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Merge remote-tracking branch 'remotes/esmci/master' into fixquerymach…
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@ekluzek
ekluzek committed Aug 30, 2016
2 parents f29b0ea + cff1801 commit d3ea142
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Showing 148 changed files with 19,019 additions and 10,623 deletions.
2 changes: 1 addition & 1 deletion cime_config/acme/config_files.xml
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Expand Up @@ -66,7 +66,7 @@

<entry id="CONFIG_TESTS_FILE">
<type>char</type>
<default_value>$CIMEROOT/scripts/Testing/Testcases/config_tests.xml</default_value>
<default_value>$CIMEROOT/cime_config/config_tests.xml</default_value>
<group>test</group>
<file>env_test.xml</file>
<desc>file containing system test descriptions </desc>
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4 changes: 1 addition & 3 deletions cime_config/acme/machines/config_batch.xml
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Expand Up @@ -79,7 +79,7 @@
<batch_query args="-u $USER" >qselect</batch_query>
<batch_submit>qsub </batch_submit>
<batch_directive>#PBS</batch_directive>
<jobid_pattern>^(\d+)\.</jobid_pattern>
<jobid_pattern>^(\d+)</jobid_pattern>
<depend_string> -W depend=afterok:jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<submit_args>
Expand Down Expand Up @@ -164,10 +164,8 @@

<!-- eos is PBS -->
<batch_system MACH="eos" type="pbs" version="x.y">
<jobid_pattern>^(\d+)</jobid_pattern>
<directives>
<directive>-A {{ project }}</directive>
<directive>-l mppwidth={{ mppwidth }}</directive>
<directive>-l nodes={{ num_nodes }}</directive>
</directives>
<queues>
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59 changes: 56 additions & 3 deletions cime_config/acme/machines/config_machines.xml
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Expand Up @@ -371,6 +371,7 @@
<cmd_path lang="sh">module</cmd_path>
<modules>
<command name="purge"/>
<command name="load">git/2.1.3</command>
<command name="load">python/2.7.9</command>
<command name="load">gcc/5.1.0/openmpi/1.8.7</command>
<command name="load">cmake/2.8.12</command>
Expand Down Expand Up @@ -1014,11 +1015,11 @@
<COMPILERS>intel</COMPILERS>
<MPILIBS>mpich,mpi-serial</MPILIBS>
<CESMSCRATCHROOT>$ENV{HOME}/acme_scratch/$PROJECT</CESMSCRATCHROOT>
<RUNDIR>$MEMBERWORK/$PROJECT/$CASE/run</RUNDIR>
<RUNDIR>$ENV{MEMBERWORK}/$PROJECT/$CASE/run</RUNDIR>
<EXEROOT>$CESMSCRATCHROOT/$CASE/bld</EXEROOT>
<DIN_LOC_ROOT>/lustre/atlas1/cli900/world-shared/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/lustre/atlas1/cli900/world-shared/cesm/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$MEMBERWORK/$PROJECT/archive/$CASE</DOUT_S_ROOT>
<DOUT_S_ROOT>$ENV{MEMBERWORK}/$PROJECT/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_MSROOT>csm/$CASE</DOUT_L_MSROOT>
<CCSM_BASELINE>/lustre/atlas1/cli900/world-shared/cesm/baselines</CCSM_BASELINE>
<CCSM_CPRNC>/lustre/atlas1/cli900/world-shared/cesm/tools/cprnc/cprnc.eos</CCSM_CPRNC>
Expand All @@ -1039,12 +1040,64 @@
<arg name="num_tasks" > -n {{ num_tasks }}</arg>
<arg name="tasks_per_node" > -N {{ tasks_per_node }}</arg>
<arg name="thread_count" > -d {{ thread_count }}</arg>
<arg name="numa_node" > -cc {{ numa_node }}</arg>
<arg name="numa_node" > -cc numa_node</arg>
</arguments>
</mpirun>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<module_system type="module">
<init_path lang="sh">$MODULESHOME/init/sh</init_path>
<init_path lang="csh">$MODULESHOME/init/csh</init_path>
<init_path lang="perl">$MODULESHOME/init/perl.pm</init_path>
<init_path lang="python">$MODULESHOME/init/python.py</init_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<cmd_path lang="perl">$MODULESHOME/bin/modulecmd perl</cmd_path>
<cmd_path lang="python">$MODULESHOME/bin/modulecmd python</cmd_path>
<modules>
<command name="rm">intel</command>
<command name="rm">cray</command>
<command name="rm">cray-parallel-netcdf</command>
<command name="rm">cray-libsci</command>
<command name="rm">cray-netcdf</command>
<command name="rm">cray-netcdf-hdf5parallel</command>
<command name="rm">netcdf</command>
</modules>
<modules compiler="intel">
<command name="load">intel/16.0.1.150</command>
<command name="load">papi</command>
</modules>
<modules compiler="cray">
<command name="load">PrgEnv-cray</command>
<command name="switch">cce cce/8.1.9</command>
<command name="load">cray-libsci/12.1.00</command>
</modules>
<modules compiler="gnu">
<command name="load">PrgEnv-gnu</command>
<command name="switch">gcc gcc/4.8.0</command>
<command name="load">cray-libsci/12.1.00</command>
</modules>
<modules mpilib="mpi-serial">
<command name="load">cray-netcdf/4.3.2</command>
</modules>
<modules mpilib="!mpi-serial">
<command name="load">cray-netcdf-hdf5parallel/4.3.3.1</command>
<command name="load">cray-parallel-netcdf/1.6.1</command>
</modules>
<modules>
<command name="load">cmake/2.8.11.2</command>
<command name="load">python/2.7.9</command>
</modules>
<environment_variables>
<env name="MPICH_ENV_DISPLAY">1</env>
<env name="MPICH_VERSION_DISPLAY">1</env>
<!-- This increases the stack size, which is necessary
for CICE to run threaded on this machine -->
<env name="OMP_STACKSIZE">64M</env>

</environment_variables>
</module_system>
</machine>

<machine MACH="mustang">
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26 changes: 13 additions & 13 deletions cime_config/cesm/config_archive.xml
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Expand Up @@ -134,33 +134,33 @@
<comp_archive_spec compname="dwav" compclass="wav">
<rest_file_extension>\.r.*</rest_file_extension>
<rest_history_varname>unset</rest_history_varname>
<rpointer_file>rpointer$NINST_STRING.wav</rpointer_file>
<rpointer_content >
$CASE.dwav$NINST_STRING.r.$DATENAME.nc,$CASE.dwav$NINST_STRING.rs1.$DATENAME.bin
</rpointer_content>
<rpointer>
<rpointer_file>rpointer$NINST_STRING.wav</rpointer_file>
<rpointer_content >$CASE.dwav$NINST_STRING.r.$DATENAME.nc,$CASE.dwav$NINST_STRING.rs1.$DATENAME.bin</rpointer_content>
</rpointer>
</comp_archive_spec>

<comp_archive_spec compname="dart" compclass="esp">
<rest_file_extension>inflate_restart.*</rest_file_extension>
<hist_file_extension>True_State.*</hist_file_extension>
<hist_file_extension>Prior_Diag.*</hist_file_extension>
<hist_file_extension>Posterior_Diag.*</hist_file_extension>
<hist_file_extension>obs_seq.*</hist_file_extension>
<rest_file_extension>inflate_restart.*</rest_file_extension>
<rest_history_varname>unset</rest_history_varname>
<rpointer_file>rpointer.unset</rpointer_file>
<rpointer_content >
unset
</rpointer_content>
<rpointer>
<rpointer_file>rpointer.unset</rpointer_file>
<rpointer_content >unset</rpointer_content>
</rpointer>
</comp_archive_spec>

<comp_archive_spec compname="cpl" compclass="cpl">
<rest_file_extension>\.r\..*</rest_file_extension>
<hist_file_extension>\.h.*</hist_file_extension>
<rest_history_varname>unset</rest_history_varname>
<rpointer_file>rpointer.cpl</rpointer_file>
<rpointer_content >
$CASE.cpl.r.$DATENAME.nc
</rpointer_content>
<rpointer>
<rpointer_file>rpointer.cpl</rpointer_file>
<rpointer_content >$CASE.cpl.r.$DATENAME.nc</rpointer_content>
</rpointer>
</comp_archive_spec>

</components>
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2 changes: 1 addition & 1 deletion cime_config/cesm/config_files.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@

<entry id="CONFIG_TESTS_FILE">
<type>char</type>
<default_value>$CIMEROOT/scripts/Testing/Testcases/config_tests.xml</default_value>
<default_value>$CIMEROOT/cime_config/config_tests.xml</default_value>
<group>test</group>
<file>env_test.xml</file>
<desc>file containing system test descriptions </desc>
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3 changes: 2 additions & 1 deletion cime_config/cesm/machines/config_batch.xml
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Expand Up @@ -424,7 +424,8 @@

<batch_system MACH="yellowstone" type="lsf" version="9.1">
<queues>
<queue walltimemax="24:00" jobmin="1" jobmax="8">caldera</queue>
<queue walltimemax="24:00" jobmin="1" jobmax="1" jobname="case.lt_archive">hpss</queue>
<queue walltimemax="24:00" jobmin="1" jobmax="8" >caldera</queue>
<queue walltimemax="12:00" jobmin="9" jobmax="16384" default="true">regular</queue>
<queue walltimemax="12:00" jobmin="16385" jobmax="65536">capability</queue>
</queues>
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62 changes: 17 additions & 45 deletions cime_config/cesm/machines/config_build.xml
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Expand Up @@ -340,20 +340,21 @@ for mct, etc.
<base> -r8 </base>
</FC_AUTO_R8>
<FFLAGS>
<!-- Yes, you really do need this huge -wmismatch flag for NAG to work. -->
<!-- More specifically, it exempts MPI functions without explicit -->
<!-- interfaces from certain argument checks. Should not be necessary in -->
<!-- libraries that only use the F90 module interface. mpibcast and -->
<!-- mpiscatterv are actually CAM wrappers for MPI. -->
<!-- <FFLAGS > -Wp,-macro=no_com -wmismatch=mpi_send,mpi_recv,mpi_bcast,mpi_allreduce,mpi_reduce,mpi_isend,mpi_irecv,mpi_irsend,mpi_rsend,mpi_gatherv,mpi_gather,mpi_scatterv,mpi_allgather,mpi_alltoallv,mpi_file_read_all,mpi_file_write_all,mpibcast,mpiscatterv -convert=BIG_ENDIAN </FFLAGS>-->
<base> -Wp,-macro=no_com -convert=BIG_ENDIAN -mismatch_all </base>
<!-- The indirect flag below is to deal with MPI functions that violate -->
<!-- the Fortran standard, by adding a large set of arguments from a file. -->
<base>-Wp,-macro=no_com -convert=BIG_ENDIAN -indirect <env>CIMEROOT</env>/cime_config/cesm/machines/nag_mpi_argument.txt</base>
<!-- DEBUG vs. non-DEBUG runs. -->
<append DEBUG="FALSE"> -ieee=full -O2 </append>
<!-- The "-gline" option is nice, but it doesn't work with OpenMP. -->
<!-- Runtime checks with OpenMP (in fact, all OpenMP cases) are WIP. -->
<append DEBUG="TRUE"> -C=all -g -time -f2003 -ieee=stop </append>
<append DEBUG="TRUE" compile_threaded="false"> -gline </append>
<append compile_threaded="true"> -openmp </append>
<!-- The SLAP library (which is part of the CISM build) has many instances of
arguments being passed to different types. So disable argument type
checking when building CISM. This can be removed once we remove SLAP from
CISM. -->
<append MODEL="cism"> -mismatch_all </append>
</FFLAGS>
<FFLAGS_NOOPT>
<base> <var>FFLAGS</var> </base>
Expand Down Expand Up @@ -944,15 +945,19 @@ for mct, etc.
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append>
</CPPDEFS>
<LAPACK_LIBDIR> /usr/lib64 </LAPACK_LIBDIR>
<MPI_LIB_NAME MPILIB="openmpi"> mpi</MPI_LIB_NAME>
<MPI_LIB_NAME MPILIB="mvapich2"> mpich</MPI_LIB_NAME>
<NETCDF_PATH><env>NETCDF_PATH</env></NETCDF_PATH>
<SLIBS>
<append><shell><var>NETCDF_PATH</var>/bin/nf-config --flibs</shell></append>
</SLIBS>
</compiler>

<compiler MACH="hobart" COMPILER="intel">
<CFLAGS>
<append> -lifcore</append>
</CFLAGS>
<FFLAGS>
<append> -lifcore</append>
<append MPILIB="mpi-serial"> -mcmodel medium </append>
</FFLAGS>
<LDFLAGS>
Expand All @@ -961,6 +966,7 @@ for mct, etc.
<append> -Wl,-rpath,<env>COMPILER_PATH</env>/lib/intel64 </append>
<append> -Wl,-rpath,<env>COMPILER_PATH</env>/mkl/lib/intel64 </append>
<append> -Wl,-rpath,<env>MPI_PATH</env>/lib</append>
<append> -lifcore</append>
</LDFLAGS>
<PFUNIT_PATH>/home/santos/pFUnit/pFUnit_Intel_3_0</PFUNIT_PATH>
<SLIBS>
Expand Down Expand Up @@ -1033,36 +1039,6 @@ for mct, etc.
</SLIBS>
</compiler>

<compiler MACH="logan">
<LAPACK_LIBDIR> /usr/lib64 </LAPACK_LIBDIR>
<MPI_LIB_NAME MPILIB="openmpi"> mpi</MPI_LIB_NAME>
<SLIBS>
<append><shell><var>NETCDF_PATH</var>/bin/nf-config --flibs</shell></append>
</SLIBS>
</compiler>

<compiler MACH="logan" COMPILER="intel">
<LDFLAGS>
<append> -Wl,-rpath,<var>NETCDF_PATH</var>/lib </append>
<append> -Wl,-rpath,<env>COMPILER_PATH</env>/lib/intel64 </append>
</LDFLAGS>
</compiler>

<compiler MACH="logan" COMPILER="pgi">
<CFLAGS>
<append DEBUG="FALSE"> -O2 </append>
</CFLAGS>
<FFLAGS>
<append DEBUG="FALSE"> -O2 </append>
</FFLAGS>
<LDFLAGS>
<append> -lgomp </append>
<append> -Wl,-R<var>NETCDF_PATH</var>/lib</append>
<append> -Wl,-R<env>COMPILER_PATH</env>/lib</append>
<append> -Wl,-R<env>COMPILER_PATH</env>/libso</append>
</LDFLAGS>
</compiler>

<compiler MACH="melvin" COMPILER="gnu">
<ALBANY_PATH>/projects/install/rhel6-x86_64/ACME/AlbanyTrilinos/Albany/build/install</ALBANY_PATH>
<CFLAGS>
Expand Down Expand Up @@ -1235,11 +1211,11 @@ for mct, etc.

<compiler MACH="stampede">
<CPPDEFS>
<!--PNETCDF_PATH>$(TACC_NETCDF_DIR)</PNETCDF_PATH-->
<append> -DHAVE_NANOTIME </append>
</CPPDEFS>
<NETCDF_PATH><env>TACC_NETCDF_DIR</env></NETCDF_PATH>
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
<PNETCDF_PATH><env>TACC_PNETCDF_DIR</env></PNETCDF_PATH>
</compiler>

<compiler MACH="stampede" COMPILER="intel">
Expand All @@ -1253,12 +1229,6 @@ for mct, etc.
<LDFLAGS>
<append>-L<env>TACC_HDF5_LIB</env> -lhdf5</append>
</LDFLAGS>
<MPICC>mpicc</MPICC>
<MPICXX>mpicxx</MPICXX>
<MPIFC>mpif90</MPIFC>
<SCC>icc</SCC>
<SCXX>icpc</SCXX>
<SFC>ifort</SFC>
<SLIBS>
<append><shell><var>NETCDF_PATH</var>/bin/nf-config --flibs</shell> -L<env>TACC_HDF5_LIB</env> -lhdf5</append>
</SLIBS>
Expand Down Expand Up @@ -1367,6 +1337,8 @@ for mct, etc.
<PAPI_LIB MPILIB="mpich2">/glade/apps/opt/papi/5.3.0/intel/12.1.5/lib64 </PAPI_LIB>
<PFUNIT_PATH><env>CESMDATAROOT</env>/tools/pFUnit/pFUnit3.1_Intel15.0.1_MPI</PFUNIT_PATH>
<!-- Needed due to the way that netcdf is loaded on yellowstone -->
<SCC MPILIB="mpi-serial">icc</SCC>
<SFC MPILIB="mpi-serial">ifort</SFC>
<SCC MPILIB="mpich2"><var>MPICC</var></SCC>
<SFC MPILIB="mpich2"><var>MPIFC</var></SFC>
<SLIBS>
Expand Down
8 changes: 1 addition & 7 deletions cime_config/cesm/machines/config_compilers.xml
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Expand Up @@ -901,17 +901,11 @@ for mct, etc.
<compiler MACH="stampede">
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS>
<NETCDF_PATH>$(TACC_NETCDF_DIR)</NETCDF_PATH>
<!--PNETCDF_PATH>$(TACC_NETCDF_DIR)</PNETCDF_PATH-->
<PNETCDF_PATH>$(TACC_PNETCDF_DIR)</PNETCDF_PATH>
<ADD_CPPDEFS> -DHAVE_NANOTIME </ADD_CPPDEFS>
</compiler>

<compiler MACH="stampede" COMPILER="intel">
<MPICC>mpicc</MPICC>
<MPIFC>mpif90</MPIFC>
<MPICXX>mpicxx</MPICXX>
<SFC>ifort</SFC>
<SCC>icc</SCC>
<SCXX>icpc</SCXX>
<ADD_FFLAGS> -xHost </ADD_FFLAGS>
<ADD_CFLAGS> -xHost </ADD_CFLAGS>
<ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nf-config --flibs) -L$(TACC_HDF5_LIB) -lhdf5</ADD_SLIBS>
Expand Down
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