Add GPTL library

share/CMakeLists.txt

@@ -1,14 +1,3 @@
-###  Fortran compiler flags
-if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  add_compile_definitions(
-    CPRGNU
-    NAMING=_ADD_UNDERSCORE)
-elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  add_compile_definitions(
-    CPRINTEL
-    NAMING=_ADD_UNDERSCORE)
-endif()
-
 # The following files are generated with a script acting on templates
 # We include pre-generated files that are committed to the repository
 list(APPEND cesm_share_generated_files
@@ -43,10 +32,23 @@ list(APPEND cesm_share_src_files
   CESM_share/src/water_isotopes/water_isotopes.F90
 )
 
-# The following files are mostly stubs.
+# GPTL timing library srcs
+list(APPEND timing_src_files
+  timing/f_wrappers.c
+  timing/gptl.c
+  timing/GPTLget_memusage.c
+  timing/gptl.h
+  timing/gptl.inc
+  timing/gptl_papi.c
+  timing/GPTLprint_memusage.c
+  timing/GPTLutil.c
+  timing/perf_mod.F90
+  timing/perf_utils.F90
+)
+
+# The following file is a stub.
 list(APPEND stubs_src_files
-  src/perf_mod.F90
-  src/mct_mod.F90
+  stubs/mct_mod.F90
 )
 
 if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
@@ -56,12 +58,13 @@ endif()
 
 
 # Collect source files for library
-add_library(share STATIC ${stubs_src_files} ${cesm_share_generated_files} ${cesm_share_src_files})
+add_library(share STATIC ${timing_src_files} ${stubs_src_files} ${cesm_share_generated_files} ${cesm_share_src_files})
 
+add_compile_definitions(NUOPC_INTERFACE HAVE_MPI)
 if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
-  target_compile_definitions(share PRIVATE CPRGNU NAMING=_ADD_UNDERSCORE)
+  target_compile_definitions(share PRIVATE CPRGNU NAMING=_ADD_UNDERSCORE FORTRANUNDERSCORE)
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "Intel")
-  target_compile_definitions(share PRIVATE CPRINTEL NAMING=_ADD_UNDERSCORE)
+  target_compile_definitions(share PRIVATE CPRINTEL NAMING=_ADD_UNDERSCORE FORTRANUNDERSCORE)
 endif()
 
 set_target_properties(share PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)

share/timing/COPYING

@@ -0,0 +1,17 @@
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the “Software”), to deal
+in the Software for any noncommercial purposes without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to permit
+persons to whom the Software is furnished to do so, subject to the following
+conditions: The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.  Any
+commercial use (including sale) of the software, and derivative development
+towards commercial use, requires written permission of the copyright
+holder. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO
+EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES
+OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

share/timing/ChangeLog

@@ -0,0 +1,238 @@
+timing_180912: Moved prefix support from perf_mod.F90 to gptl.c
+               and also added support for setting prefixes in
+               threaded regions.
+               [Patrick Worley]
+timing_180911: Moved detail to end of timer name when specify
+               profile_add_detail (so that will not interfere with
+               planned move of the prefix logic into gptl.c)
+               [Patrick Worley]
+timing_180910: Removed addition of double quotes to timer names in
+               perf_mod.F90 and added this as an output option in
+               gptl.c (so internally the names do not have the quotes)
+               [Patrick Worley]
+timing_180822: Fixed perf_mod.F90 bug that prevents PAPI derived events
+               from being recognized.
+               [Patrick Worley]
+timing_180731: Refactored implementation of append/write modes;
+               collected and output "on" events for global statistics
+               [Patrick Worley]
+timing_180730: Added support for setting GPTLmaxthreads. Cleaned up white space.
+               Added SEQUENTIAL to fortran open, to avoid problems on some systems.
+               Added timing overhead measurement to perf_mod. Fixed errors in
+               f_wrappers.c in definition of gptlpr_query_append and
+               gptlpr_XXX_write.
+               [Patrick Worley (some from Jim Rosinksi)]
+timing_180403: Added GPTLstartstop_val(f) to gptl.h, to provide explicit
+               typing and eliminate compile-time warning for some compilers.
+               Also do not define the CPP tokens HAVE_COMM_F2C and
+               HAVE_GETTIMEOFDAY in private.h if they have already been
+               defined, also eliminating compile-time warnings.
+               [Patrick Worley]
+timing_171028: Backported GPTLstartstop_val from a more recent version
+               of GPTL, added a callcount parameter, and renamed it
+               GPTLstartstop_vals. Also added a version for non-null
+               terminated timing event names (GPTLstartstop_valsf).
+               Added t_startstop_valsf to perf_mod. Also replaced
+               all strncpy calls in f_wrapper.c, just to be safe.
+               [Patrick Worley (but primarily Jim Rosinksi)]
+timing_171027: Mitigated against nonmonotonic timing calls by
+               setting negative deltas to zero in gptl.c .
+               [Patrick Worley]
+timing_160816: Added quotes to timing event names in t_startf and t_stopf
+               before calling GPTL routines.
+               [Patrick Worley and Sean Patrick Santos]
+timing_161207: Replaced strncpy and snprintf where applied to
+               non-null-terminated strings, to avoid memory issues
+               when strncpy and snprintf implementations use strnlen
+               to check validity of passed in string length parameter.
+               (Why this causes problems is still a mystery.)
+               [Patrick Worley and Gautam Bisht]
+timing_160320: Added routines t_set_prefixf and t_unset_prefixf.
+               Setting the prefix adds this to the beginning of all subsequent
+               timer event names (defined in t_startf/t_stopf).
+               Also doubling default hash index tablesize to 2048.
+               [Patrick Worley]
+timing_160124: Added option to prefix timer names with detail level. This is
+               controlled by a new namelist variable (profile_add_detail).
+               The default is to not enable this option. It is meant to be
+               used for inspecting the profile detail definitions and
+               associated logic.
+               [Patrick Worley]
+timing_150903: Changed API to be compatible with NCAR CIME version of timing
+               library: (a) changed handle argument from integer8 to integer
+               in t_startf and t_stopf, and disabled use of handles in these
+               routines until gptl.c can be updated; (b) added MaxThreads
+               optional argument to t_initf, though it does not do anything
+               yet.
+               [Patrick Worley]
+timing_150518: Disabled abort when calling GPTL routines before GPTLinitialize
+               (so can use with Chombo library, for example); changed top
+               level default from nanotimer to MPI_WTIME.
+               [Patrick Worley]
+timing_150327: Added option to more accurately measure measurement overhead
+               (incurring additional overhead, so not on by default).
+               [Patrick Worley]
+timing_150217: Added support for enabling/disabling start/stop timers from
+               perf_mod even when calling GPTL routines directly from C/C++
+               libraries; increased maximum timer name length.
+               [Patrick Worley]
+timing_141119: Enabled cmake build of timing library.
+               [Jayesh Krishna]
+timing_140805: Disabled GPTL autoinstrumentation, as this conflicts with the
+               VampirTrace tool. (We do not use the autoinstrumentation
+               capability.) [Patrick Worley, from B. Jamroz]
+timing_140416: Changed Makefile so that .mods and the static library are copied to
+               LIBROOT
+timing_140317: Modified Makefile to deal with shared mpi-serial builds
+timing_131108: Added memory retrieval commands for BG/Q [S Mickelson]
+timing_131023: Added explicit include path for gptl.h [J Edwards]
+timing_130827: added routines supporting non-null terminated timer labels, for use with
+               with C++ std:string (and more efficient usage with Fortran); also CMake
+               logic fixes
+               [Patrick Worley]
+timing_130506: Copy all modules to the include directory on install
+timing_130417: Made nano time the default timer if available.
+timing_130316: Changed declarations of functions used in qsort in gptl.c, to eliminate
+	       error with Cray compiler (and warnings from other compilers)
+               [Patrick Worley]
+timing_130214: NAG port: Put mpif.h include before "save", and don't use
+	       "abort" and "flush" extensions for NAG. [Sean Patrick Santos]
+timing_120921: Add code for cmake build, should not have any affect otherwise
+timing_120731: Correction in Makefile for serial build [Jim Edwards]
+timing_120728: Replace process subset optional parameter in t_prf with
+	       outpe_thispe optional parameter. Change def_perf_outpe_num to 0.
+	       [Patrick Worley]
+timing_120717: Retain timestamp on cp in Makefile   [Jim Edwards]
+timing_120710: Correct issue in Makefile [Jim Edwards]
+timing_120709: Change for BGP to measure on compute nodes rather than IO nodes only,
+               minor Change in Makefile so that gptl can build seperate from csm_share
+               in cesm [Jim Edwards]
+timing_120512: Bug fix in global statistics logic for when a thread has no events
+	       to contribute to the merge (mods to gptl.c)
+	       [Patrick Worley]
+timing_120419: Minor changes for mpi-serial compile (jedwards)
+timing_120408: Make HAVE_COMM_F2C default to true. (jedwards)
+timing_120110: Update to GPTL 4.1 source (mods to gptl.c and GPTLprint_memusage)
+               [Jim Rosinski (GPTL 4.1), Patrick Worley]
+timing_120109: Bug fix (adding shr_kind_i8 to shr_kind_mod list)
+timing_111205: Update to gptl 4.0 (introducing CESM customizations);
+               support for handles in t_startf/t_stopf;
+               support for restricting output to explicitly named process subsets
+               [Jim Rosinski (gptl 4.0), Patrick Worley]
+timing_111101: Workaround for mpi_rsend issue on cray/gemini
+timing_110928: Add a Makefile and build as a library usable by mct and pio
+timing_101215: No changes from previous tag other than updating Changelog
+timing_101210: Fix interface to cesm build system, add workaround for xlf bug
+timing_101202: updated get_memusage and print_memusage from GPTL version 3.7; adds
+	       improved support for MacOS and SLASHPROC
+	       [Jim Rosinski, Chuck Bardeen (integrated by P. Worley)]
+timing_091021: update to GPTL version 3.5; rewrite of GPTLpr_summary: much faster, merging
+	       events from all processes and all threads (not just process 0/thread 0);
+	       miscellaneous fixes
+	       [Jim Rosinski (gptl 3.5), Joseph Singh, Patrick Worley]
+timing_090929: added explicit support for the GPTL-native token HAVE_MPI (indicating
+	       presence of MPI library)
+	       [Patrick Worley]
+timing_081221: restore default assumption that gettimeofday available
+timing_081028: bug fix in include order in gptl_papi.c
+timing_081026: change in output format to make postprocessing simpler
+timing_081024: support for up to one million processes and writing timing files to
+	       subdirectories
+timing_081017: updated to gptl version 3_4_2. Changed some defaults.
+               [Jim Rosinski, Patrick Worley]
+timing_080629: added optional parameters perf_outpe_num and perf_outpe_stride to t_prf.
+	       These are used to override the user specified values for timing data
+	       written out before the end of a simulation.
+               [Patrick Worley]
+timing_071213: changed default to disable inline keyword; changed global statistics
+	       logic to avoid problems at scale; moved shr and CAM routine equivalencies
+	       to a new module (in perf_utils.F90); added t_getLogUnit/t_setLogUnit
+	       routines to control Log output in same way as shr_file_get/setLogUnit;
+               modified GPTLpr logic to support output of timing data during a run
+               [Patrick Worley]
+timing_071023: updated to gptl version 2.16, added support for output of global
+               statistics; removed dependencies on shr and CAM routines; renamed
+               gptlutil.c to GPTLutil.c
+               [Patrick Worley, Jim Rosinski]
+timing_071019: modified namelist logic to abort if try to set unknown namelist parameters;
+	       changed default number of reporting processes to 1;
+               reversed meaning and changed names of CPP tokens to NO_C99_INLINE and NO_VPRINTF
+               [Patrick Worley]
+timing_071010: modified gptl.c to remove the 'inline' specification unless the
+	       CPP token C99 is defined.
+               [Patrick Worley]
+timing_070810: added ChangeLog
+               updated to latest version of GPTL (from Jim Rosinski)
+               modified perf_mod.F90:
+               - added perf_outpe_num and perf_outpe_stride to perf_inparm
+	         namelist to control which processes output timing data
+	       - added perf_papi_enable to perf_inparm namelist to enable
+	         PAPI counters
+               - added papi_inparm namelist and papi_ctr1,2,3,4 namelist
+	         parameters to specify PAPI counters
+               [Patrick Worley, Jim Rosinski]
+timing_070525: bug fix in gptl.c
+               - unitialized pointer, testing for null pter
+                 before traversing
+               [Patrick Worley]
+timing_070328: modified perf_mod.F90
+	       - deleted HIDE_MPI cpp token
+	       [Erik Kluzek]
+timing_070327: bug fixes in gptl.c
+	       - testing for null pters before traversing
+                 links; added missing type declaration to GPTLallocate for sum
+	       bug fixes in perf_mod.F90
+	       - fixed OMP-related logic, modified settings reporting,
+	         modified to work when namelist input is
+                 missing; moved timer depth logic back into gptl.c
+	       [Patrick Worley]
+timing_070308: added perf_mod.F90
+	       - defines all t_xxx entry points - calling gptlxxx directly
+	         and removing all external gptlxxx dependencies,
+                 added detail option as an alternative way to disable
+	         event timing, added runtime selection of timing_disable,
+	         perf_timer, timer_depth_limit, timing_detail_limit,
+	         timing_barrier, perf_single_file via namelist parameters
+	       modified f_wrappers.c
+	       - replaced all t_xxx entry points with gptlxxx entry points,
+	         added new gptlxxx entry points, deleted _fcd support
+	       modified gptl.c
+	       - deleted DISABLE_TIMERS cpp token, modified GPTLpr call
+	         and logic to move some of support for concatenating timing
+	         output into a single file to perf_mod.F90
+	       modified gptl.h
+	       - exposed gptlxxx entry points and to add support for choice
+	         of GPTL timer
+	       modified gptl.inc
+	       - removed t_xxx entry points and expose gptlxxx entry points
+	       [Patrick Worley]
+timing_061207: modified gptl.c
+	       - improved event output ordering
+	       [Jim Edwards]
+timing_061124: modified gptl.c
+	       - modified GPTLpr to add option to concatenate
+	         all timing data in a single output file, added GPTL_enable
+	         and GPTL_disable as runtime control of event timing,
+	         process 0-only reporting of timing options - unless DEBUG
+	         cpp token defined
+	       modified gptl.h
+	       - redefined GPTLpr parameters
+	       modified f_wrappers.c
+	       - added t_enablef and t_disablef to call GPTL_enable and
+	         GPTL_disable, added t_pr_onef, added string.h include
+	       bug fix in f_wrappers.c
+	       - changed character string size declaration from int to size_t
+	       bug fix in gptl_papi.c
+	       - modified error message - from Jim Edwards
+	       modified private.h
+	       - increased maximum event name length
+	       [Patrick Worley]
+timing_061028: modified f_wrappers.c
+	       - deleted dependency on cfort.h
+	       [Patrick Worley]
+timing_060524: modified f_wrappers.c
+	       - added support for CRAY cpp token and fixed routine
+	         type declarations
+	       [Patrick Worley]
+timing_051212: original subversion version
+	       - see CAM ChangeLog for earlier history