Merge pull request pmodels#7284 from hzhou/2501_yaksa

yaksa: move yaksa into mpich

Approved-by: Ken Raffenetti

Author: hzhou

.gitmodules

@@ -11,9 +11,6 @@
 	path = modules/json-c
 	url = https://github.com/pmodels/json-c
         branch = mpich/main
-[submodule "modules/yaksa"]
-	path = modules/yaksa
-	url = https://github.com/pmodels/yaksa
 [submodule "modules/mydef_boot"]
 	path = modules/mydef_boot
 	url = https://github.com/pmodels/mydef_boot

CHANGES

@@ -7,6 +7,11 @@
 # Rename MPIR_CVAR_DEBUG_PROGRESS_TIMEOUT to MPIR_CVAR_PROGRESS_TIMEOUT, and
   enable it whether or not --enable-g=progress is used in configure.
 
+# MPICH now generates the MPI-IO bindings when ROMIO is build inside MPICH. It
+  remains the same for using ROMIO outside MPICH.
+
+# Yaksa is now maintained inside MPICH rather than as an external submodule.  
+
 ===============================================================================
                                Changes in 4.3
 ===============================================================================

autogen.sh

@@ -228,8 +228,7 @@ set_externals() {
         fi
 
         if [ "yes" = "$do_yaksa" ] ; then
-            check_submodule_presence "modules/yaksa"
-            externals="${externals} modules/yaksa"
+            externals="${externals} src/mpi/datatype/typerep/yaksa"
         fi
     fi
 }
@@ -594,7 +593,7 @@ autogen_external() {
     if [ -d "$_dir" -o -L "$_dir" ] ; then
         echo "------------------------------------------------------------------------"
         echo "running third-party initialization in $_dir"
-        if test "$_dir" = "modules/yaksa" -a -n "$yaksa_depth" ; then
+        if test "$_dir" = "src/mpi/datatype/typerep/yaksa" -a -n "$yaksa_depth" ; then
             (cd $_dir && ./autogen.sh --pup-max-nesting=$yaksa_depth) || exit 1
         else
             (cd $_dir && ./autogen.sh) || exit 1

modules/yaksa

@@ -43,21 +43,21 @@ yaksalib=""
 AC_SUBST([yaksalib])
 
 AM_COND_IF([BUILD_YAKSA_ENGINE], [
-m4_define([yaksa_embedded_dir],[modules/yaksa])
+m4_define([yaksa_embedded_dir],[src/mpi/datatype/typerep/yaksa])
 PAC_CHECK_HEADER_LIB_EXPLICIT([yaksa],[yaksa.h],[$YAKSALIBNAME],[yaksa_init])
 if test "$with_yaksa" = "embedded" ; then
-    yaksalib="modules/yaksa/lib${YAKSALIBNAME}.la"
-    if test ! -e "${use_top_srcdir}/modules/PREBUILT"; then
+    yaksalib="yaksa_embedded_dir/lib${YAKSALIBNAME}.la"
+    if test ! -e "${use_top_srcdir}/modules/PREBUILT-yaksa"; then
         PAC_PUSH_ALL_FLAGS()
         PAC_RESET_ALL_FLAGS()
         # no need for libtool versioning when embedding YAKSA
         yaksa_subdir_args="--enable-embedded"
-        PAC_CONFIG_SUBDIR_ARGS([modules/yaksa],[$yaksa_subdir_args],[],[AC_MSG_ERROR(YAKSA configure failed)])
+        PAC_CONFIG_SUBDIR_ARGS(yaksa_embedded_dir,[$yaksa_subdir_args],[],[AC_MSG_ERROR(YAKSA configure failed)])
         PAC_POP_ALL_FLAGS()
-        yaksasrcdir="modules/yaksa"
+        yaksasrcdir="yaksa_embedded_dir"
     fi
-    PAC_APPEND_FLAG([-I${main_top_builddir}/modules/yaksa/src/frontend/include], [CPPFLAGS])
-    PAC_APPEND_FLAG([-I${use_top_srcdir}/modules/yaksa/src/frontend/include], [CPPFLAGS])
+    PAC_APPEND_FLAG(-I${main_top_builddir}/yaksa_embedded_dir/src/frontend/include, [CPPFLAGS])
+    PAC_APPEND_FLAG(-I${use_top_srcdir}/yaksa_embedded_dir/src/frontend/include, [CPPFLAGS])
 fi
 ])
 

src/mpi/datatype/typerep/src/subconfigure.m4

@@ -0,0 +1,23 @@
+## Pull Request Description
+
+<!--
+By submitting a PR, you are confirming that you have read and agree to
+the terms in the Yaksa contributor license agreement
+(https://github.com/pmodels/yaksa/wiki/Yaksa-Contributor-License-Agreement).
+-->
+
+<!--
+Insert description of the work in this merge request (above this comment),
+particularly focused on _why_ the work is necessary, not _what_ you did.
+-->
+
+<!-- AUTHOR: After creating this merge request, check off each of the following items as you complete them. -->
+
+## Expected Impact
+
+## Author Checklist
+* [ ] Reference appropriate issues (with "Fixes" or "See" as appropriate)
+* [ ] Commits are self-contained and do not do two things at once
+* [ ] Commit message is of the form: `module: short description` and follows [good practice](https://chris.beams.io/posts/git-commit/)
+* [ ] Add comments such that someone without knowledge of the code could understand
+* [ ] Have read and agree to the Yaksa CLA terms (https://github.com/pmodels/yaksa/wiki/Yaksa-Contributor-License-Agreement)

src/mpi/datatype/typerep/yaksa/.github/pull_request_template.md

@@ -0,0 +1,72 @@
+# generic files
+.libs
+.tmp
+.deps
+.dirstamp
+Makefile
+Makefile.in
+aclocal.m4
+autom4te.cache
+config.log
+config.status
+configure
+stamp-h1
+libtool
+*~
+*.la
+*.lo
+*.o
+__pycache__
+
+# m4 temporary files
+ar-lib
+compile
+config.guess
+config.sub
+depcomp
+install-sh
+libtool.m4
+ltmain.sh
+ltoptions.m4
+ltsugar.m4
+ltversion.m4
+lt~obsolete.m4
+missing
+
+# directory specific files
+/Doxyfile
+/src/frontend/include/yaksa.h
+/src/frontend/include/yaksa_config.h
+/src/frontend/include/yaksa_config.h.in
+/maint/Version
+/maint/yaksa.pc
+/maint/yutils.pyc
+/README
+
+# autogenerated files
+/src/backend/gencomm.pyc
+/src/backend/cuda/pup/Makefile.populate_pupfns.mk
+/src/backend/cuda/pup/Makefile.pup.mk
+/src/backend/cuda/pup/yaksuri_cudai_populate_pupfns*
+/src/backend/cuda/pup/yaksuri_cudai_pup.h
+/src/backend/cuda/pup/yaksuri_cudai_pup_*
+/src/backend/ze/pup/Makefile.populate_pupfns.mk
+/src/backend/ze/pup/Makefile.pup.mk
+/src/backend/ze/pup/yaksuri_zei_populate_pupfns*
+/src/backend/ze/pup/yaksuri_zei_pup.h
+/src/backend/ze/pup/yaksuri_zei_pup_*
+/src/backend/ze/pup/yaksuri_zei_pup_kernels.cl
+/src/backend/ze/pup/yaksuri_zei_pup_kernels.ll
+/src/backend/ze/pup/yaksuri_zei_pup_kernels.c
+/src/backend/ze/hooks/yaksuri_zei_init_kernels.c
+/src/backend/ze/hooks/yaksuri_zei_finalize_kernels.c
+/src/backend/hip/pup/Makefile.populate_pupfns.mk
+/src/backend/hip/pup/Makefile.pup.mk
+/src/backend/hip/pup/yaksuri_hipi_populate_pupfns*
+/src/backend/hip/pup/yaksuri_hipi_pup.h
+/src/backend/hip/pup/yaksuri_hipi_pup_*
+/src/backend/seq/pup/Makefile.populate_pupfns.mk
+/src/backend/seq/pup/Makefile.pup.mk
+/src/backend/seq/pup/yaksuri_seqi_populate_pupfns*
+/src/backend/seq/pup/yaksuri_seqi_pup.h
+/src/backend/seq/pup/yaksuri_seqi_pup_*

src/mpi/datatype/typerep/yaksa/.gitignore

@@ -0,0 +1,49 @@
+===============================================================================
+                               Changes in 0.3
+===============================================================================
+
+# Default to detecting the CUDA device capabilities at configure
+  time. If no device is found on the build system, build all "major"
+  CUDA capabilities to cut down on build time and library size. (thanks
+  to Jeff Hammond for contributing)
+
+# Add support for mixed memory types (thanks to ParTec AG for
+  contributing)
+
+# Add HIP backend for stream APIs
+
+# Add automatic HIP SM detection
+
+# Add automatic CUDA SM detection
+
+# Add support for user-specified CUDA compiler
+
+# Add support in --ze-native option to compile for multiple devices
+
+# Add support for --pup-max-nesting < 2 in genpup.py
+
+# Add support for --ze-revision-id to pass to ocloc compiler
+
+# Other bug fixes and code cleanup
+
+===============================================================================
+                               Changes in 0.2
+===============================================================================
+
+# Add support for reduction operations (e.g. sum, prod, min, max, ...)
+
+# Add support for AMD GPUs via HIP backend
+
+# Add "nogpu" info hint to avoid unnecessary pointer attribute queries
+
+# Add stream-based pack/unpack APIs
+
+# Add blocking pack/unpack APIs
+
+# Add support for NVIDIA HPC SDK compilers
+
+# Improve compile time for Level Zero kernels
+
+# Extend tests to support subdevices (tiles) of Intel GPUs
+
+# Many bug fixes and code cleanups

src/mpi/datatype/typerep/yaksa/CHANGES

@@ -0,0 +1,46 @@
+                   Copyright (C) 2020, UChicago Argonne, LLC
+                             All Rights Reserved
+                            Software Name: Yaksa
+                      By: Argonne National Laboratory
+
+                             OPEN SOURCE LICENSE
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the
+   distribution.
+
+3. Neither the names of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+
+********************************************************************************
+                           DISCLAIMER
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+********************************************************************************
+
+                           EXTERNAL CONTRIBUTIONS
+
+Portions of this code have been contributed under the above license by:
+
+ * Intel Corporation
+ * ParTec AG