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<machine MACH="singularity"> <DESC>Singularity container</DESC> <NODENAME_REGEX>localhost<REGEX>singularity</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>gnu</COMPILERS> <MPILIBS>mpich</MPILIBS> <CIME_OUTPUT_ROOT>$ENV{HOME}/projects/e3sm/scratch</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>$ENV{HOME}/projects/e3sm/cesm-inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>$ENV{HOME}/projects/e3sm/ptclm-data</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$ENV{HOME}/projects/e3sm/scratch/archive/$CASE</DOUT_S_ROOT> <BASELINE_ROOT>$ENV{HOME}/projects/e3sm/baselines/$COMPILER</BASELINE_ROOT> <CCSM_CPRNC>$CCSMROOT/tools/cprnc/build/cprnc</CCSM_CPRNC> <GMAKE>make</GMAKE> <GMAKE_J>16</GMAKE_J> <TESTS>e3sm_developer</TESTS> <BATCH_SYSTEM>none</BATCH_SYSTEM> <SUPPORTED_BY>lukasz at uchicago dot edu</SUPPORTED_BY> <MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>16</MAX_MPITASKS_PER_NODE> <mpirun mpilib="default"> <executable>mpirun</executable> <arguments> <arg name="num_tasks"> -launcher fork -hosts localhost -np {{ total_tasks }}</arg> </arguments> </mpirun> <module_system type="none"/> <RUNDIR>$ENV{HOME}/projects/e3sm/scratch/$CASE/run</RUNDIR> <EXEROOT>$ENV{HOME}/projects/e3sm/scratch/$CASE/bld</EXEROOT> <environment_variables> <env name="E3SM_SRCROOT">$SRCROOT</env> </environment_variables> <environment_variables mpilib="mpi-serial"> <env name="NETCDF_PATH">/usr/local/packages/netcdf-serial</env> <env name="PATH">/usr/local/packages/cmake/bin:/usr/local/packages/hdf5-serial/bin:/usr/local/packages/netcdf-serial/bin:$ENV{PATH}</env> <env name="LD_LIBRARY_PATH">/usr/local/packages/szip/lib:/usr/local/packages/hdf5-serial/lib:/usr/local/packages/netcdf-serial/lib</env> </environment_variables> <environment_variables mpilib="!mpi-serial"> <env name="NETCDF_PATH">/usr/local/packages/netcdf-parallel</env> <env name="PNETCDF_PATH">/usr/local/packages/pnetcdf</env> <env name="HDF5_PATH">/usr/local/packages/hdf5-parallel</env> <env name="PATH">/usr/local/packages/cmake/bin:/usr/local/packages/mpich/bin:/usr/local/packages/hdf5-parallel/bin:/usr/local/packages/netcdf-parallel/bin:/usr/local/packages/pnetcdf/bin:$ENV{PATH}</env> <env name="LD_LIBRARY_PATH">/usr/local/packages/mpich/lib:/usr/local/packages/szip/lib:/usr/local/packages/hdf5-parallel/lib:/usr/local/packages/netcdf-parallel/lib:/usr/local/packages/pnetcdf/lib</env> </environment_variables> </machine> |
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<compiler COMPILER="gnu" MACH="singularity"> <HDF5_PATH> $ENV{HDF5_PATH}</HDF5_PATH> <NETCDF_PATH> $(NETCDF_PATH)</NETCDF_PATH> <PNETCDF_PATH> $(PNETCDF_PATH)</PNETCDF_PATH> <ADD_SLIBS> $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -lblas -llapack</ADD_SLIBS> </compiler> |
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singularity shell --hostname localhost singularity e3sm.sif
Singularity> cd <E3SM_SRC_DIR>/cime/scripts
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[lukasz@blueslogin4 ~]$ srun --pty -p acme-small -t 01:00:00 /bin/bash
[lukasz@b566]$ singularity shell --hostname localhost singularity e3sm.sif
Singularity> cd E3SM/cime/scripts/
Singularity> ./create_newcase --case singularity.A_WCYCL1850.ne4_oQU240.baseline --compset A_WCYCL1850 --res ne4_oQU240
Singularity> cd singularity.A_WCYCL1850.ne4_oQU240.baseline/
Singularity> ./case.setup
Singularity> ./case.build
Singularity> ./case.submit