case.build error

[B.S.Wei]

Hello everyone,
I encountered a problem with build a case for clm5.0 and it show the error comment like this:

[phouta@localhost I1850CLM50_001]$ ./case.build
Building case in directory /home/phouta/clm_new_case/I1850CLM50_001
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
Calling /home/phouta/clm5.0_2024_model/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/home/phouta/projects/cesm-inputdata/share/domains/domain.lnd.fv1.9x2.5_gx1v7.181205.nc", will attempt to download in check_input_data phase
Calling /home/phouta/clm5.0_2024_model/cime_config/buildnml
ERROR: Command /home/phouta/clm5.0_2024_model/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /home/phouta/clm5.0_2024_model/bld /home/phouta/clm5.0_2024_model/bld /home/phouta/clm5.0_2024_model/cime/utils/perl5lib /home/phouta/clm5.0_2024_model/bld /home/phouta/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/phouta/clm5.0_2024_model/cime/utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /home/phouta/clm5.0_2024_model/cime/utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /home/phouta/clm5.0_2024_model/bld/CLMBuildNamelist.pm line 414.

Could anyone help me to solve this problem?
I appreciate for you help so much.

 

[jedwards]

XML::LibXML is a perl module that should be installed on your system - you can install it as a user
using cpan but I recommend you contact your system administrators to do a system wide install.

 

[B.S.Wei]

Dear jedwards,
Thank you for your reply. I have contact my system administrators and can you give me the specific name of the library for install?

 

[B.S.Wei]

Dear @jedwards,
after I solve the error. Now I am facing the new problem as shown below:

[phouta@localhost I1850CLM50_001]$ ./case.build
Building case in directory /home/phouta/clm_new_case/I1850CLM50_001
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (8388608, -1)
Generating component namelists as part of build
Creating component namelists
Calling /home/phouta/clm5.0_2024_model/cime/src/components/data_comps/datm/cime_config/buildnml
File not found: domainfile = "/home/phouta/projects/cesm-inputdata/share/domains/domain.lnd.fv1.9x2.5_gx1v7.181205.nc", will attempt to download in check_input_data phase
Calling /home/phouta/clm5.0_2024_model/cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/cime/src/components/stub_comps/sice/cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/cime/src/components/stub_comps/socn/cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/components/mosart//cime_config/buildnml
File not found: frivinp_rtm = "/home/phouta/projects/cesm-inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc", will attempt to download in check_input_data phase
Running /home/phouta/clm5.0_2024_model/components/cism//cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/cime/src/components/stub_comps/swav/cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/cime/src/components/stub_comps/sesp/cime_config/buildnml
Calling /home/phouta/clm5.0_2024_model/cime/src/drivers/mct/cime_config/buildnml
File not found: lnd2rof_fmapname = "lnd/clm2/mappingdata/maps/1.9x2.5/map_1.9x2.5_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/1.9x2.5/map_0.5x0.5_nomask_to_1.9x2.5_nomask_aave_da_c120709.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_fmapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_TO_gland4km_aave.170429.nc", will attempt to download in check_input_data phase
File not found: lnd2glc_smapname = "cpl/gridmaps/fv1.9x2.5/map_fv1.9x2.5_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_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
File not found: glc2lnd_smapname = "cpl/gridmaps/gland4km/map_gland4km_TO_fv1.9x2.5_aave.170429.nc", will attempt to download in check_input_data phase
Finished creating component namelists
Building gptl with output to file /home/phouta/projects/scratch/I1850CLM50_001/bld/gptl.bldlog.240724-203407
Calling /home/phouta/clm5.0_2024_model/cime/src/build_scripts/buildlib.gptl
ERROR: /home/phouta/clm5.0_2024_model/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/phouta/projects/scratch/I1850CLM50_001/bld/gptl.bldlog.240724-203407

 

[jedwards]

What is in the gptl.bldlog file it refers to?

ERROR: /home/phouta/clm5.0_2024_model/cime/src/build_scripts/buildlib.gptl FAILED, cat /home/phouta/projects/scratch/I1850CLM50_001/bld/gptl.bldlog.240724-203407

 

[B.S.Wei]

I am sure about that but I will attached the file for you. Could you help me to check?

 

[jedwards]

It appears that you are trying to use intel compiler options but with a gcc compiler. If you intend to use intel you need to make sure that it's found before gcc in your path. If you intend to use gnu you need to set that compiler in config_machines.xml

 

[B.S.Wei]

Dear jedwards,
I hope you are doing well. Now, I am still encountering on ./case build. I am trying to compile my machine using gnu compiler with gcc11.4.0. But I got an error comment Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/LOGICAL(4)). You will find in the attachment below.

 

[jedwards]

Add the following flags for gnu 11 and newer:
-fallow-argument-mismatch -fallow-invalid-boz

 

[B.S.Wei]

Add the following flags for gnu 11 and newer:
-fallow-argument-mismatch -fallow-invalid-boz

Thank you for your responses.
After I have added this comment. Now I'm seeing a new problem, and I've attached the files below.

Is there something wrong with my installation of software requirements? Below is the version of the software that I had install.
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 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.

GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 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.

GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <The GNU General Public License v3.0 - GNU Project - Free Software Foundation>
This is free software: you are free to change and redistribute it.

netCDF 4.8.1
netCDF-Fortran 4.5.4
Python 3.10.12

mpirun (Open MPI) 4.1.2
Report bugs to 2. Getting help — Open MPI main documentation

Thank you very much for your assistance.

 

[jedwards]

I suspect that for some reason the mpif90 command is not passing flags through to your compiler - otherwise the errors you are getting don't make any sense.