Resolve merge conflicts

Signed-off-by: Mikhail Kurnosov <mkurnosov@gmail.com>

Author: mkurnosov

LICENSE

@@ -53,7 +53,7 @@ Copyright (c) 2014-2015 Hewlett-Packard Development Company, LP.  All
                         rights reserved.
 Copyright (c) 2013-2017 Research Organization for Information Science (RIST).
                         All rights reserved.
-Copyright (c) 2017      Amazon.com, Inc. or its affiliates.  All Rights
+Copyright (c) 2017-2018 Amazon.com, Inc. or its affiliates.  All Rights
                         reserved.
 Copyright (c) 2018      DataDirect Networks. All rights reserved.
 

NEWS

@@ -80,6 +80,53 @@ Master (not on release branches yet)
   Currently, this means the Open SHMEM layer will only build if
   a MXM or UCX library is found.
 
+3.1.2 -- August, 2018
+------------------------
+
+- A subtle race condition bug was discovered in the "vader" BTL
+  (shared memory communications) that, in rare instances, can cause
+  MPI processes to crash or incorrectly classify (or effectively drop)
+  an MPI message sent via shared memory.  If you are using the "ob1"
+  PML with "vader" for shared memory communication (note that vader is
+  the default for shared memory communication with ob1), you need to
+  upgrade to v3.1.2 or later to fix this issue.  You may also upgrade
+  to the following versions to fix this issue:
+  - Open MPI v2.1.5 (expected end of August, 2018) or later in the
+    v2.1.x series
+  - Open MPI v3.0.1 (released March, 2018) or later in the v3.0.x
+    series
+- Assorted Portals 4.0 bug fixes.
+- Fix for possible data corruption in MPI_BSEND.
+- Move shared memory file for vader btl into /dev/shm on Linux.
+- Fix for MPI_ISCATTER/MPI_ISCATTERV Fortran interfaces with MPI_IN_PLACE.
+- Upgrade PMIx to v2.1.3.
+- Numerous One-sided bug fixes.
+- Fix for race condition in uGNI BTL.
+- Improve handling of large number of interfaces with TCP BTL.
+- Numerous UCX bug fixes.
+
+3.1.1 -- June, 2018
+-------------------
+
+- Fix potential hang in UCX PML during MPI_FINALIZE
+- Update internal PMIx to v2.1.2rc2 to fix forward version compatibility.
+- Add new MCA parameter osc_sm_backing_store to allow users to specify
+  where in the filesystem the backing file for the shared memory
+  one-sided component should live.  Defaults to /dev/shm on Linux.
+- Fix potential hang on non-x86 platforms when using builds with
+  optimization flags turned off.
+- Disable osc/pt2pt when using MPI_THREAD_MULTIPLE due to numerous
+  race conditions in the component.
+- Fix dummy variable names for the mpi and mpi_f08 Fortran bindings to
+  match the MPI standard.  This may break applications which use
+  name-based parameters in Fortran which used our internal names
+  rather than those documented in the MPI standard.
+- Revamp Java detection to properly handle new Java versions which do
+  not provide a javah wrapper.
+- Fix RMA function signatures for use-mpi-f08 bindings to have the
+  asynchonous property on all buffers.
+- Improved configure logic for finding the UCX library.
+
 3.1.0 -- May, 2018
 ------------------
 

README

@@ -8,7 +8,7 @@ Copyright (c) 2004-2008 High Performance Computing Center Stuttgart,
                         University of Stuttgart.  All rights reserved.
 Copyright (c) 2004-2007 The Regents of the University of California.
                         All rights reserved.
-Copyright (c) 2006-2017 Cisco Systems, Inc.  All rights reserved.
+Copyright (c) 2006-2018 Cisco Systems, Inc.  All rights reserved.
 Copyright (c) 2006-2011 Mellanox Technologies. All rights reserved.
 Copyright (c) 2006-2012 Oracle and/or its affiliates.  All rights reserved.
 Copyright (c) 2007      Myricom, Inc.  All rights reserved.
@@ -605,7 +605,6 @@ Network Support
     - Loopback (send-to-self)
     - Shared memory
     - TCP
-    - Intel Phi SCIF
     - SMCUDA
     - Cisco usNIC
     - uGNI (Cray Gemini, Aries)
@@ -768,6 +767,26 @@ Open MPI is unable to find relevant support for <foo>, configure will
 assume that it was unable to provide a feature that was specifically
 requested and will abort so that a human can resolve out the issue.
 
+Additionally, if a search directory is specified in the form
+--with-<foo>=<dir>, Open MPI will:
+
+1. Search for <foo>'s header files in <dir>/include.
+2. Search for <foo>'s library files:
+   2a. If --with-<foo>-libdir=<libdir> was specified, search in
+       <libdir>.
+   2b. Otherwise, search in <dir>/lib, and if they are not found
+       there, search again in <dir>/lib64.
+3. If both the relevant header files and libraries are found:
+   3a. Open MPI will build support for <foo>.
+   3b. If the root path where the <foo> libraries are found is neither
+       "/usr" nor "/usr/local", Open MPI will compile itself with
+       RPATH flags pointing to the directory where <foo>'s libraries
+       are located.  Open MPI does not RPATH /usr/lib[64] and
+       /usr/local/lib[64] because many systems already search these
+       directories for run-time libraries by default; adding RPATH for
+       them could have unintended consequences for the search path
+       ordering.
+
 INSTALLATION OPTIONS
 
 --prefix=<directory>
@@ -1000,9 +1019,6 @@ NETWORKING SUPPORT / OPTIONS
   covers most cases.  This option is only needed for special
   configurations.
 
---with-scif=<dir>
-  Look in directory for Intel SCIF support libraries
-
 --with-verbs=<directory>
   Specify the directory where the verbs (also known as OpenFabrics
   verbs, or Linux verbs, and previously known as OpenIB) libraries and

autogen.pl

@@ -61,7 +61,7 @@
 my $exclude_list;
 
 # Minimum versions
-my $ompi_automake_version = "1.12.2";
+my $ompi_automake_version = "1.13.4";
 my $ompi_autoconf_version = "2.69";
 my $ompi_libtool_version = "2.4.2";
 

config/ompi_config_files.m4

@@ -1,7 +1,7 @@
 # -*- shell-script -*-
 #
 # Copyright (c) 2009-2017 Cisco Systems, Inc.  All rights reserved
-# Copyright (c) 2017      Research Organization for Information Science
+# Copyright (c) 2017-2018 Research Organization for Information Science
 #                         and Technology (RIST). All rights reserved.
 # Copyright (c) 2018      Los Alamos National Security, LLC. All rights
 #                         reserved.
@@ -38,6 +38,7 @@ AC_DEFUN([OMPI_CONFIG_FILES],[
         ompi/mpi/fortran/use-mpi-ignore-tkr/mpi-ignore-tkr-file-interfaces.h
         ompi/mpi/fortran/use-mpi-ignore-tkr/mpi-ignore-tkr-removed-interfaces.h
         ompi/mpi/fortran/use-mpi-f08/Makefile
+        ompi/mpi/fortran/use-mpi-f08/bindings/Makefile
         ompi/mpi/fortran/use-mpi-f08/mod/Makefile
         ompi/mpi/fortran/mpiext-use-mpi/Makefile
         ompi/mpi/fortran/mpiext-use-mpi-f08/Makefile

config/opal_check_pmi.m4

@@ -347,7 +347,8 @@ AC_DEFUN([OPAL_CHECK_PMIX],[
                                                             ], [])],
                                             [AC_MSG_RESULT([found])
                                              opal_external_pmix_version=4x
-                                             opal_external_pmix_version_found=1],
+                                             opal_external_pmix_version_found=1
+                                             opal_external_pmix_happy=yes],
                                             [AC_MSG_RESULT([not found])])])
 
                   AS_IF([test "$opal_external_pmix_version_found" = "0"],
@@ -437,9 +438,11 @@ AC_DEFUN([OPAL_CHECK_PMIX],[
                        [Whether the external PMIx library is v1])
     AM_CONDITIONAL([OPAL_WANT_PRUN], [test "$opal_prun_happy" = "yes"])
 
-    AS_IF([test "$opal_external_pmix_version" = "1x"],
-          [OPAL_SUMMARY_ADD([[Miscellaneous]],[[PMIx support]], [opal_pmix], [1.2.x: WARNING - DYNAMIC OPS NOT SUPPORTED])],
-          [OPAL_SUMMARY_ADD([[Miscellaneous]],[[PMIx support]], [opal_pmix], [$opal_external_pmix_version])])
+    AS_IF([test "$opal_external_pmix_happy" = "yes"],
+          [AS_IF([test "$opal_external_pmix_version" = "1x"],
+                 [OPAL_SUMMARY_ADD([[Miscellaneous]],[[PMIx support]], [opal_pmix], [External (1.2.5) WARNING - DYNAMIC OPS NOT SUPPORTED])],
+                 [OPAL_SUMMARY_ADD([[Miscellaneous]],[[PMIx support]], [opal_pmix], [External ($opal_external_pmix_version)])])],
+          [OPAL_SUMMARY_ADD([[Miscellaneous]], [[PMIx support]], [opal_pmix], [Internal])])
 
     OPAL_VAR_SCOPE_POP
 ])

config/opal_config_asm.m4

@@ -13,7 +13,7 @@ dnl Copyright (c) 2008-2018 Cisco Systems, Inc.  All rights reserved.
 dnl Copyright (c) 2010      Oracle and/or its affiliates.  All rights reserved.
 dnl Copyright (c) 2015-2017 Research Organization for Information Science
 dnl                         and Technology (RIST). All rights reserved.
-dnl Copyright (c) 2014-2017 Los Alamos National Security, LLC. All rights
+dnl Copyright (c) 2014-2018 Los Alamos National Security, LLC. All rights
 dnl                         reserved.
 dnl Copyright (c) 2017      Amazon.com, Inc. or its affiliates.  All Rights
 dnl                         reserved.
@@ -122,6 +122,57 @@ int main(int argc, char** argv)
 }
 ]])
 
+dnl This is a C test to see if 128-bit __atomic_compare_exchange_n()
+dnl actually works (e.g., it compiles and links successfully on
+dnl ARM64+clang, but returns incorrect answers as of August 2018).
+AC_DEFUN([OPAL_ATOMIC_COMPARE_EXCHANGE_STRONG_TEST_SOURCE],[[
+#include <stdint.h>
+#include <stdbool.h>
+#include <stdlib.h>
+#include <stdatomic.h>
+
+typedef union {
+    uint64_t fake@<:@2@:>@;
+    _Atomic __int128 real;
+} ompi128;
+
+static void test1(void)
+{
+    // As of Aug 2018, we could not figure out a way to assign 128-bit
+    // constants -- the compilers would not accept it.  So use a fake
+    // union to assign 2 uin64_t's to make a single __int128.
+    ompi128 ptr      = { .fake = { 0xFFEEDDCCBBAA0099, 0x8877665544332211 }};
+    ompi128 expected = { .fake = { 0x11EEDDCCBBAA0099, 0x88776655443322FF }};
+    ompi128 desired  = { .fake = { 0x1122DDCCBBAA0099, 0x887766554433EEFF }};
+    bool r = atomic_compare_exchange_strong (&ptr.real, &expected.real,
+                                             desired.real, true,
+					     atomic_relaxed, atomic_relaxed);
+    if ( !(r == false && ptr.real == expected.real)) {
+        exit(1);
+    }
+}
+
+static void test2(void)
+{
+    ompi128 ptr =      { .fake = { 0xFFEEDDCCBBAA0099, 0x8877665544332211 }};
+    ompi128 expected = ptr;
+    ompi128 desired =  { .fake = { 0x1122DDCCBBAA0099, 0x887766554433EEFF }};
+    bool r = atomic_compare_exchange_strong (&ptr.real, &expected.real,
+                                             desired.real, true,
+					     atomic_relaxed, atomic_relaxed);
+    if (!(r == true && ptr.real == desired.real)) {
+        exit(2);
+    }
+}
+
+int main(int argc, char** argv)
+{
+    test1();
+    test2();
+    return 0;
+}
+]])
+
 dnl ------------------------------------------------------------------
 
 dnl
@@ -329,6 +380,71 @@ __atomic_add_fetch(&tmp64, 1, __ATOMIC_RELAXED);],
   OPAL_CHECK_GCC_BUILTIN_CSWAP_INT128
 ])
 
+AC_DEFUN([OPAL_CHECK_C11_CSWAP_INT128], [
+  OPAL_VAR_SCOPE_PUSH([atomic_compare_exchange_result atomic_compare_exchange_CFLAGS_save atomic_compare_exchange_LIBS_save])
+
+  atomic_compare_exchange_CFLAGS_save=$CFLAGS
+  atomic_compare_exchange_LIBS_save=$LIBS
+
+  # Do we have C11 atomics on 128-bit integers?
+  # Use a special macro because we need to check with a few different
+  # CFLAGS/LIBS.
+  OPAL_ASM_CHECK_ATOMIC_FUNC([atomic_compare_exchange_strong_16],
+      [AC_LANG_SOURCE(OPAL_ATOMIC_COMPARE_EXCHANGE_STRONG_TEST_SOURCE)],
+      [atomic_compare_exchange_result=1],
+      [atomic_compare_exchange_result=0])
+
+  # If we have it and it works, check to make sure it is always lock
+  # free.
+  AS_IF([test $atomic_compare_exchange_result -eq 1],
+        [AC_MSG_CHECKING([if C11 __int128 atomic compare-and-swap is always lock-free])
+         AC_RUN_IFELSE([AC_LANG_PROGRAM([#include <stdatomic.h>], [_Atomic __int128_t x; if (!atomic_is_lock_free(&x)) { return 1; }])],
+              [AC_MSG_RESULT([yes])],
+              [atomic_compare_exchange_result=0
+               # If this test fails, need to reset CFLAGS/LIBS (the
+               # above tests atomically set CFLAGS/LIBS or not; this
+               # test is running after the fact, so we have to undo
+               # the side-effects of setting CFLAGS/LIBS if the above
+               # tests passed).
+               CFLAGS=$atomic_compare_exchange_CFLAGS_save
+               LIBS=$atomic_compare_exchange_LIBS_save
+               AC_MSG_RESULT([no])],
+              [AC_MSG_RESULT([cannot test -- assume yes (cross compiling)])])
+        ])
+
+  AC_DEFINE_UNQUOTED([OPAL_HAVE_C11_CSWAP_INT128],
+        [$atomic_compare_exchange_result],
+        [Whether C11 atomic compare swap is both supported and lock-free on 128-bit values])
+
+  dnl If we could not find decent support for 128-bits atomic let's
+  dnl try the GCC _sync
+  AS_IF([test $atomic_compare_exchange_result -eq 0],
+      [OPAL_CHECK_SYNC_BUILTIN_CSWAP_INT128])
+
+  OPAL_VAR_SCOPE_POP
+])
+
+AC_DEFUN([OPAL_CHECK_GCC_ATOMIC_BUILTINS], [
+  AC_MSG_CHECKING([for __atomic builtin atomics])
+
+  AC_TRY_LINK([
+#include <stdint.h>
+uint32_t tmp, old = 0;
+uint64_t tmp64, old64 = 0;], [
+__atomic_thread_fence(__ATOMIC_SEQ_CST);
+__atomic_compare_exchange_n(&tmp, &old, 1, 0, __ATOMIC_RELAXED, __ATOMIC_RELAXED);
+__atomic_add_fetch(&tmp, 1, __ATOMIC_RELAXED);
+__atomic_compare_exchange_n(&tmp64, &old64, 1, 0, __ATOMIC_RELAXED, __ATOMIC_RELAXED);
+__atomic_add_fetch(&tmp64, 1, __ATOMIC_RELAXED);],
+    [AC_MSG_RESULT([yes])
+     $1],
+    [AC_MSG_RESULT([no])
+     $2])
+
+  # Check for 128-bit support
+  OPAL_CHECK_GCC_BUILTIN_CSWAP_INT128
+])
+
 
 dnl #################################################################
 dnl
@@ -1020,17 +1136,27 @@ AC_DEFUN([OPAL_CONFIG_ASM],[
     AC_REQUIRE([OPAL_SETUP_CC])
     AC_REQUIRE([AM_PROG_AS])
 
+    AC_ARG_ENABLE([c11-atomics],[AC_HELP_STRING([--enable-c11-atomics],
+                  [Enable use of C11 atomics if available (default: enabled)])])
+
     AC_ARG_ENABLE([builtin-atomics],
       [AC_HELP_STRING([--enable-builtin-atomics],
-         [Enable use of __sync builtin atomics (default: enabled)])])
-
-    opal_cv_asm_builtin="BUILTIN_NO"
-    AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" != "no"],
-          [OPAL_CHECK_GCC_ATOMIC_BUILTINS([opal_cv_asm_builtin="BUILTIN_GCC"], [])])
-    AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" != "no"],
-          [OPAL_CHECK_SYNC_BUILTINS([opal_cv_asm_builtin="BUILTIN_SYNC"], [])])
-    AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" = "yes"],
-          [AC_MSG_ERROR([__sync builtin atomics requested but not found.])])
+         [Enable use of __sync builtin atomics (default: disabled)])])
+
+    OPAL_CHECK_C11_CSWAP_INT128
+
+    if test "x$enable_c11_atomics" != "xno" && test "$opal_cv_c11_supported" = "yes" ; then
+        opal_cv_asm_builtin="BUILTIN_C11"
+        OPAL_CHECK_C11_CSWAP_INT128
+    else
+        opal_cv_asm_builtin="BUILTIN_NO"
+        AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" = "yes"],
+              [OPAL_CHECK_GCC_ATOMIC_BUILTINS([opal_cv_asm_builtin="BUILTIN_GCC"], [])])
+        AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" = "yes"],
+              [OPAL_CHECK_SYNC_BUILTINS([opal_cv_asm_builtin="BUILTIN_SYNC"], [])])
+        AS_IF([test "$opal_cv_asm_builtin" = "BUILTIN_NO" && test "$enable_builtin_atomics" = "yes"],
+              [AC_MSG_ERROR([__sync builtin atomics requested but not found.])])
+    fi
 
         OPAL_CHECK_ASM_PROC
         OPAL_CHECK_ASM_TEXT

config/opal_config_subdir_args.m4

@@ -10,7 +10,7 @@ dnl Copyright (c) 2004-2005 High Performance Computing Center Stuttgart,
 dnl                         University of Stuttgart.  All rights reserved.
 dnl Copyright (c) 2004-2005 The Regents of the University of California.
 dnl                         All rights reserved.
-dnl Copyright (c) 2014-2015 Intel, Inc. All rights reserved.
+dnl Copyright (c) 2014-2018 Intel, Inc.  All rights reserved.
 dnl Copyright (c) 2015      Cisco Systems, Inc.  All rights reserved.
 dnl $COPYRIGHT$
 dnl
@@ -60,6 +60,8 @@ do
 	    ;;
 	-with-platform=* | --with-platform=*)
 	    ;;
+        -with*=internal)
+            ;;
 	*)
 	    case $subdir_arg in
 	    *\'*) subdir_arg=`echo "$subdir_arg" | sed "s/'/'\\\\\\\\''/g"` ;;

configure.ac

@@ -100,7 +100,7 @@ OPAL_VAR_SCOPE_POP
 #
 # Init automake
 #
-AM_INIT_AUTOMAKE([foreign dist-bzip2 subdir-objects no-define 1.12.2 tar-ustar])
+AM_INIT_AUTOMAKE([foreign dist-bzip2 subdir-objects no-define 1.13.4 tar-ustar])
 
 # SILENT_RULES is new in AM 1.11, but we require 1.11 or higher via
 # autogen.  Limited testing shows that calling SILENT_RULES directly
@@ -858,7 +858,7 @@ OPAL_SEARCH_LIBS_CORE([ceil], [m])
 # -lrt might be needed for clock_gettime
 OPAL_SEARCH_LIBS_CORE([clock_gettime], [rt])
 
-AC_CHECK_FUNCS([asprintf snprintf vasprintf vsnprintf openpty isatty getpwuid fork waitpid execve pipe ptsname setsid mmap tcgetpgrp posix_memalign strsignal sysconf syslog vsyslog regcmp regexec regfree _NSGetEnviron socketpair strncpy_s usleep mkfifo dbopen dbm_open statfs statvfs setpgid setenv __malloc_initialize_hook __clear_cache])
+AC_CHECK_FUNCS([asprintf snprintf vasprintf vsnprintf openpty isatty getpwuid fork waitpid execve pipe ptsname setsid mmap tcgetpgrp posix_memalign strsignal sysconf syslog vsyslog regcmp regexec regfree _NSGetEnviron socketpair usleep mkfifo dbopen dbm_open statfs statvfs setpgid setenv __malloc_initialize_hook __clear_cache])
 
 # Sanity check: ensure that we got at least one of statfs or statvfs.
 if test $ac_cv_func_statfs = no && test $ac_cv_func_statvfs = no; then

contrib/Makefile.am

@@ -88,12 +88,8 @@ EXTRA_DIST = \
         platform/lanl/darwin/mic-common \
         platform/lanl/darwin/debug \
         platform/lanl/darwin/debug.conf \
-        platform/lanl/darwin/debug-mic \
-        platform/lanl/darwin/debug-mic.conf \
         platform/lanl/darwin/optimized \
         platform/lanl/darwin/optimized.conf \
-        platform/lanl/darwin/optimized-mic \
-        platform/lanl/darwin/optimized-mic.conf \
 	platform/snl/portals4-m5 \
 	platform/snl/portals4-orte \
 	platform/ibm/debug-ppc32-gcc \