fix incorrect merge with upstream

java: try do dlopen libmpi with the full path

Since OS X 10.11 (aka El Capitan) DYLD_LIBRARY_PATH is no more
propagated to children, so try to dlopen libmpi with the full path
using the directory of libmpi_java

Fixes open-mpi#1220

Thanks Alexander Daryin for reporting this

Update symbol-hiding script

btl/sm: rename file after file descriptor has been closed.

Thanks George for spotting this.

Author: annu13

config/ompi_setup_java.m4

@@ -74,6 +74,9 @@ AC_DEFUN([OMPI_SETUP_JAVA_BINDINGS],[
         # header file needs this file, so we need to check for
         # it/include it in our sources when compiling on Mac).
         AC_CHECK_HEADERS([TargetConditionals.h])
+
+        # dladdr and Dl_info are required to build the full path to libmpi on OS X 10.11 aka El Capitan
+        AC_CHECK_TYPES([Dl_info], [], [], [[#include <dlfcn.h>]])
     else
         AC_MSG_RESULT([no])
         WANT_MPI_JAVA_SUPPORT=0

contrib/symbol-hiding.pl

@@ -12,6 +12,7 @@
 my $mylib;
 my $myprefix;
 my $mysuffix;
+my $mycapprefix;
 
 # Set to true if the script should merely check for symbols in
 # the library that are not in the provided output file - useful
@@ -63,6 +64,8 @@ sub quiet_print {
 
 #-------------------------------------------------------------------------------
 
+$mycapprefix = uc $myprefix;
+
 # get the symbol output for this lib
 my $output = qx(nm $mylib);
 
@@ -84,8 +87,7 @@ sub quiet_print {
     # next token indicates a public symbol by
     # being a 'T' or a 'B'
     $val = shift(@values);
-    if ("T" eq $val || "B" eq $val || "D" eq $val ||
-        "t" eq $val || "b" eq $val || "d" eq $val) {
+    if ("T" eq $val || "B" eq $val || "D" eq $val) {
         $val = shift(@values);
         # if this symbol contains a '.', then we
         # need to ignore it
@@ -105,10 +107,24 @@ sub quiet_print {
 if ($myfile ne "") {
     open FILE, ">$myfile" || die "file could not be opened";
 }
+sub checkCase {
+    if ($_[0] =~ /^[[:upper:]]/) {
+        return 1;
+    }
+    else {
+        return 0;
+    }
+}
+
 foreach my $sym (@symbols) {
     my $out;
     if ($REVERSE) {
-        $out = "#define " . $myprefix . $sym . $mysuffix;
+        # if the first char is a cap, then use the cap prefix
+        if (checkCase($sym)) {
+            $out = "#define " . $mycapprefix . $sym . $mysuffix;
+        } else {
+            $out = "#define " . $myprefix . $sym . $mysuffix;
+        }
     } else {
         $out = "#define " . $sym;
     }
@@ -119,7 +135,12 @@ sub quiet_print {
     if ($REVERSE) {
         $out = $out . $sym . "\n";
     } else {
-        $out = $out . $myprefix . $sym . $mysuffix . "\n";
+        # if the first char is a cap, then use the cap prefix
+        if (checkCase($sym)) {
+            $out = $out . $mycapprefix . $sym . $mysuffix . "\n";
+        } else {
+            $out = $out . $myprefix . $sym . $mysuffix . "\n";
+        }
     }
     if ($myfile ne "") {
         print FILE $out;

ompi/mpi/java/c/Makefile.am

@@ -1,9 +1,11 @@
 # -*- makefile -*-
 #
 # Copyright (c) 2011-2013 Cisco Systems, Inc.  All rights reserved.
-# Copyright (c) 2012	Oracle and/or its affiliates.  All rights reserved.
+# Copyright (c) 2012      Oracle and/or its affiliates.  All rights reserved.
 # Copyright (c) 2015      Los Alamos National Security, LLC. All rights
 #                         reserved.
+# Copyright (c) 2015      Research Organization for Information Science
+#                         and Technology (RIST). All rights reserved.
 # $COPYRIGHT$
 #
 # Additional copyrights may follow
@@ -44,7 +46,7 @@ libmpi_java_la_SOURCES = \
 	mpi_Status.c \
 	mpi_Win.c
 
-libmpi_java_la_LIBADD = $(top_builddir)/ompi/libmpi.la
+libmpi_java_la_LIBADD = -ldl $(top_builddir)/ompi/libmpi.la
 libmpi_java_la_LDFLAGS = -version-info $(libmpi_java_so_version)
 
 endif

ompi/mpi/java/c/mpi_MPI.c

@@ -14,6 +14,8 @@
  *                         reserved.
  * Copyright (c) 2015      Cisco Systems, Inc.  All rights reserved.
  * Copyright (c) 2015      Intel, Inc. All rights reserved.
+ * Copyright (c) 2015      Research Organization for Information Science
+ *                         and Technology (RIST). All rights reserved.
  * $COPYRIGHT$
  *
  * Additional copyrights may follow
@@ -62,8 +64,13 @@
 #ifdef HAVE_SYS_STAT_H
 #include <sys/stat.h>
 #endif
+#ifdef HAVE_DLFCN_H
 #include <dlfcn.h>
+#endif
 #include <poll.h>
+#ifdef HAVE_LIBGEN_H
+#include <libgen.h>
+#endif
 
 #include "opal/util/output.h"
 #include "opal/datatype/opal_convertor.h"
@@ -126,7 +133,27 @@ jint JNI_OnLoad(JavaVM *vm, void *reserved)
 {
     libmpi = dlopen("libmpi." OPAL_DYN_LIB_SUFFIX, RTLD_NOW | RTLD_GLOBAL);
 
-    if(libmpi == NULL)
+#if defined(HAVE_DL_INFO) && defined(HAVE_LIBGEN_H)
+    /*
+     * OS X El Capitan does not propagate DYLD_LIBRARY_PATH to children any more
+     * so if previous dlopen failed, try to open libmpi in the same directory
+     * than the current libmpi_java
+     */
+    if(NULL == libmpi) {
+        Dl_info info;
+        if(0 != dladdr((void *)JNI_OnLoad, &info)) {
+            char libmpipath[OPAL_PATH_MAX];
+            char *libmpijavapath = strdup(info.dli_fname);
+            if (NULL != libmpijavapath) {
+                snprintf(libmpipath, OPAL_PATH_MAX-1, "%s/libmpi." OPAL_DYN_LIB_SUFFIX, dirname(libmpijavapath));
+                free(libmpijavapath);
+                libmpi = dlopen(libmpipath, RTLD_NOW | RTLD_GLOBAL);
+            }
+        }
+    }
+#endif
+
+    if(NULL == libmpi)
     {
         fprintf(stderr, "Java bindings failed to load libmpi: %s\n",dlerror());
         exit(1);

opal/mca/btl/sm/btl_sm_component.c

@@ -696,6 +696,8 @@ create_rndv_file(mca_btl_sm_component_t *comp_ptr,
         /* only do this for the mpool case */
         OBJ_RELEASE(tmp_modp);
     }
+    (void)close(fd);
+    fd = -1;
     if (0 != rename(tmpfname, fname)) {
         rc = OPAL_ERR_IN_ERRNO;
         goto out;

orte/mca/ess/base/ess_base_std_orted.c

@@ -510,77 +510,6 @@ int orte_ess_base_orted_setup(char **hosts)
             goto error;
         }
     }
-    /* setup the global job and node arrays */
-    orte_job_data = OBJ_NEW(opal_pointer_array_t);
-    if (ORTE_SUCCESS != (ret = opal_pointer_array_init(orte_job_data,
-                                                       1,
-                                                       ORTE_GLOBAL_ARRAY_MAX_SIZE,
-                                                       1))) {
-        ORTE_ERROR_LOG(ret);
-        error = "setup job array";
-        goto error;
-    }
-    orte_node_pool = OBJ_NEW(opal_pointer_array_t);
-    if (ORTE_SUCCESS != (ret = opal_pointer_array_init(orte_node_pool,
-                                                       ORTE_GLOBAL_ARRAY_BLOCK_SIZE,
-                                                       ORTE_GLOBAL_ARRAY_MAX_SIZE,
-                                                       ORTE_GLOBAL_ARRAY_BLOCK_SIZE))) {
-        ORTE_ERROR_LOG(ret);
-        error = "setup node array";
-        goto error;
-    }
-    orte_node_topologies = OBJ_NEW(opal_pointer_array_t);
-    if (ORTE_SUCCESS != (ret = opal_pointer_array_init(orte_node_topologies,
-                                                       ORTE_GLOBAL_ARRAY_BLOCK_SIZE,
-                                                       ORTE_GLOBAL_ARRAY_MAX_SIZE,
-                                                       ORTE_GLOBAL_ARRAY_BLOCK_SIZE))) {
-        ORTE_ERROR_LOG(ret);
-        error = "setup node topologies array";
-        goto error;
-    }
-    /* Setup the job data object for the daemons */
-    /* create and store the job data object */
-    jdata = OBJ_NEW(orte_job_t);
-    jdata->jobid = ORTE_PROC_MY_NAME->jobid;
-    opal_pointer_array_set_item(orte_job_data, 0, jdata);
-    /* every job requires at least one app */
-    app = OBJ_NEW(orte_app_context_t);
-    opal_pointer_array_set_item(jdata->apps, 0, app);
-    jdata->num_apps++;
-    /* create and store a node object where we are */
-    node = OBJ_NEW(orte_node_t);
-    node->name = strdup(orte_process_info.nodename);
-    node->index = opal_pointer_array_set_item(orte_node_pool, ORTE_PROC_MY_NAME->vpid, node);
-    /* point our topology to the one detected locally */
-    node->topology = opal_hwloc_topology;
-
-    /* create and store a proc object for us */
-    proc = OBJ_NEW(orte_proc_t);
-    proc->name.jobid = ORTE_PROC_MY_NAME->jobid;
-    proc->name.vpid = ORTE_PROC_MY_NAME->vpid;
-    proc->pid = orte_process_info.pid;
-    proc->rml_uri = orte_rml.get_contact_info();
-    proc->state = ORTE_PROC_STATE_RUNNING;
-    opal_pointer_array_set_item(jdata->procs, proc->name.vpid, proc);
-    /* record that the daemon (i.e., us) is on this node
-     * NOTE: we do not add the proc object to the node's
-     * proc array because we are not an application proc.
-     * Instead, we record it in the daemon field of the
-     * node object
-     */
-    OBJ_RETAIN(proc);   /* keep accounting straight */
-    node->daemon = proc;
-    ORTE_FLAG_SET(node, ORTE_NODE_FLAG_DAEMON_LAUNCHED);
-    node->state = ORTE_NODE_STATE_UP;
-    /* now point our proc node field to the node */
-    OBJ_RETAIN(node);   /* keep accounting straight */
-    proc->node = node;
-    /* record that the daemon job is running */
-    jdata->num_procs = 1;
-    jdata->state = ORTE_JOB_STATE_RUNNING;
-    /* obviously, we have "reported" */
-    jdata->num_reported = 1;
-
     /* setup the PMIx framework - ensure it skips all non-PMIx components,
      * but do not override anything we were given */
     opal_setenv("OMPI_MCA_pmix", "^s1,s2,cray", false, &environ);