Error while generating new case compset - F20TR_MMF1

[gourikadam]

Dear team,

I am getting below mentioned error in ./case.build and the message says

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(647): error: identifier "MADV_SEQUENTIAL" is undefined
          madvise(m, l, MADV_SEQUENTIAL); // optimize for sequential access
                        ^

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(649): error: identifier "MADV_NORMAL" is undefined
          madvise(m, root->len = l, MADV_NORMAL); // put it back to normal
                                    ^

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(647): warning #266: function "madvise" declared implicitly
          madvise(m, l, MADV_SEQUENTIAL); // optimize for sequential access
          ^

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(647): error: identifier "MADV_SEQUENTIAL" is undefined
          madvise(m, l, MADV_SEQUENTIAL); // optimize for sequential access
                        ^

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(649): error: identifier "MADV_NORMAL" is undefined
          madvise(m, root->len = l, MADV_NORMAL); // put it back to normal
                                    ^

/scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/mpas-framework/src/external/ezxml/ezxml.c(935): warning #266: function "strdup" declared implicitly
              xml->attr[1] = strdup(""); // empty list of malloced names/vals

Please help me in resolving this.

Thank you
Regards,
Gouri

[whannah1]

@gourikadam what machine/compiler are you trying to use?

[gourikadam]

Hi. I am using unsupported machine with intel compiler. my cmake file looks like below
"if (COMP_NAME STREQUAL gptl)
string(APPEND CMAKE_C_FLAGS " -DHAVE_SLASHPROC")
endif()
string(APPEND CMAKE_C_FLAGS " -std=c99")
if (compile_threaded)
string(APPEND CMAKE_C_FLAGS " -qopenmp")
string(APPEND CMAKE_CXX_FLAGS " -qopenmp")
string(APPEND CMAKE_Fortran_FLAGS " -qopenmp")
string(APPEND CMAKE_EXE_LINKER_FLAGS " -qopenmp")
endif()
string(APPEND CMAKE_C_FLAGS_RELEASE " -O2 -debug minimal")
string(APPEND CMAKE_CXX_FLAGS_RELEASE " -O2")
string(APPEND CMAKE_Fortran_FLAGS_RELEASE " -O2 -debug minimal")
string(APPEND CMAKE_C_FLAGS_DEBUG " -O0 -g")
string(APPEND CMAKE_CXX_FLAGS_DEBUG " -O0 -g")
string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created -init=snan,arrays")
#string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -L/scratch/um_cdac2/met_models/CDACP_Int/all-dep/lib -lpnetcdf -O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created -init=snan,arrays")
string(APPEND CMAKE_CXX_FLAGS " -std=c++17 -xHost -fp-model fast")
if (COMP_NAME STREQUAL cice)
string(APPEND CMAKE_Fortran_FLAGS_DEBUG " -init=nosnan,arrays")
endif()
if (COMP_NAME MATCHES "^pio")
string(APPEND SPIO_CMAKE_OPTS " -DPIO_ENABLE_TOOLS:BOOL=ON")
endif()
string(APPEND CPPDEFS " -DFORTRANUNDERSCORE -DNO_R16 -DCPRINTEL")
string(APPEND CMAKE_Fortran_FLAGS " -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs")
string(APPEND CMAKE_Fortran_FORMAT_FIXED_FLAG " -fixed -132")
string(APPEND CMAKE_Fortran_FORMAT_FREE_FLAG " -free")
string(APPEND LDFLAGS " ")
set(HAS_F2008_CONTIGUOUS "TRUE")
set(MPICC "mpiicc")
set(MPICXX "mpiicpc")
set(MPIFC "mpiifort")
set(SCC "icc")
set(SCXX "icpc")
set(SFC "ifort")
#set(LDFLAGS "-L/scratch/um_cdac2/met_models/CDACP_Int/all-dep/lib -lnetcdf -lpnetcdf")

Intel has to link fortran mains with fortran

set(E3SM_LINK_WITH_FORTRAN "TRUE")
"

[whannah1]

Also, a few other sanity check things - are you using a recent version of the E3SM repo?
Did you make sure the submodules are synced and up-to-date?

[gourikadam]

Yes, I am using the recent version of E3SM downloaded from Github. As and when error occurs, installing respective submodules. Hopefully everything is updated.

[rljacob]

still looks like some submodule isn't checked out completely. At the top of the code, do "git submodule update --init --recursive". If you get an error, repeat until you don't.

[gourikadam]

I tried using "git submodule update --init --recursive" but it is not working as access issue from the server and i downloaded the original code using git clone.
Cloning into 'components/eam/src/physics/cosp2/external'.. .
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Clone of '[email protected]:CFMIP/COSPv2.0.git' into submodul e path 'components/eam/src/physics/cosp2/external' failed

I manuaaly tried to clone few submodules in the path "E3SM/cime/CIME"like cprnc. But still error is there. I have following doubts

1. wether cmake file which I posted in reply above is correct or any setting is missing
2. the Compset "F20TR_MMF1" which I am using for creating new EAM is correct or not?

[rljacob]

You either need to set up ssh keys with github or do "git config --global url."https://github.com/".insteadOf "[email protected]:"

[gourikadam]

Hi,

Thank you foryour support. Able to resolve most of the errors related to submodules. Now getting errro in e3sm.bld.log as below
" elm/src/main/elm_interface_pflotranMod.F90.o.provides.build
/tmp/iforthpJeIj.i90: catastrophic error: Internal compiler error: segmentation violation signal raised Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for /scratch/um_cdac2/met_models/CDACP_Int/E3SM/components/elm/src/external_models/fates/main/FatesHistoryInterfaceMod.F90 (code 1)
Target CMakeFiles/lnd.dir///elm/src/external_models/fates/main/FatesHistoryInterfaceMod.F90.o built in 2.777128 seconds
Target CMakeFiles/lnd.dir///elm/src/external_models/fates/fire/SFMainMod.F90.o built in 2.484418 seconds
make[2]: *** [cmake/lnd/CMakeFiles/lnd.dir///elm/src/external_models/fates/main/FatesHistoryInterfaceMod.F90.o] Error 1
"