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Error building CESM 1.2.1 on Pleiades-san

A

andrew_kren@colorado_edu

Member
I just installed WACCM, version CESM 1.2.1 on NASA Pleiades. I ran cesm_setup with no problems. When I ran the build script, I got an error message like this below:ERROR: buildlib.gptl failed, see /nobackup/akren/waccm_1850/bld/gptl/gptl.bldlog.140210-123329
ERROR: cat /nobackup/akren/waccm_1850/bld/gptl/gptl.bldlog.140210-123329

When I looked into the error, this is what it said: Mon Feb 10 11:46:53 PST 2014 /nobackup/akren/waccm_1850/bld/gptl/gptl.bldlog.140210-114649Copying source to CESM EXEROOT...mpicc   -c   -O2 -fp-model precise  -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_MPI /home6/akren/cesm1_2_1/models/utils/timing/gptl.cgcc: precise: No such file or directorycc1: error: unrecognized command line option "-fp-model"gmake: *** [gptl.o] Error 1 Question is, how can this be reconciled? Is this due to the newer version of WACCM?
 
J

jedwards

CSEG and Liaisons
Staff member
CESM is expectiing the intel compiler but your mpicc is pointing to the gcc compiler.    Check the env_mach_specific file and make sure that the intel module is still available, it may be that thatmodule has aged off the machine.    
 
J

jedwards

CSEG and Liaisons
Staff member
CESM is expectiing the intel compiler but your mpicc is pointing to the gcc compiler.    Check the env_mach_specific file and make sure that the intel module is still available, it may be that thatmodule has aged off the machine.    
 
J

jedwards

CSEG and Liaisons
Staff member
CESM is expectiing the intel compiler but your mpicc is pointing to the gcc compiler.    Check the env_mach_specific file and make sure that the intel module is still available, it may be that thatmodule has aged off the machine.    
 
E

eaton

CSEG and Liaisons
The problem appears to be that mpicc is not invoking an intel version of the C compiler.  "-fp-model" is an arg that intel compilers recognize. 
 
E

eaton

CSEG and Liaisons
The problem appears to be that mpicc is not invoking an intel version of the C compiler.  "-fp-model" is an arg that intel compilers recognize. 
 
E

eaton

CSEG and Liaisons
The problem appears to be that mpicc is not invoking an intel version of the C compiler.  "-fp-model" is an arg that intel compilers recognize. 
 
A

andrew_kren@colorado_edu

Member
Here is my env_mach_specific file below. It looks to load the intel compiler. And, I also see this in the module avail on the machine. #! /bin/csh -f

#-------------------------------------------------------------------------------
# pleiades machine specific settings
#-------------------------------------------------------------------------------

#-------------------------------------------------------------------------------
# build-time environment variables
#-------------------------------------------------------------------------------

if (-e /usr/share/modules/init/csh) then
  source /usr/share/modules/init/csh
  module purge
  module load comp-intel/2013.5.192
  module load mpi-sgi/mpt.2.08r7
  module load netcdf/4.0-i10.1
  module load nas
endif

#-------------------------------------------------------------------------------
# run-time environment variables
#-------------------------------------------------------------------------------
#setenv P4_GLOBMEMSIZE 500000000

setenv MPI_GROUP_MAX 1024
setenv MPI_TYPE_MAX 100000

setenv KMP_AFFINITY noverbose,disabled
setenv KMP_SCHEDULE static,balanced
setenv KMP_LIBRARY throughput
setenv KMP_BLOCKTIME infinite
setenv OMP_DYNAMIC FALSE

setenv MPI_TYPE_DEPTH 10
setenv PNETCDF_PATH /home1/fvitt/parallel-netcdf-1.3.1
 
A

andrew_kren@colorado_edu

Member
Here is my env_mach_specific file below. It looks to load the intel compiler. And, I also see this in the module avail on the machine. #! /bin/csh -f

#-------------------------------------------------------------------------------
# pleiades machine specific settings
#-------------------------------------------------------------------------------

#-------------------------------------------------------------------------------
# build-time environment variables
#-------------------------------------------------------------------------------

if (-e /usr/share/modules/init/csh) then
  source /usr/share/modules/init/csh
  module purge
  module load comp-intel/2013.5.192
  module load mpi-sgi/mpt.2.08r7
  module load netcdf/4.0-i10.1
  module load nas
endif

#-------------------------------------------------------------------------------
# run-time environment variables
#-------------------------------------------------------------------------------
#setenv P4_GLOBMEMSIZE 500000000

setenv MPI_GROUP_MAX 1024
setenv MPI_TYPE_MAX 100000

setenv KMP_AFFINITY noverbose,disabled
setenv KMP_SCHEDULE static,balanced
setenv KMP_LIBRARY throughput
setenv KMP_BLOCKTIME infinite
setenv OMP_DYNAMIC FALSE

setenv MPI_TYPE_DEPTH 10
setenv PNETCDF_PATH /home1/fvitt/parallel-netcdf-1.3.1
 
A

andrew_kren@colorado_edu

Member
Here is my env_mach_specific file below. It looks to load the intel compiler. And, I also see this in the module avail on the machine. #! /bin/csh -f

#-------------------------------------------------------------------------------
# pleiades machine specific settings
#-------------------------------------------------------------------------------

#-------------------------------------------------------------------------------
# build-time environment variables
#-------------------------------------------------------------------------------

if (-e /usr/share/modules/init/csh) then
  source /usr/share/modules/init/csh
  module purge
  module load comp-intel/2013.5.192
  module load mpi-sgi/mpt.2.08r7
  module load netcdf/4.0-i10.1
  module load nas
endif

#-------------------------------------------------------------------------------
# run-time environment variables
#-------------------------------------------------------------------------------
#setenv P4_GLOBMEMSIZE 500000000

setenv MPI_GROUP_MAX 1024
setenv MPI_TYPE_MAX 100000

setenv KMP_AFFINITY noverbose,disabled
setenv KMP_SCHEDULE static,balanced
setenv KMP_LIBRARY throughput
setenv KMP_BLOCKTIME infinite
setenv OMP_DYNAMIC FALSE

setenv MPI_TYPE_DEPTH 10
setenv PNETCDF_PATH /home1/fvitt/parallel-netcdf-1.3.1
 
S

santos

Member
I don't know why (or exactly when this changed), but it seems that the Intel modules are not setting MPICC_CC or MPIF90_F90, which are what the MPI compiler wrappers are trying to use to autodetect the compiler.I would try adding this to env_mach_specific:setenv MPICC_CC iccsetenv MPIF90_F90 ifort(I can try a run, but it's been a while since I've used pleaides.)
 
S

santos

Member
I don't know why (or exactly when this changed), but it seems that the Intel modules are not setting MPICC_CC or MPIF90_F90, which are what the MPI compiler wrappers are trying to use to autodetect the compiler.I would try adding this to env_mach_specific:setenv MPICC_CC iccsetenv MPIF90_F90 ifort(I can try a run, but it's been a while since I've used pleaides.)
 
S

santos

Member
I don't know why (or exactly when this changed), but it seems that the Intel modules are not setting MPICC_CC or MPIF90_F90, which are what the MPI compiler wrappers are trying to use to autodetect the compiler.I would try adding this to env_mach_specific:setenv MPICC_CC iccsetenv MPIF90_F90 ifort(I can try a run, but it's been a while since I've used pleaides.)
 
A

andrew_kren@colorado_edu

Member
Sean,I did what you said and it got past that section of the build. But when it got to pio.bldlog.140210-145411, it gave me this error on the buildlib.pio:checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
configure: WARNING: NETCDF_PATH not found in environment,                            defaulting to /usr/local/netcdf
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... yes
checking for library containing nc_inq_libvers... -lnetcdf
checking for library containing NF_INQ_LIBVERS... none required
checking for f90 netCDF interface... yes
checking for netcdf 4 API...
checking for nf90_inq_grps... yes
configure: error: netcdf.mod not found in NETCDF_PATH/include                             check the environment variable NETCDF_PATH
gmake: *** [/nobackup/akren/waccm_1850/bld/pio/Makefile.conf] Error 1
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:25: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.

 
A

andrew_kren@colorado_edu

Member
Sean,I did what you said and it got past that section of the build. But when it got to pio.bldlog.140210-145411, it gave me this error on the buildlib.pio:checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
configure: WARNING: NETCDF_PATH not found in environment,                            defaulting to /usr/local/netcdf
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... yes
checking for library containing nc_inq_libvers... -lnetcdf
checking for library containing NF_INQ_LIBVERS... none required
checking for f90 netCDF interface... yes
checking for netcdf 4 API...
checking for nf90_inq_grps... yes
configure: error: netcdf.mod not found in NETCDF_PATH/include                             check the environment variable NETCDF_PATH
gmake: *** [/nobackup/akren/waccm_1850/bld/pio/Makefile.conf] Error 1
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:25: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.

 
A

andrew_kren@colorado_edu

Member
Sean,I did what you said and it got past that section of the build. But when it got to pio.bldlog.140210-145411, it gave me this error on the buildlib.pio:checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
configure: WARNING: NETCDF_PATH not found in environment,                            defaulting to /usr/local/netcdf
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... yes
checking for library containing nc_inq_libvers... -lnetcdf
checking for library containing NF_INQ_LIBVERS... none required
checking for f90 netCDF interface... yes
checking for netcdf 4 API...
checking for nf90_inq_grps... yes
configure: error: netcdf.mod not found in NETCDF_PATH/include                             check the environment variable NETCDF_PATH
gmake: *** [/nobackup/akren/waccm_1850/bld/pio/Makefile.conf] Error 1
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:25: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.

 
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