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Merge branch 'bogensch/cime/ACMEv1_LC_Machines' into nexti (PR #1367)
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Provide support for Livermore Computing Machines

Provide support for Livermore Computing (LC) clusters.  Specifically for the machines
Cab and Syrah.  Added a generic module load for environment management system that does
not have python interface (such as LC).

[BFB]
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Peter Bogenschutz committed May 22, 2017
2 parents d96bce9 + 84d585f commit fb388e0
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23 changes: 23 additions & 0 deletions cime/config/acme/machines/config_batch.xml
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Expand Up @@ -130,6 +130,29 @@
<directive default="/bin/bash" > -S {{ shell }}</directive>
</directives>
</batch_system>

<!-- for cab llnl -->
<batch_system type="lc_slurm">
<batch_submit>msub</batch_submit>
<batch_directive>#MSUB</batch_directive>
<jobid_pattern>(\d+)$</jobid_pattern>
<depend_string> -l depend=jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<directives>
<directive>-V</directive>
<directive>-q {{ job_queue }}</directive>
<directive>-N {{ job_id }}</directive>
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
<directive>-l walltime={{ job_wallclock_time }}</directive>
<directive>-o {{ output_error_path }}.out</directive>
<directive>-e {{ output_error_path }}.err</directive>
<directive>-m be</directive>
<directive> -A {{ project }} </directive>
</directives>
<queues>
<queue walltimemax="01:00:00" jobmin="1" jobmax="4320" default="true">pbatch</queue>
</queues>
</batch_system>

<batch_system type="slurm" >
<batch_query>squeue</batch_query>
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44 changes: 44 additions & 0 deletions cime/config/acme/machines/config_compilers.xml
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Expand Up @@ -783,6 +783,50 @@ for mct, etc.
<ADD_CPPDEFS MODEL="pop"> -D_USE_FLOW_CONTROL </ADD_CPPDEFS>
</compiler>

<compiler COMPILER="pgi" MACH="cab">
<NETCDF_PATH>/usr/local/tools/netcdf-pgi-4.1.3</NETCDF_PATH>
<MPI_PATH>/usr/local/tools/mvapich2-pgi-1.7/</MPI_PATH>
<MPI_LIB_NAME> mpich</MPI_LIB_NAME>
<ADD_CPPDEFS> -DNO_SHR_VMATH -DCNL </ADD_CPPDEFS>
<ADD_SLIBS>$(shell /usr/local/tools/netcdf-pgi-4.1.3/bin/nc-config --flibs)</ADD_SLIBS>
<ADD_LDFLAGS> -Wl,-rpath /usr/local/tools/netcdf-pgi-4.1.3/lib -llapack -lblas</ADD_LDFLAGS>
</compiler>

<compiler COMPILER="intel" MACH="cab">
<ADD_CFLAGS DEBUG="FALSE"> -O2 </ADD_CFLAGS>
<ADD_FFLAGS DEBUG="FALSE"> -O2 </ADD_FFLAGS>
<NETCDF_PATH>/usr/local/tools/netcdf-intel-4.1.3</NETCDF_PATH>
<CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
<MPI_PATH>/usr/local/tools/mvapich2-intel-2.1/</MPI_PATH>
<MPI_LIB_NAME> mpich</MPI_LIB_NAME>
<ADD_CPPDEFS> -DNO_SHR_VMATH -DCNL </ADD_CPPDEFS>
<ADD_FFLAGS DEBUG="TRUE"> -g -traceback -O0 -fpe0 -check all -check noarg_temp_created -ftrapuv </ADD_FFLAGS>
<ADD_SLIBS>$(shell /usr/local/tools/netcdf-intel-4.1.3/bin/nc-config --flibs)</ADD_SLIBS>
<ADD_LDFLAGS> -llapack -lblas</ADD_LDFLAGS>
</compiler>

<compiler COMPILER="pgi" MACH="syrah">
<NETCDF_PATH>/usr/local/tools/netcdf-pgi-4.1.3</NETCDF_PATH>
<MPI_PATH>/usr/local/tools/mvapich2-pgi-1.7/</MPI_PATH>
<MPI_LIB_NAME> mpich</MPI_LIB_NAME>
<ADD_CPPDEFS> -DNO_SHR_VMATH -DCNL </ADD_CPPDEFS>
<ADD_SLIBS>$(shell /usr/local/tools/netcdf-pgi-4.1.3/bin/nc-config --flibs)</ADD_SLIBS>
<ADD_LDFLAGS> -Wl,-rpath /usr/local/tools/netcdf-pgi-4.1.3/lib -llapack -lblas</ADD_LDFLAGS>
</compiler>

<compiler COMPILER="intel" MACH="syrah">
<ADD_CFLAGS DEBUG="FALSE"> -O2 </ADD_CFLAGS>
<ADD_FFLAGS DEBUG="FALSE"> -O2 </ADD_FFLAGS>
<NETCDF_PATH>/usr/local/tools/netcdf-intel-4.1.3</NETCDF_PATH>
<CONFIG_ARGS> --host=Linux </CONFIG_ARGS>
<MPI_PATH>/usr/local/tools/mvapich2-intel-2.1/</MPI_PATH>
<MPI_LIB_NAME> mpich</MPI_LIB_NAME>
<ADD_CPPDEFS> -DNO_SHR_VMATH -DCNL </ADD_CPPDEFS>
<ADD_FFLAGS DEBUG="TRUE"> -g -traceback -O0 -fpe0 -check all -check noarg_temp_created -ftrapuv </ADD_FFLAGS>
<ADD_SLIBS>$(shell /usr/local/tools/netcdf-intel-4.1.3/bin/nc-config --flibs)</ADD_SLIBS>
<ADD_LDFLAGS> -llapack -lblas</ADD_LDFLAGS>
</compiler>

<compiler MACH="oic2" COMPILER="gnu">
<NETCDF_PATH>/projects/cesm/devtools/netcdf-4.1.3-gcc4.8.1-mpich3.0.4/</NETCDF_PATH>
<ADD_SLIBS>-L/user/lib64 -llapack -lblas -lnetcdff </ADD_SLIBS>
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112 changes: 89 additions & 23 deletions cime/config/acme/machines/config_machines.xml
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Expand Up @@ -1085,44 +1085,110 @@
</environment_variables>
</machine>

<machine MACH="sierra">
<DESC>LLNL Linux Cluster, Linux (pgi), 12 pes/node, batch system is Moab</DESC>
<machine MACH="cab">
<DESC>LLNL Linux Cluster, Linux (pgi), 16 pes/node, batch system is Slurm</DESC>
<COMPILERS>intel, pgi</COMPILERS>
<MPILIBS>mpich,mpi-serial</MPILIBS>
<RUNDIR>/p/lscratche/$CCSMUSER/ACME/$CASE/run</RUNDIR>
<EXEROOT>/p/lscratche/$CCSMUSER/$CASE/bld</EXEROOT>
<CIME_OUTPUT_ROOT>/p/lscratche/$USER</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/p/lscratchd/ma21/ccsm3data/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/p/lscratchd/ma21/ccsm3data/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DIN_LOC_ROOT>/usr/gdata/climdat/ccsm3data/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/usr/gdata/climdat/ccsm3data/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/p/lscratche/$CCSMUSER/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_HTAR>FALSE</DOUT_L_HTAR>
<DOUT_L_MSROOT>UNSET</DOUT_L_MSROOT>
<BASELINE_ROOT>/p/lscratchd/$CCSMUSER/ccsm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/p/lscratchd/ma21/ccsm3data/tools/cprnc/cprnc</CCSM_CPRNC>
<OS>LINUX</OS>
<BATCHQUERY>mshow</BATCHQUERY>
<BATCHSUBMIT>msub</BATCHSUBMIT>
<BATCHREDIRECT></BATCHREDIRECT>
<SUPPORTED_BY>wlin -at- bnl.gov</SUPPORTED_BY>
<SUPPORTED_BY>bogenschutz1 -at- llnl.gov</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
<MAX_TASKS_PER_NODE>12</MAX_TASKS_PER_NODE>
<batch_system type="sierra_slurm" version="x.y">
<queues>
<queue jobmin="1" jobmax="9999" default="true">pbatch</queue>
</queues>
<walltimes>
<walltime default="true">walltime=01:00:00</walltime>
</walltimes>
</batch_system>
<mpirun mpilib="mpich">
<executable>srun</executable>
<arguments>
<arg name="num_nodes"> -N {{ num_nodes }}</arg>
</arguments>
<MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE>
<PES_PER_NODE>16</PES_PER_NODE>
<BATCH_SYSTEM>lc_slurm</BATCH_SYSTEM>
<SAVE_TIMING_DIR>/usr/gdata/climdat/timing_performance</SAVE_TIMING_DIR>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<mpirun mpilib="default">
<executable>srun</executable>
</mpirun>
<module_system type="generic">
<cmd_path lang="sh">use</cmd_path>
<cmd_path lang="csh">use</cmd_path>
<init_path lang="csh">/usr/global/tools/dotkit/init.csh</init_path>
<init_path lang="sh">/usr/global/tools/dotkit/init.sh</init_path>
<modules compiler="pgi">
<command name="-q">pgi-14.3</command>
<command name="-q">mvapich2-pgi-1.7</command>
<command name="-q">netcdf-pgi-4.1.3</command>
</modules>
<modules compiler="intel">
<command name="-q">ic-14.0.211</command>
<command name="-q">mvapich2-intel-2.1</command>
<command name="-q">netcdf-intel-4.1.3</command>
</modules>
</module_system>
<environment_variables compiler="pgi">
<env name="NETCDF">/usr/local/tools/netcdf-pgi-4.1.3/</env>
<env name="PNETCDF_PATH" mpilib="!mpi-serial">/usr/local/tools/parallel-netcdf-pgi-1.6.1/</env>
</environment_variables>
<environment_variables compiler="intel">
<env name="NETCDF">/usr/local/tools/netcdf-intel-4.1.3/</env>
<env name="PNETCDF_PATH" mpilib="!mpi-serial">/usr/local/tools/parallel-netcdf-intel-1.6.1/</env>
</environment_variables>
</machine>

<machine MACH="syrah">
<DESC>LLNL Linux Cluster, Linux (pgi), 16 pes/node, batch system is Slurm</DESC>
<COMPILERS>intel, pgi</COMPILERS>
<MPILIBS>mpich,mpi-serial</MPILIBS>
<RUNDIR>/p/lscratche/$CCSMUSER/ACME/$CASE/run</RUNDIR>
<EXEROOT>/p/lscratche/$CCSMUSER/$CASE/bld</EXEROOT>
<CIME_OUTPUT_ROOT>/p/lscratche/$USER</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/usr/gdata/climdat/ccsm3data/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/usr/gdata/climdat/ccsm3data/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/p/lscratche/$CCSMUSER/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_HTAR>FALSE</DOUT_L_HTAR>
<DOUT_L_MSROOT>UNSET</DOUT_L_MSROOT>
<BASELINE_ROOT>/p/lscratchd/$CCSMUSER/ccsm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/p/lscratchd/ma21/ccsm3data/tools/cprnc/cprnc</CCSM_CPRNC>
<OS>LINUX</OS>
<SUPPORTED_BY>bogenschutz1 -at- llnl.gov</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
<MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE>
<PES_PER_NODE>16</PES_PER_NODE>
<BATCH_SYSTEM>lc_slurm</BATCH_SYSTEM>
<SAVE_TIMING_DIR>/usr/gdata/climdat/timing_performance</SAVE_TIMING_DIR>
<mpirun mpilib="mpi-serial">
<executable></executable>
<executable></executable>
</mpirun>
<mpirun mpilib="default">
<executable>srun</executable>
</mpirun>
<module_system type="generic">
<cmd_path lang="sh">use</cmd_path>
<cmd_path lang="csh">use</cmd_path>
<init_path lang="csh">/usr/global/tools/dotkit/init.csh</init_path>
<init_path lang="sh">/usr/global/tools/dotkit/init.sh</init_path>
<modules compiler="pgi">
<command name="-q">pgi-14.3</command>
<command name="-q">mvapich2-pgi-1.7</command>
<command name="-q">netcdf-pgi-4.1.3</command>
</modules>
<modules compiler="intel">
<command name="-q">ic-14.0.211</command>
<command name="-q">mvapich2-intel-2.1</command>
<command name="-q">netcdf-intel-4.1.3</command>
</modules>
</module_system>
<environment_variables compiler="pgi">
<env name="NETCDF">/usr/local/tools/netcdf-pgi-4.1.3/</env>
<env name="PNETCDF_PATH" mpilib="!mpi-serial">/usr/local/tools/parallel-netcdf-pgi-1.6.1/</env>
</environment_variables>
<environment_variables compiler="intel">
<env name="NETCDF">/usr/local/tools/netcdf-intel-4.1.3/</env>
<env name="PNETCDF_PATH" mpilib="!mpi-serial">/usr/local/tools/parallel-netcdf-intel-1.6.1/</env>
</environment_variables>
</machine>

<machine MACH="mira">
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27 changes: 10 additions & 17 deletions cime/scripts/lib/CIME/XML/env_mach_specific.py
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Expand Up @@ -89,9 +89,9 @@ def load_modules(self, modules_to_load):
if (module_system == "module"):
self._load_module_modules(modules_to_load)
elif (module_system == "soft"):
self._load_soft_modules(modules_to_load)
elif (module_system == "dotkit"):
self._load_dotkit_modules(modules_to_load)
self._load_modules_generic(modules_to_load)
elif (module_system == "generic"):
self._load_modules_generic(modules_to_load)
elif (module_system == "none"):
self._load_none_modules(modules_to_load)
else:
Expand All @@ -114,7 +114,7 @@ def list_modules(self):
elif (module_system == "soft"):
# Does soft really not provide this capability?
return ""
elif (module_system == "dotkit"):
elif (module_system == "generic"):
return run_cmd_no_fail("%suse -lv" % source_cmd)
elif (module_system == "none"):
return ""
Expand Down Expand Up @@ -227,18 +227,14 @@ def _load_module_modules(self, modules_to_load):
"module command %s failed with message:\n%s"%(cmd,errout))
exec(py_module_code)

def _load_soft_modules(self, modules_to_load):
def _load_modules_generic(self, modules_to_load):
sh_init_cmd = self.get_module_system_init_path("sh")
sh_mod_cmd = self.get_module_system_cmd_path("sh")

# Some machines can set the environment
# variables using a script (such as /etc/profile.d/00softenv.sh
# on mira or /etc/profile.d/a_softenv.sh on blues)
# which load the new environment variables using softenv-load.

# Other machines need to run soft-dec.sh and evaluate the output,
# which may or may not have unresolved variables such as
# PATH=/soft/com/packages/intel/16/initial/bin:${PATH}
# Purpose is for environment management system that does not have
# a python interface and therefore can only determine what they
# do by running shell command and looking at the changes
# in the environment.

cmd = "source %s" % sh_init_cmd

Expand Down Expand Up @@ -285,10 +281,7 @@ def _load_soft_modules(self, modules_to_load):
if key in os.environ and key not in newenv:
del(os.environ[key])
else:
os.environ[key] = newenv[key]

def _load_dotkit_modules(self, _):
expect(False, "Not yet implemented")
os.environ[key] = newenv[key]

def _load_none_modules(self, modules_to_load):
"""
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2 changes: 1 addition & 1 deletion cime/src/drivers/mct/cime_config/config_component.xml
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Expand Up @@ -560,7 +560,7 @@
<entry id="BATCH_SYSTEM">
<type>char</type>
<default_value>none</default_value>
<valid_values>moab,pbs,lsf,slurm,cobalt,cobalt_theta,none</valid_values>
<valid_values>lc_slurm,moab,pbs,lsf,slurm,cobalt,cobalt_theta,none</valid_values>
<group>config_batch</group>
<file>env_batch.xml</file>
<desc>The batch system type to use for this machine.</desc>
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2 changes: 2 additions & 0 deletions cime/src/externals/pio1/pio/pionfput_mod.F90.in
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Expand Up @@ -696,9 +696,11 @@ contains
#endif
#endif
#ifdef _NETCDF
#ifdef _NETCDF4
case(pio_iotype_netcdf4p)
ierr=nf90_var_par_access(File%fh, varid, NF90_COLLECTIVE)
ierr = nf90_put_var(File%fh, varid, ival, start=int(pstart), count=int(pcount))
#endif
case(pio_iotype_netcdf, pio_iotype_netcdf4c)
! Only io proc 0 will do writing
if (Ios%io_rank == 0) then
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