Describe every step you took leading up to the problem:
Dear Scientists:
I am currently using the Intel compiler, but it seems that my mpiicc cannot be used. Perhaps it is related to my previous use of the GNU compiler that comes with the Ubuntu system. I have now passed it/ The case.setup step cannot be passed/ Step case.build. I have previously modified the Depend-INtel file, and my logs have been pasted below
Building a single executable version of target coupled model
ERROR: Command make exec_se -j 2 EXEC_SE=/home/cx123/cesm/scratch/AB4/bld/cesm.exe MODEL=driver LIBROOT=/home/cx123/cesm/scratch/AB4/bld/lib -f /home/cx123/clm5.0/cime/scripts/AB4/Tools/Makefile failed rc=2
out=/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkSrcfiles
cp -f Filepath Deppath
/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkDepends Deppath Srcfiles > Depends
/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkSrcfiles
mpifort -o /home/cx123/cesm/scratch/AB4/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o -L/home/cx123/cesm/scratch/AB4/bld/lib/ -latm -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lice -L/home/cx123/cesm/scratch/AB4/bld/lib/ -llnd -L/home/cx123/cesm/scratch/AB4/bld/lib/ -locn -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lrof -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lglc -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lwav -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lesp -L../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib -lcsm_share -L../../intel/impi/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/netcdf4/lib -lnetcdf -lcurl -lm -lnetcdff -lhdf5_hl -lhdf5 -lz -L/usr/lib/x86_64-linux-gnu/lapack -llapack -L/usr/lib/x86_64-linux-gnu/blas -lblas
../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib/libcsm_share.a(shr_sys_mod.o): In function `__shr_sys_mod_MOD_shr_sys_chdir':
shr_sys_mod.F90:(.text+0x1d4): undefined reference to `chdir_'
../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib/libcsm_share.a(shr_sys_mod.o): In function `__shr_sys_mod_MOD_shr_sys_system':
shr_sys_mod.F90:(.text+0x1fd): undefined reference to `system_'
collect2: error: ld returned 1 exit status
/home/cx123/clm5.0/cime/scripts/AB4/Tools/Makefile:878: recipe for target '/home/cx123/cesm/scratch/AB4/bld/cesm.exe' failed
make: *** [/home/cx123/cesm/scratch/AB4/bld/cesm.exe] Error 1
Because the XML format file cannot be pasted here, I have pasted some of the contents of my confic_compiler. xml and config.machine.xml files that I created when creating the case, as well as the Depend. intel file that I previously modified, below. I don't know if my question is related to the following content.
config_compilers.xml
<compiler COMPILER="intel">
<CFLAGS>
<base> </base>
<append compile_threaded="true"> -qopenmp </append>
<append DEBUG="FALSE"> -O2 -debug </append>
<append DEBUG="TRUE"> -O0 -g </append>
</CFLAGS>
<CPPDEFS>
<!-- Technical Library -->
<append> -DFORTRANUNDERSCORE -DCPRINTEL</append>
</CPPDEFS>
<CXX_LDFLAGS>
<base> -cxxlib </base>
</CXX_LDFLAGS>
<CXX_LINKER>FORTRAN</CXX_LINKER>
<FC_AUTO_R8>
<base> -r8 </base>
</FC_AUTO_R8>
<FFLAGS>
<append compile_threaded="true"> -qopenmp </append>
<append DEBUG="TRUE"> -O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created </append>
<append DEBUG="FALSE"> -O2 -debug </append>
</FFLAGS>
<FFLAGS_NOOPT>
<base> -O
ree </base>
</FREEFLAGS>
<HAS_F2008_CONTIGUOUS>TRUE</HAS_F2008_CONTIGUOUS>
<LDFLAGS>
<append compile_threaded="true"> -qopenmp </append>
</LDFLAGS>
<MPICC> mpicc </MPICC>
<MPICXX> mpiicpc </MPICXX>
<MPIFC> mpifort</MPIFC>
<SCC> icc </SCC>
<SCXX> icpc </SCXX>
<SFC> ifort </SFC>
<SLIBS>
<append MPILIB="mpich"> -mkl=cluster </append>
<append MPILIB="mpich2"> -mkl=cluster </append>
<append MPILIB="mvapich"> -mkl=cluster </append>
<append MPILIB="mvapich2"> -mkl=cluster </append>
<append MPILIB="mpt"> -mkl=cluster </append>
<append MPILIB="openmpi"> -mkl=cluster </append>
<append MPILIB="impi">-qmkl=cluster -L/home/u4/netcdf-intel/lib -lnetcdf -lnetcdff</append>
<append MPILIB="mpi-serial"> -mkl </append>
</SLIBS>
<SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
</compiler>
config_machines.xml
<machine MACH="myintel">
<DESC>
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
</DESC>
<NODENAME_REGEX>regex.expression.matching.your.machine</NODENAME_REGEX>
<OS>LINUX</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>intel</COMPILERS>
<MPILIBS>impi</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>$ENV{HOME}/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$ENV{HOME}/cesm/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>2</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>2</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>2</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="none"/>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
<env name="NETCDF_PATH">/home/cx123/netcdf-intel</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
Depend.intel
#
PERFOBJS=\
prim_advection_mod.o \
edge_mod.o \
derivative_mod.o \
bndry_mod.o \
prim_advance_mod.o
# CLM's SatellitePhenologyMod is compiled incorrectly with intel 15.0.0 at -O2
REDUCED_OPT_OBJS=\
SatellitePhenologyMod.o
# shr_wv_sat_mod does not need to have better than ~0.1% precision, and benefits
# enormously from a lower precision in the vector functions.
REDUCED_PRECISION_OBJS=\
shr_wv_sat_mod.o
SHR_RANDNUM_FORT_OBJS=\
kissvec_mod.o \
mersennetwister_mod.o \
dSFMT_interface.o \
shr_RandNum_mod.o
SHR_RANDNUM_C_OBJS=\
dSFMT.o \
dSFMT_utils.o \
kissvec.o
ifeq ($(DEBUG),FALSE)
$(PERFOBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(REDUCED_OPT_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O1 $<
$(REDUCED_PRECISION_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(SHR_RANDNUM_FORT_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(SHR_RANDNUM_C_OBJS): %.o: %.c
$(CC) -c $(INCLDIR) $(INCS) $(CFLAGS) -O3 $<
endif
Looking forward to your early reply!
Yours
sincerely.
Describe your problem or question:
Dear Scientists:
I am currently using the Intel compiler, but it seems that my mpiicc cannot be used. Perhaps it is related to my previous use of the GNU compiler that comes with the Ubuntu system. I have now passed it/ The case.setup step cannot be passed/ Step case.build. I have previously modified the Depend-INtel file, and my logs have been pasted below
Building a single executable version of target coupled model
ERROR: Command make exec_se -j 2 EXEC_SE=/home/cx123/cesm/scratch/AB4/bld/cesm.exe MODEL=driver LIBROOT=/home/cx123/cesm/scratch/AB4/bld/lib -f /home/cx123/clm5.0/cime/scripts/AB4/Tools/Makefile failed rc=2
out=/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkSrcfiles
cp -f Filepath Deppath
/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkDepends Deppath Srcfiles > Depends
/home/cx123/clm5.0/cime/scripts/AB4/Tools/mkSrcfiles
mpifort -o /home/cx123/cesm/scratch/AB4/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o -L/home/cx123/cesm/scratch/AB4/bld/lib/ -latm -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lice -L/home/cx123/cesm/scratch/AB4/bld/lib/ -llnd -L/home/cx123/cesm/scratch/AB4/bld/lib/ -locn -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lrof -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lglc -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lwav -L/home/cx123/cesm/scratch/AB4/bld/lib/ -lesp -L../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib -lcsm_share -L../../intel/impi/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/usr/local/netcdf4/lib -lnetcdf -L/usr/local/netcdf4/lib -lnetcdf -lcurl -lm -lnetcdff -lhdf5_hl -lhdf5 -lz -L/usr/lib/x86_64-linux-gnu/lapack -llapack -L/usr/lib/x86_64-linux-gnu/blas -lblas
../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib/libcsm_share.a(shr_sys_mod.o): In function `__shr_sys_mod_MOD_shr_sys_chdir':
shr_sys_mod.F90:(.text+0x1d4): undefined reference to `chdir_'
../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib/libcsm_share.a(shr_sys_mod.o): In function `__shr_sys_mod_MOD_shr_sys_system':
shr_sys_mod.F90:(.text+0x1fd): undefined reference to `system_'
collect2: error: ld returned 1 exit status
/home/cx123/clm5.0/cime/scripts/AB4/Tools/Makefile:878: recipe for target '/home/cx123/cesm/scratch/AB4/bld/cesm.exe' failed
make: *** [/home/cx123/cesm/scratch/AB4/bld/cesm.exe] Error 1
Because the XML format file cannot be pasted here, I have pasted some of the contents of my confic_compiler. xml and config.machine.xml files that I created when creating the case, as well as the Depend. intel file that I previously modified, below. I don't know if my question is related to the following content.
config_compilers.xml
<compiler COMPILER="intel">
<CFLAGS>
<base> </base>
<append compile_threaded="true"> -qopenmp </append>
<append DEBUG="FALSE"> -O2 -debug </append>
<append DEBUG="TRUE"> -O0 -g </append>
</CFLAGS>
<CPPDEFS>
<!-- Technical Library -->
<append> -DFORTRANUNDERSCORE -DCPRINTEL</append>
</CPPDEFS>
<CXX_LDFLAGS>
<base> -cxxlib </base>
</CXX_LDFLAGS>
<CXX_LINKER>FORTRAN</CXX_LINKER>
<FC_AUTO_R8>
<base> -r8 </base>
</FC_AUTO_R8>
<FFLAGS>
<append compile_threaded="true"> -qopenmp </append>
<append DEBUG="TRUE"> -O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created </append>
<append DEBUG="FALSE"> -O2 -debug </append>
</FFLAGS>
<FFLAGS_NOOPT>
<base> -O
ree </base>
</FREEFLAGS>
<HAS_F2008_CONTIGUOUS>TRUE</HAS_F2008_CONTIGUOUS>
<LDFLAGS>
<append compile_threaded="true"> -qopenmp </append>
</LDFLAGS>
<MPICC> mpicc </MPICC>
<MPICXX> mpiicpc </MPICXX>
<MPIFC> mpifort</MPIFC>
<SCC> icc </SCC>
<SCXX> icpc </SCXX>
<SFC> ifort </SFC>
<SLIBS>
<append MPILIB="mpich"> -mkl=cluster </append>
<append MPILIB="mpich2"> -mkl=cluster </append>
<append MPILIB="mvapich"> -mkl=cluster </append>
<append MPILIB="mvapich2"> -mkl=cluster </append>
<append MPILIB="mpt"> -mkl=cluster </append>
<append MPILIB="openmpi"> -mkl=cluster </append>
<append MPILIB="impi">-qmkl=cluster -L/home/u4/netcdf-intel/lib -lnetcdf -lnetcdff</append>
<append MPILIB="mpi-serial"> -mkl </append>
</SLIBS>
<SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
</compiler>
config_machines.xml
<machine MACH="myintel">
<DESC>
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from Environment Modules – A Great Tool for Clusters » ADMIN Magazine
</DESC>
<NODENAME_REGEX>regex.expression.matching.your.machine</NODENAME_REGEX>
<OS>LINUX</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>intel</COMPILERS>
<MPILIBS>impi</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>$ENV{HOME}/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$ENV{HOME}/cesm/archive/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>2</GMAKE_J>
<BATCH_SYSTEM>none</BATCH_SYSTEM>
<SUPPORTED_BY>me@my.address</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>2</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>2</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="none"/>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
<env name="NETCDF_PATH">/home/cx123/netcdf-intel</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
Depend.intel
#
PERFOBJS=\
prim_advection_mod.o \
edge_mod.o \
derivative_mod.o \
bndry_mod.o \
prim_advance_mod.o
# CLM's SatellitePhenologyMod is compiled incorrectly with intel 15.0.0 at -O2
REDUCED_OPT_OBJS=\
SatellitePhenologyMod.o
# shr_wv_sat_mod does not need to have better than ~0.1% precision, and benefits
# enormously from a lower precision in the vector functions.
REDUCED_PRECISION_OBJS=\
shr_wv_sat_mod.o
SHR_RANDNUM_FORT_OBJS=\
kissvec_mod.o \
mersennetwister_mod.o \
dSFMT_interface.o \
shr_RandNum_mod.o
SHR_RANDNUM_C_OBJS=\
dSFMT.o \
dSFMT_utils.o \
kissvec.o
ifeq ($(DEBUG),FALSE)
$(PERFOBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(REDUCED_OPT_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O1 $<
$(REDUCED_PRECISION_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(SHR_RANDNUM_FORT_OBJS): %.o: %.F90
$(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O3 $<
$(SHR_RANDNUM_C_OBJS): %.o: %.c
$(CC) -c $(INCLDIR) $(INCS) $(CFLAGS) -O3 $<
endif
Looking forward to your early reply!
Yours
sincerely.
Describe your problem or question: