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Provide support for Livermore Computing (LC) #1367

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merged 10 commits into from
May 23, 2017
Merged

Provide support for Livermore Computing (LC) #1367

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2f96813
modify files for support for LC machines
Mar 29, 2017
0cda7f4
updates to allow ACME to run on LC
Apr 4, 2017
475cfa6
Code clean ups
Apr 4, 2017
acb0c14
modifications for PR review
Apr 18, 2017
2a22d16
remove white space
Apr 19, 2017
0ad988a
add support for mpi-serial builds (for SCM)
Apr 19, 2017
31b68bd
change soft to generic for PR approval
May 4, 2017
5f3d09a
update comments for generic module load
May 10, 2017
d3dde85
remove whitespace
May 10, 2017
84d585f
revert unintended change to slurm
May 15, 2017
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27 changes: 25 additions & 2 deletions cime/config/acme/machines/config_batch.xml
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Expand Up @@ -130,11 +130,34 @@
<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>
<batch_submit>sbatch</batch_submit>
<batch_directive>#SBATCH</batch_directive>
<batch_submit>msub</batch_submit>
<batch_directive>#MSUB</batch_directive>
<jobid_pattern>(\d+)$</jobid_pattern>
<depend_string> --dependency=afterok:jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
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44 changes: 44 additions & 0 deletions cime/config/acme/machines/config_compilers.xml
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Expand Up @@ -749,6 +749,50 @@ 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>
Expand Down
112 changes: 89 additions & 23 deletions cime/config/acme/machines/config_machines.xml
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Expand Up @@ -1076,44 +1076,110 @@
</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">
Expand Down
24 changes: 7 additions & 17 deletions cime/scripts/lib/CIME/XML/env_mach_specific.py
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Expand Up @@ -87,9 +87,9 @@ 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 @@ -112,7 +112,7 @@ 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 @@ -221,18 +221,11 @@ 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}
# Load dotkit modules, similar to soft module load
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@jgfouca jgfouca May 9, 2017 •
edited
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This comment is no longer valid. We should explain that this is for environment management systems that do not have a python interface and therefore we can only replicate what they do by running shell commands and looking at the changes in the environment.


cmd = "source %s" % sh_init_cmd

Expand Down Expand Up @@ -279,10 +272,7 @@ 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):
"""
Expand Down
2 changes: 1 addition & 1 deletion cime/src/drivers/mct/cime_config/config_component.xml
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Expand Up @@ -544,7 +544,7 @@
<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>
Expand Down
2 changes: 2 additions & 0 deletions cime/src/externals/pio1/pio/pionfput_mod.F90.in
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Expand Up @@ -697,9 +697,11 @@ 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
Expand Down