Hi everyone,
I’m trying to run one of the test cases in NEMO and encountering a compilation error during a linking step. I’m following this example configuration: apptainer-nemo.def.
The command I’m using to compile the test is:
./makenemo -m local -a DOME -n DOME_v2
Here’s my local configuration file:
%NCDF_HOME /nemo/installs
%HDF5_HOME /nemo/installs
%XIOS_HOME /nemo/sources/XIOS/xios
%OASIS_HOME
%NCDF_INC -I%NCDF_HOME/include
%NCDF_LIB -L%NCDF_HOME/lib -lnetcdf -lnetcdff -L%HDF5_HOME/lib -lhdf5_hl -lhdf5 -lcurl
%XIOS_INC -I%XIOS_HOME/inc
%XIOS_LIB -L%XIOS_HOME/lib -lxios -lstdc++
%OASIS_INC
%OASIS_LIB
%CPP cpp -Dkey_nosignedzero
%FC mpif90 -c -cpp
%FCFLAGS -O3 -fdefault-real-8 -ffree-line-length-none -fno-second-underscore -Dgfortran -funroll-all-loops -fcray-pointer -fallow-argument-mismatch
%FFLAGS %FCFLAGS
%LD mpif90
%LDFLAGS -Wl,-rpath,$INSTDIR/lib
%FPPFLAGS -P -C -traditional
%AR ar
%ARFLAGS rs
%MK make
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC gcc
%CFLAGS
When I run the makenemo command, I get this error:
2/AGRIFLIB/obj/main.o:(.bss+0x4ef8): first defined here
/usr/bin/ld: /nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/lib/lib__fcm__conv.a(writeinfile.o):(.bss+0x4efc): multiple definition of `value_char_size3'; /nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/obj/main.o:(.bss+0x4efc): first defined here
...
collect2: error: ld returned 1 exit status
fcm_internal load failed (256)
make: *** [/nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/Makefile:406: conv] Error 1
make -f /nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/Makefile -j 1 all failed (2) at /nemo/sources/NEMO/NEMOGCM/ext/FCM/bin/../lib/Fcm/Build.pm line 597.
On further inspection, this seems to be the problematic command:
gcc -o conv /nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/obj/main.o -L/nemo/sources/NEMO/NEMOGCM/tests/DOME_v2/AGRIFLIB/lib -l__fcm__conv
The error is:
/usr/bin/ld: cannot find -l__fcm__conv: No such file or directory
collect2: error: ld returned 1 exit status
I’ve verified the FCM installation, and the bin and lib directories seem to be present:
root@88e9669300bd:/nemo/sources/NEMO/NEMOGCM# ls ext/FCM/bin/
fcm fcm_graphic_diff fcm_graphic_merge fcm_gui fcm_internal fcm_setup_konqueror fcm_update_version_dir.pl
root@88e9669300bd:/nemo/sources/NEMO/NEMOGCM# ls ext/FCM/lib/Fcm/
Base.pm BuildSrc.pm CLI.pm Cm.pm CmUrl.pm Dest.pm ExtractConfigComparator.pm Interactive Keyword.pm Timer.pm
Build BuildTask.pm CfgFile.pm CmBranch.pm Config.pm Exception.pm ExtractFile.pm Interactive.pm ReposBranch.pm Util
Build.pm CLI CfgLine.pm CmCommitMessage.pm ConfigSystem.pm Extract.pm ExtractSrc.pm Keyword SrcDirLayer.pm Util.pm
I’m stuck on how to resolve this linkage issue. Does anyone have any tips or suggestions?
Thanks in advance! 