Merge pull request #7026 from raffenet/4.2.x-fixes

[4.2.x] backport fixes for upcoming 4.2.2

autogen.sh

@@ -237,12 +237,23 @@ set_externals() {
 check_python3() {
     echo_n "Checking for Python 3... "
     PYTHON=
-    if test 3 = `python -c 'import sys; print(sys.version_info[0])' 2> /dev/null || echo "0"`; then
-        PYTHON=python
-    fi
 
-    if test -z "$PYTHON" -a 3 = `python3 -c 'import sys; print(sys.version_info[0])' 2> /dev/null || echo "0"`; then
-        PYTHON=python3
+    python_one_liner="import sys; print(sys.version_info[0])"
+    PYTHON_PATH=`command -v python`
+    if test "x$PYTHON_PATH" != x ; then
+        version=`$PYTHON_PATH -c "$python_one_liner"`
+        if test "$version" = 3 ; then
+            PYTHON=$PYTHON_PATH
+        fi
+    fi
+    if test "x$PYTHON" = x ; then
+        PYTHON_PATH=`command -v python3`
+        if test "x$PYTHON_PATH" != x ; then
+            version=`$PYTHON_PATH -c "$python_one_liner"`
+            if test "$version" = 3 ; then
+                PYTHON=$PYTHON_PATH
+            fi
+        fi
     fi
 
     if test -z "$PYTHON" ; then

confdb/aclocal_misc.m4

@@ -3,17 +3,33 @@ dnl
 AC_DEFUN([PAC_CHECK_PYTHON],[
     AC_ARG_VAR([PYTHON], [set to Python 3])
     if test -z "$PYTHON" ; then
-        AC_MSG_CHECKING([Python 3])
         PYTHON=
         python_one_liner="import sys; print(sys.version_info[[0]])"
-        if test 3 = `python -c "$python_one_liner"`; then
-            PYTHON=python
-        elif test 3 = `python3 -c "$python_one_liner"`; then
-            PYTHON=python3
+
+        dnl check command 'python'
+        PYTHON_PATH=
+        AC_PATH_PROG(PYTHON_PATH, python)
+        if test "x$PYTHON_PATH" != x ; then
+            py_version=`$PYTHON_PATH -c "$python_one_liner"`
+            if test "x$py_version" = x3 ; then
+                PYTHON=$PYTHON_PATH
+            fi
+        fi
+        dnl PYTHON is still not set, check command 'python3'
+        if test "x$PYTHON" = x ; then
+            PYTHON3_PATH=
+            AC_PATH_PROG(PYTHON3_PATH, python3)
+            if test "x$PYTHON3_PATH" != x ; then
+                py3_version=`$PYTHON3_PATH -c "$python_one_liner"`
+                if test "x$py3_version" = x3 ; then
+                    PYTHON=$PYTHON3_PATH
+                fi
+            fi
         fi
-        AC_MSG_RESULT($PYTHON)
         if test -z "$PYTHON" ; then
-            AC_MSG_WARN([Python 3 not found! Bindings need to be generated before configure.])
+            AC_MSG_WARN([Python version 3 not found! Bindings need to be generated before configure.])
+        else
+            AC_MSG_NOTICE([Python version 3 is $PYTHON])
         fi
     fi
 ])

configure.ac

@@ -626,7 +626,6 @@ AC_CANONICAL_TARGET
 # We also need to do this before the F77 and FC test to ensure that we
 # find the C preprocessor reliably.
 AC_PROG_CC
-AC_PROG_CC_C99
 AM_PROG_CC_C_O dnl needed for automake "silent-rules"
 PAC_PUSH_FLAG([CFLAGS])
 AC_PROG_CPP

maint/fcrosscompile/configure.ac

@@ -12,7 +12,6 @@ AC_ARG_WITH(aint-size,
 
 AC_PROG_CPP
 AC_PROG_CC
-AC_PROG_CC_C99
 AC_CHECK_SIZEOF([char])
 AC_CHECK_SIZEOF([short])
 AC_CHECK_SIZEOF([int])

maint/local_python/binding_f08.py

@@ -322,7 +322,12 @@ def process_index(p):
         if p['param_direction'] == 'in' or p['param_direction'] == 'inout':
             convert_list_pre.append("%s = %s - 1" % (arg, p['name']))
         if p['param_direction'] == 'out' or p['param_direction'] == 'inout':
-            convert_list_post.append("%s = %s + 1" % (p['name'], arg))
+            uses['MPI_UNDEFINED'] = 1
+            convert_list_post.append("IF (%s == MPI_UNDEFINED) THEN" % arg)
+            convert_list_post.append("    %s = %s" % (p['name'], arg))
+            convert_list_post.append("ELSE")
+            convert_list_post.append("    %s = %s + 1" % (p['name'], arg))
+            convert_list_post.append("END IF")
         return (arg, arg)
 
     def process_string(p):

src/mpi/romio/adio/common/flatten.c

@@ -182,6 +182,9 @@ static void flatlist_node_grow(ADIOI_Flatlist_node * flat, int idx)
     }
 }
 
+static MPI_Count ADIOI_Count_contiguous_blocks(MPI_Datatype datatype, MPI_Count * curr_index);
+static void ADIOI_Flatten(MPI_Datatype datatype, ADIOI_Flatlist_node * flat,
+                          ADIO_Offset st_offset, MPI_Count * curr_index);
 static void ADIOI_Optimize_flattened(ADIOI_Flatlist_node * flat_type);
 /* flatten datatype and add it to Flatlist */
 static ADIOI_Flatlist_node *ADIOI_Flatten_datatype(MPI_Datatype datatype)

src/mpi/romio/configure.ac

@@ -31,7 +31,6 @@ AM_MAINTAINER_MODE([enable])
 
 dnl must come before LT_INIT, which AC_REQUIREs AC_PROG_CC
 AC_PROG_CC
-AC_PROG_CC_C99
 AM_PROG_CC_C_O
 PAC_CHECK_VISIBILITY
 AC_SUBST(VISIBILITY_CFLAGS)

src/mpid/ch4/netmod/ofi/init_settings.c

@@ -187,7 +187,9 @@ int MPIDI_OFI_init_hints(struct fi_info *hints)
         }
     }
     hints->tx_attr->op_flags = FI_COMPLETION;
+    /* apply SAS hint to both tx and rx or else ordering may not be guaranteed */
     hints->tx_attr->msg_order = FI_ORDER_SAS;
+    hints->rx_attr->msg_order = FI_ORDER_SAS;
     /* direct RMA operations supported only with delivery complete mode,
      * else (AM mode) delivery complete is not required */
     if (MPIDI_OFI_ENABLE_RMA || MPIDI_OFI_ENABLE_ATOMICS) {

src/mpid/ch4/netmod/ofi/ofi_nic.c

@@ -80,18 +80,22 @@ bool MPIDI_OFI_nic_already_used(const struct fi_info * prov, struct fi_info ** o
 
 /* Setup the multi-NIC data structures to use the fi_info structure given in prov */
 static int setup_single_nic(void);
+#ifdef HAVE_LIBFABRIC_NIC
 static int setup_multi_nic(int nic_count);
+#endif
 
 int MPIDI_OFI_init_multi_nic(struct fi_info *prov)
 {
     int mpi_errno = MPI_SUCCESS;
     int nic_count = 0;
-    int max_nics = MPIR_CVAR_CH4_OFI_MAX_NICS;
 
+#ifdef HAVE_LIBFABRIC_NIC
+    int max_nics = MPIR_CVAR_CH4_OFI_MAX_NICS;
     if (MPIR_CVAR_CH4_OFI_MAX_NICS == 0 || MPIR_CVAR_CH4_OFI_MAX_NICS <= -2) {
         /* Invalid values for the CVAR will default to single nic */
         max_nics = 1;
     }
+#endif
 
     /* Count the number of NICs */
     struct fi_info *first_prov = NULL;

src/mpid/ch4/src/mpidig_win.h

@@ -537,7 +537,7 @@ MPL_STATIC_INLINE_PREFIX int MPIDIG_mpi_win_fence(int massert, MPIR_Win * win)
 MPL_STATIC_INLINE_PREFIX int MPIDIG_win_shared_query_self(MPIR_Win * win, int rank, MPI_Aint * size,
                                                           int *disp_unit, void *baseptr)
 {
-    if (rank == win->comm_ptr->rank) {
+    if (rank == win->comm_ptr->rank || (rank == MPI_PROC_NULL && win->comm_ptr->local_size == 1)) {
         *size = win->size;
         *disp_unit = win->disp_unit;
         *((void **) baseptr) = win->base;

src/mpl/configure.ac

@@ -16,7 +16,6 @@ AM_INIT_AUTOMAKE([subdir-objects] [-Wall -Werror foreign 1.12.3])
 
 dnl must come before LT_INIT, which AC_REQUIREs AC_PROG_CC
 AC_PROG_CC
-AC_PROG_CC_C99
 AM_PROG_CC_C_O
 
 AC_USE_SYSTEM_EXTENSIONS

src/mpl/src/sock/mpl_host.c

@@ -11,15 +11,24 @@
 #define MAX_HOSTNAME_LEN MAXHOSTNAMELEN
 #endif
 
+/* we use a static array here to avoid cleaning up (e.g. with uthash) */
 #define MAX_LOCAL_HOSTNAMES  (100)
 static char lhost[MAX_LOCAL_HOSTNAMES][MAX_HOSTNAME_LEN];
 static int lhost_count = 0;
 
 static void append_lhost(const char *host)
 {
-    int i;
+    if (lhost_count == MAX_LOCAL_HOSTNAMES) {
+        /* For the rare case when there are more than 100 local IP
+         * addresses, we only check against the first 100.
+         *
+         * MPL_host_is_local is only used in Hydra, and it is not
+         * fatal to miss some localhost detections.
+         */
+        return;
+    }
 
-    for (i = 0; i < lhost_count; i++)
+    for (int i = 0; i < lhost_count; i++)
         if (!strcmp(lhost[i], host))
             return;
 

src/pm/hydra/configure.ac

@@ -21,7 +21,6 @@ AC_ARG_PROGRAM
 dnl must come before LT_INIT, which AC_REQUIREs AC_PROG_CC
 dnl must also come before AC_USE_SYSTEM_EXTENSIONS
 AC_PROG_CC
-AC_PROG_CC_C99
 AM_PROG_CC_C_O
 
 # also needed by hwloc in embedded mode, must also come early for expansion

src/pm/hydra/lib/tools/bootstrap/external/ll.h

@@ -15,6 +15,6 @@ HYD_status HYDT_bscd_ll_launch_procs(char **args, struct HYD_proxy *proxy_list,
 HYD_status HYDT_bscd_ll_query_proxy_id(int *proxy_id);
 HYD_status HYDT_bscd_ll_query_native_int(int *ret);
 HYD_status HYDT_bscd_ll_query_node_list(struct HYD_node **node_list);
-HYD_status HYDT_bscd_ll_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_ll_query_env_inherit(const char *env_name, int *should_inherit);
 
 #endif /* LL_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/ll_env.c

@@ -7,7 +7,7 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_ll_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_ll_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "LOADL_STEP_CLASS", "LOADL_STEP_ARGS",
         "LOADL_STEP_ID", "LOADL_STARTD_PORT",
@@ -49,7 +49,7 @@ HYD_status HYDT_bscd_ll_query_env_inherit(const char *env_name, int *ret)
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();
 

src/pm/hydra/lib/tools/bootstrap/external/lsf.h

@@ -10,6 +10,6 @@
 
 HYD_status HYDT_bscd_lsf_query_native_int(int *ret);
 HYD_status HYDT_bscd_lsf_query_node_list(struct HYD_node **node_list);
-HYD_status HYDT_bscd_lsf_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_lsf_query_env_inherit(const char *env_name, int *should_inherit);
 
 #endif /* LSF_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/lsf_env.c

@@ -7,7 +7,7 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_lsf_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_lsf_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "DISPLAY", "EGO_SERVERDIR", "LSB_TRAPSIGS",
         "LSF_SERVERDIR", "HOSTTYPE", "LSB_HOSTS",
@@ -30,7 +30,7 @@ HYD_status HYDT_bscd_lsf_query_env_inherit(const char *env_name, int *ret)
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();
 

src/pm/hydra/lib/tools/bootstrap/external/pbs.h

@@ -21,7 +21,7 @@ extern struct HYDT_bscd_pbs_sys_s *HYDT_bscd_pbs_sys;
 
 HYD_status HYDT_bscd_pbs_launch_procs(char **args, struct HYD_proxy *proxy_list, int num_hosts,
                                       int use_rmk, int *control_fd);
-HYD_status HYDT_bscd_pbs_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_pbs_query_env_inherit(const char *env_name, int *should_inherit);
 HYD_status HYDT_bscd_pbs_wait_for_completion(int timeout);
 HYD_status HYDT_bscd_pbs_launcher_finalize(void);
 #endif /* if defined(HAVE_TM_H) */

src/pm/hydra/lib/tools/bootstrap/external/pbs_env.c

@@ -7,7 +7,7 @@
 #include "common.h"
 #include "pbs.h"
 
-HYD_status HYDT_bscd_pbs_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_pbs_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "PBSCOREDUMP",
         "PBSDEBUG",
@@ -47,7 +47,7 @@ HYD_status HYDT_bscd_pbs_query_env_inherit(const char *env_name, int *ret)
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();
 

src/pm/hydra/lib/tools/bootstrap/external/rsh.h

@@ -8,6 +8,6 @@
 
 #include "hydra.h"
 
-HYD_status HYDT_bscd_rsh_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_rsh_query_env_inherit(const char *env_name, int *should_inherit);
 
 #endif /* RSH_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/rsh_env.c

@@ -7,13 +7,13 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_rsh_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_rsh_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "DISPLAY", NULL };
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();
 

src/pm/hydra/lib/tools/bootstrap/external/sge.h

@@ -10,6 +10,6 @@
 
 HYD_status HYDT_bscd_sge_query_native_int(int *ret);
 HYD_status HYDT_bscd_sge_query_node_list(struct HYD_node **node_list);
-HYD_status HYDT_bscd_sge_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_sge_query_env_inherit(const char *env_name, int *should_inherit);
 
 #endif /* SGE_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/sge_env.c

@@ -7,7 +7,7 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_sge_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_sge_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "DISPLAY", "SGE_ROOT", "SGE_CELL", "SGE_DEBUG_LEVEL",
         "SGE_QMASTER_PORT", "SGE_O_HOME", "SGE_O_HOST",
@@ -26,7 +26,7 @@ HYD_status HYDT_bscd_sge_query_env_inherit(const char *env_name, int *ret)
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();
 

src/pm/hydra/lib/tools/bootstrap/external/slurm.h

@@ -13,6 +13,6 @@ HYD_status HYDT_bscd_slurm_launch_procs(char **args, struct HYD_proxy *proxy_lis
 HYD_status HYDT_bscd_slurm_query_proxy_id(int *proxy_id);
 HYD_status HYDT_bscd_slurm_query_native_int(int *ret);
 HYD_status HYDT_bscd_slurm_query_node_list(struct HYD_node **node_list);
-HYD_status HYDT_bscd_slurm_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_slurm_query_env_inherit(const char *env_name, int *should_inherit);
 
 #endif /* SLURM_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/slurm_env.c

@@ -7,16 +7,16 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_slurm_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_slurm_query_env_inherit(const char *env_name, int *should_inherit)
 {
     HYDU_FUNC_ENTER();
 
     /* check if envvar starts with SBATCH_, SLURMD_, or SLURM_ */
     if (strncmp(env_name, "SBATCH_", 7) == 0 || strncmp(env_name, "SLURMD_", 7) == 0 ||
         strncmp(env_name, "SLURM_", 6) == 0) {
-        *ret = 1;
+        *should_inherit = 0;
     } else {
-        *ret = 0;
+        *should_inherit = 1;
     }
 
     HYDU_FUNC_EXIT();

src/pm/hydra/lib/tools/bootstrap/external/ssh.h

@@ -32,7 +32,7 @@ extern struct HYDT_bscd_ssh_time *HYDT_bscd_ssh_time;
 
 HYD_status HYDTI_bscd_ssh_store_launch_time(char *hostname);
 
-HYD_status HYDT_bscd_ssh_query_env_inherit(const char *env_name, int *ret);
+HYD_status HYDT_bscd_ssh_query_env_inherit(const char *env_name, int *should_inherit);
 HYD_status HYDT_bscd_ssh_launcher_finalize(void);
 
 #endif /* SSH_H_INCLUDED */

src/pm/hydra/lib/tools/bootstrap/external/ssh_env.c

@@ -7,13 +7,13 @@
 #include "bsci.h"
 #include "common.h"
 
-HYD_status HYDT_bscd_ssh_query_env_inherit(const char *env_name, int *ret)
+HYD_status HYDT_bscd_ssh_query_env_inherit(const char *env_name, int *should_inherit)
 {
     const char *env_list[] = { "DISPLAY", NULL };
 
     HYDU_FUNC_ENTER();
 
-    *ret = !HYDTI_bscd_in_env_list(env_name, env_list);
+    *should_inherit = !HYDTI_bscd_in_env_list(env_name, env_list);
 
     HYDU_FUNC_EXIT();