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Merge branch 'jgfouca/update_netcdf_for_sandia_machines' into master …
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…(PR #1640)

Update netcdf for sandia machines.

This is necessary to support the cdf5 file type which is needed
for internal CIME testing.

Machines that do not use PIO in pnetcdf mode do not need to need
to worry about updating netcdf. If they do, netcdf 4.4 is needed.

[BFB]

* jgfouca/update_netcdf_for_sandia_machines:
  Point to new cprnc build
  Update netcdf for sandia machines.
  • Loading branch information
@jgfouca
jgfouca committed Jul 14, 2017
2 parents ee805fb + e6dccd6 commit 3605215
Showing 1 changed file with 27 additions and 104 deletions.
131 changes: 27 additions & 104 deletions config/acme/machines/config_machines.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -522,7 +522,7 @@
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_MSROOT>csm/$CASE</DOUT_L_MSROOT>
<BASELINE_ROOT>/sems-data-store/ACME/baselines</BASELINE_ROOT>
<CCSM_CPRNC>/sems-data-store/ACME/cprnc/build/cprnc</CCSM_CPRNC>
<CCSM_CPRNC>/sems-data-store/ACME/cprnc/build.new/cprnc</CCSM_CPRNC>
<SUPPORTED_BY>jgfouca at sandia dot gov</SUPPORTED_BY>
<!-- <GMAKE>make</GMAKE> <- this doesn't actually work! -->
<GMAKE_J>32</GMAKE_J>
Expand Down Expand Up @@ -553,7 +553,7 @@
<command name="load" compiler="intel">sems-intel/16.0.3</command>
<command name="load">sems-openmpi/1.8.7</command>
<command name="load">sems-cmake/2.8.12</command>
<command name="load">sems-netcdf/4.3.2/parallel</command>
<command name="load">sems-netcdf/4.4.1/exo_parallel</command>
</modules>
</module_system>
<environment_variables>
Expand Down Expand Up @@ -615,7 +615,7 @@
<modules>
<command name="load">sems-openmpi/1.8.7</command>
<command name="load">sems-cmake/2.8.12</command>
<command name="load">sems-netcdf/4.3.2/parallel</command>
<command name="load">sems-netcdf/4.4.1/exo_parallel</command>
</modules>
</module_system>
<environment_variables>
Expand Down Expand Up @@ -703,7 +703,7 @@
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT> <!-- complete path to a short term archiving directory -->
<DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT> <!-- complete path to a long term archiving directory -->
<BASELINE_ROOT>/projects/ccsm/ccsm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/projects/ccsm/cprnc/build/cprnc_wrap</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<CCSM_CPRNC>/projects/ccsm/cprnc/build.new/cprnc_wrap</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<BATCH_SYSTEM>slurm</BATCH_SYSTEM>
<SUPPORTED_BY>jgfouca at sandia dot gov</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
Expand Down Expand Up @@ -743,6 +743,7 @@
<command name="load">intel/intel-15.0.3.187</command>
<command name="load" mpilib="!mpi-serial">openmpi-intel/1.6</command>
<command name="load">libraries/intel-mkl-15.0.2.164</command>
<command name="load">sems-netcdf/4.4.1/exo_parallel</command>
<!-- We want to use these modules but the segfault comes back if we do, maybe wait for new PIO? -->
<!-- <command name="load" mpilib="!mpi-serial">sems-hdf5/1.8.12/parallel</command> -->
<!-- <command name="load" mpilib="!mpi-serial">sems-netcdf/4.3.2/parallel</command> -->
Expand All @@ -752,16 +753,16 @@
</module_system>
<environment_variables>
<!-- <env name="PATH">/projects/ccsm/cmake-2.8.10.2-Linux-i386/bin:$PATH</env> -->
<env name="PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/bin:$ENV{PATH}</env>
<env name="LD_LIBRARY_PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib:$ENV{LD_LIBRARY_PATH}</env>
<env name="NETCDF_INCLUDES">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/include</env>
<env name="NETCDF_LIBS">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib</env>
<env name="NETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<env name="PNETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<!-- <env name="NETCDFROOT">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="PNETCDFROOT" mpilib="!mpi-serial">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="NETCDF_INCLUDES">$ENV{SEMS_NETCDF_ROOT}/include</env> -->
<!-- <env name="NETCDF_LIBS">$ENV{SEMS_NETCDF_ROOT}/lib</env> -->
<!-- <env name="PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/bin:$ENV{PATH}</env> -->
<!-- <env name="LD_LIBRARY_PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib:$ENV{LD_LIBRARY_PATH}</env> -->
<!-- <env name="NETCDF_INCLUDES">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/include</env> -->
<!-- <env name="NETCDF_LIBS">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib</env> -->
<!-- <env name="NETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env> -->
<!-- <env name="PNETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env> -->
<env name="NETCDFROOT">$ENV{SEMS_NETCDF_ROOT}</env>
<env name="PNETCDFROOT" mpilib="!mpi-serial">$ENV{SEMS_NETCDF_ROOT}</env>
<env name="NETCDF_INCLUDES">$ENV{SEMS_NETCDF_ROOT}/include</env>
<env name="NETCDF_LIBS">$ENV{SEMS_NETCDF_ROOT}/lib</env>
<env name="OMP_STACKSIZE">64M</env>
</environment_variables>
</machine>
Expand All @@ -782,7 +783,7 @@
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT> <!-- complete path to a short term archiving directory -->
<DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT> <!-- complete path to a long term archiving directory -->
<BASELINE_ROOT>/projects/ccsm/ccsm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/projects/ccsm/cprnc/build/cprnc_wrap</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<CCSM_CPRNC>/projects/ccsm/cprnc/build.new/cprnc_wrap</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<BATCH_SYSTEM>slurm</BATCH_SYSTEM>
<SUPPORTED_BY>jgfouca at sandia dot gov</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
Expand Down Expand Up @@ -822,6 +823,7 @@
<command name="load">intel/intel-15.0.3.187</command>
<command name="load" mpilib="!mpi-serial">openmpi-intel/1.6</command>
<command name="load">libraries/intel-mkl-15.0.2.164</command>
<command name="load">sems-netcdf/4.4.1/exo_parallel</command>
<!-- We want to use these modules but the segfault comes back if we do, maybe wait for new PIO? -->
<!-- <command name="load" mpilib="!mpi-serial">sems-hdf5/1.8.12/parallel</command> -->
<!-- <command name="load" mpilib="!mpi-serial">sems-netcdf/4.3.2/parallel</command> -->
Expand All @@ -831,95 +833,16 @@
</module_system>
<environment_variables>
<!-- <env name="PATH">/projects/ccsm/cmake-2.8.10.2-Linux-i386/bin:$PATH</env> -->
<env name="PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/bin:$ENV{PATH}</env>
<env name="LD_LIBRARY_PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib:$ENV{LD_LIBRARY_PATH}</env>
<env name="NETCDF_INCLUDES">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/include</env>
<env name="NETCDF_LIBS">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib</env>
<env name="NETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<env name="PNETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<!-- <env name="NETCDFROOT">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="PNETCDFROOT" mpilib="!mpi-serial">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="NETCDF_INCLUDES">$ENV{SEMS_NETCDF_ROOT}/include</env> -->
<!-- <env name="NETCDF_LIBS">$ENV{SEMS_NETCDF_ROOT}/lib</env> -->
<env name="OMP_STACKSIZE">64M</env>
</environment_variables>
</machine>

<machine MACH="redsky">
<DESC>SNL clust</DESC>
<NODENAME_REGEX>redsky-login</NODENAME_REGEX>
<PROXY>wwwproxy.sandia.gov:80</PROXY>
<TESTS>acme_integration</TESTS>
<COMPILERS>intel</COMPILERS>
<MPILIBS>openmpi,mpi-serial</MPILIBS>
<OS>LINUX</OS>
<CIME_OUTPUT_ROOT>/gscratch/$USER/acme_scratch</CIME_OUTPUT_ROOT>
<RUNDIR>$CIME_OUTPUT_ROOT/$CASE/run</RUNDIR>
<EXEROOT>$CIME_OUTPUT_ROOT/$CASE/bld</EXEROOT>
<DIN_LOC_ROOT>/projects/ccsm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/projects/ccsm/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT> <!-- complete path to a short term archiving directory -->
<DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT> <!-- complete path to a long term archiving directory -->
<BASELINE_ROOT>/projects/ccsm/ccsm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>/projects/ccsm/cprnc/build/cprnc_wrap</CCSM_CPRNC> <!-- path to the cprnc tool used to compare netcdf history files in testing -->
<BATCH_SYSTEM>slurm</BATCH_SYSTEM>
<SUPPORTED_BY>jgfouca at sandia dot gov</SUPPORTED_BY>
<GMAKE_J>8</GMAKE_J>
<MAX_TASKS_PER_NODE>8</MAX_TASKS_PER_NODE>
<PES_PER_NODE>8</PES_PER_NODE>
<PIO_BUFFER_SIZE_LIMIT>1</PIO_BUFFER_SIZE_LIMIT>
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>
<PROJECT>fy150001</PROJECT>

<mpirun mpilib="default">
<executable>mpiexec</executable>
<arguments>
<arg name="bind"> --bind-to-core</arg>
<arg name="num_tasks"> --n $TOTALPES</arg>
<arg name="tasks_per_node"> --npernode $PES_PER_NODE</arg>
</arguments>
</mpirun>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<module_system type="module">
<init_path lang="python">/usr/share/Modules/init/python.py</init_path>
<init_path lang="perl">/usr/share/Modules/init/perl.pm</init_path>
<init_path lang="sh">/usr/share/Modules/init/sh</init_path>
<init_path lang="csh">/usr/share/Modules/init/csh</init_path>
<cmd_path lang="python">/usr/bin/modulecmd python</cmd_path>
<cmd_path lang="perl">/usr/bin/modulecmd perl</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<cmd_path lang="sh">module</cmd_path>
<modules>
<command name="purge"/>
<command name="load">sems-env</command>
<command name="load">sems-git</command>
<command name="load">sems-python/2.7.9</command>
<command name="load">sems-cmake</command>
<command name="load">gnu/4.9.2</command>
<command name="load">intel/intel-15.0.3.187</command>
<command name="load" mpilib="!mpi-serial">openmpi-intel/1.6</command>
<command name="load">libraries/intel-mkl-15.0.2.164</command>
<!-- We want to use these modules but the segfault comes back if we do, maybe wait for new PIO? -->
<!-- <command name="load" mpilib="!mpi-serial">sems-hdf5/1.8.12/parallel</command> -->
<!-- <command name="load" mpilib="!mpi-serial">sems-netcdf/4.3.2/parallel</command> -->
<!-- <command name="load" mpilib="mpi-serial">sems-hdf5/1.8.11/base</command> -->
<!-- <command name="load" mpilib="mpi-serial">sems-netcdf/4.3.2/base</command> -->
</modules>
</module_system>
<environment_variables>
<!-- <env name="PATH">/projects/ccsm/cmake-2.8.10.2-Linux-i386/bin:$PATH</env> -->
<env name="PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/bin:$ENV{PATH}</env>
<env name="LD_LIBRARY_PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib:$ENV{LD_LIBRARY_PATH}</env>
<env name="NETCDF_INCLUDES">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/include</env>
<env name="NETCDF_LIBS">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib</env>
<env name="NETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<env name="PNETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env>
<!-- <env name="NETCDFROOT">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="PNETCDFROOT" mpilib="!mpi-serial">$ENV{SEMS_NETCDF_ROOT}</env> -->
<!-- <env name="NETCDF_INCLUDES">$ENV{SEMS_NETCDF_ROOT}/include</env> -->
<!-- <env name="NETCDF_LIBS">$ENV{SEMS_NETCDF_ROOT}/lib</env> -->
<!-- <env name="PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/bin:$ENV{PATH}</env> -->
<!-- <env name="LD_LIBRARY_PATH">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib:$ENV{LD_LIBRARY_PATH}</env> -->
<!-- <env name="NETCDF_INCLUDES">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/include</env> -->
<!-- <env name="NETCDF_LIBS">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5/lib</env> -->
<!-- <env name="NETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env> -->
<!-- <env name="PNETCDFROOT">/projects/ccsm/tpl/netcdf/4.3.2/intel/13.0.1/openmpi/1.6.5</env> -->
<env name="NETCDFROOT">$ENV{SEMS_NETCDF_ROOT}</env>
<env name="PNETCDFROOT" mpilib="!mpi-serial">$ENV{SEMS_NETCDF_ROOT}</env>
<env name="NETCDF_INCLUDES">$ENV{SEMS_NETCDF_ROOT}/include</env>
<env name="NETCDF_LIBS">$ENV{SEMS_NETCDF_ROOT}/lib</env>
<env name="OMP_STACKSIZE">64M</env>
</environment_variables>
</machine>
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