

But, I have no idea how to link -and perhaps adding those missing libraries.
I would appreciate any suggestions.

 

[slevis]

For organizational purposes, I am linking here the thread where we are waiting/hoping for another user to share how they solved this.

 

[MS_CLM]

For organizational purposes, I am linking here the thread where we are waiting/hoping for another user to share how they solved this.

Thanks a lot. I appreciate it.
Actually, I could solve it myself by adding “-mkl” into the config_compilers.xml -- I'm using Niagara cluster, as follows:



Thanks again.