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Issue when building cases for CESM2

T

tongh

hao tong
New Member
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.
 
J

jedwards

CSEG and Liaisons
Staff member
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
 
T

tongh

hao tong
New Member
jedwards said:
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
Click to expand...
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?
 
T

tongh

hao tong
New Member
<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'
 
T

tongh

hao tong
New Member
<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>
 
M

MabelSue

MabelSue
New Member
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
 
J

jedwards

CSEG and Liaisons
Staff member
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>
 
A

abanks

Alison Banks
New Member
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
 
T

thakur.abubakar

Abu Bakar Siddiqui Thakur
Member
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
 
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