Issue when building cases for CESM2

[tongh]

I am getting an error while building a test case using CESM2,
the error is down below.
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/deac/classes/csc391/tongh18/cesm/scratch/b.e20.B1850.f19_g17.test/bld/gnu/openmpi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
/usr/bin/ar: two different operation options specified
gmake[1]: *** [libmpeu.a] Error 1
gmake: *** [subdirs] Error 2
ERROR: f951: Warning: Nonexistent include directory

The error that we found was the noesmf folder does not exist, and on the site it said esmf is optional for running the app. Do we need the esmf or is there a way bypass the issue?
Thank you.

 

[jedwards]

Most compilers warn or ignore when an include directory is not present, but recent gnu compilers make it an error,
you can turn this off with -Wno-missing-include-dirs

 

[tongh]

Most compilers warn or ignore when an include directory is not present, but recent gnu compilers make it an error,
you can turn this off with -Wno-missing-include-dirs

how do I do that? Do I do it with the case.build, or is it something I have to do for the compilers separately?

 

[jedwards]

Add this flag to the section for your system in config_compilers.xml .

 

[tongh]

<compiler COMPILER="gnu">
<CFLAGS>
<base> -std=gnu99 </base>
<append compile_threaded="true"> -fopenmp </append>
<append DEBUG="TRUE"> -g -Wall -Og -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds </append>
<append DEBUG="FALSE"> -O </append>
</CFLAGS>
<CPPDEFS>
Since I am using gnu, would I just add it to the debug='true'

 

[jedwards]

Yes you can add it there.

 

[tongh]

<compiler COMPILER="gnu">
<CFLAGS>
<base> -std=gnu99 </base>
<append compile_threaded="true"> -fopenmp </append>
<append DEBUG="TRUE"> -g -Wall -Og -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds -Wno-missing-include-dirs </append>
<append DEBUG="FALSE"> -O </append>
</CFLAGS>
<CPPDEFS>
This is what I did, and I tried to create a new case, and I still got the same error, is there something wrong with my machine files?

<machine MACH="a1a-u2-c4-b5">
<DESC>
deac cluster
</DESC>
<NODENAME_REGEX>a1a-u2-c4-b5</NODENAME_REGEX>
<OS>LINUX</OS>
<COMPILERS>gnu</COMPILERS>
<MPILIBS>openmpi</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>/deac/classes/csc391/tongh18/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/deac/classes/csc391/tongh18/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/deac/classes/csc391/tongh18/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/deac/classes/csc391/tongh18/cesm/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>/deac/classes/csc391/tongh18/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/deac/classes/csc391/tongh18/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>gmake</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>8</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>8</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpiexec</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<mpirun mpilib="openmpi">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks">-n {{ total_tasks }}</arg>
</arguments>
</mpirun>

<module_system type="module">
<init_path lang="perl">/usr/share/Modules/init/perl.pm</init_path>
<init_path lang="python">/usr/share/Modules/init/python.py</init_path>
<init_path lang="csh">/usr/share/Modules/init/csh</init_path>
<init_path lang="sh">/usr/share/Modules/init/sh</init_path>
<cmd_path lang="perl">/usr/bin/modulecmd perl</cmd_path>
<cmd_path lang="python">/usr/bin/modulecmd python</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<modules>
<command name="purge"/>
</modules>
<modules compiler="gnu">
<command name="load">compilers/gcc/9.3.0</command>
<command name="load">openmpi/4.0.3-gcc-9.3.0-xmy2xef</command>
<command name="load">netcdf-c/4.7.3-gcc-9.3.0-oe74wmu</command>
<command name="load">parallel-netcdf/1.12.1-gcc-9.3.0-bmlq6qi</command>
<command name="load">netcdf-fortran/4.5.2-gcc-9.3.0-7w6olqk</command>
</modules>
</module_system>
<environment_variables>
<env name="NETCDF_C_PATH">/home/tongh18/spack/opt/spack/linux-rhel7-x86_64/gcc-9.3.0/netcdf-c-4.7.3-oe74wmumkzj5rd5jihaktoxspqvw2l4p</env>
<env name="NETCDF_FORTRAN_PATH">/home/tongh18/spack/opt/spack/linux-rhel7-x86_64/gcc-9.3.0/netcdf-fortran-4.5.2-7w6olqkwpd7z5ddv3ycgqora7zh3yfmo</env>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>

 

[MabelSue]

Hi, I get the same error.Have you figured it out?

_________________________________

/usr/bin/ar: two different operation options specified
make[1]: *** [Makefile:55: libmpeu.a] Error 1
make: *** [/my_cesm_sandbox/cime/src/externals/mct/Makefile:10: subdirs] Error 2

 

[jedwards]

If you add it to the DEBUG=TRUE section it will only apply if DEBUG=TRUE in your case,
to add it in general try a line
<append>-Wno-missing-include-dirs</append>

 

[MabelSue]

If you add it to the DEBUG=TRUE section it will only apply if DEBUG=TRUE in your case,
to add it in general try a line
<append>-Wno-missing-include-dirs</append>

Thank you.

It didn't work.

 

[abanks]

Hello,
I have a similar build issue. Appending -Wno-missing-include-dirs isn't working for me either. @MabelSue have you found a solution?
Thanks

 

[MabelSue]

Hello,
I have a similar build issue. Appending -Wno-missing-include-dirs isn't working for me either. @MabelSue have you found a solution?
Thanks

I fixed it. The compiler was not congfigured correctly.

 

[thakur.abubakar]

Hi Mabel,

I'm facing a similar problem with gnu. Can you please post the changes you made to your config_compilers.xml?

Thanks in advance,
Abu