bug fixes, cleanup, doc update, etc. Refer to ChangeLog for full list.

Author: Gregory L. Lee

ChangeLog

@@ -1,3 +1,29 @@
+2013-02-15 Gregory L. Lee <[email protected]>
+	* src/STAT_FrontEnd.C : need to strdup remoteNode into proctab for serial attach
+	* doc/src/* : updated documentation
+
+2013-02-08 Gregory L. Lee <[email protected]>
+	* src/STAT_FrontEnd.C : added STAT_FE_HOSTNAME env variable
+	* scripts/*.in : check for [STAT|LMON|MRNET]_PREFIX env vars and adjust	paths accordingly
+	* config/x_ac_debuglibs.m4 : added --enable-[libdwarf|stackwalker|-rpm to look for includes/libs in /usr
+
+2013-01-30 Gregory L. Lee <[email protected]>
+	* src/STAT_FrontEnd.C : use std::string instead of char * for topo generation
+	* : Fixed memory leaks, dead code, etc. identified by Intel's Static Security Analysis Tool
+
+2013-01-30 Gregory L. Lee <[email protected]>
+	* scripts/STATGUI.py : clear proctab on detach
+	* : MRNet 3.0 and MRNet 3.1 backwards compatibility fixes
+	* : StackWalker 8.0 and 2.0 backwards compatibility fixes
+	* src/STAT_GraphRoutines.[C,h], src/STAT_BackEnd.[C,h] : fixed count+rep graph (need to translate daemon-local rank to MPI rank)
+
+2013-01-29 Gregory L. Lee <[email protected]>
+	* : Fixed some memory leaks identified by Inspector
+	* src/STAT_BackEnd.C : fixed Python truncating of "[call|fast]_function"
+
+2013-01-28 Gregory L. Lee <[email protected]>
+	* src/STAT_GraphRoutines.C : fixed handling of function tables when	previously allocated
+
 2013-01-22 Gregory L. Lee <[email protected]>
 	* : code clean up
 	* src/STAT_BackEnd.C : fixed Python offset caching

Doxyfile

@@ -23,7 +23,7 @@ PROJECT_NAME           = STAT
 # This could be handy for archiving the generated documentation or 
 # if some version control system is used.
 
-PROJECT_NUMBER         = 1.0
+PROJECT_NUMBER         = 2.0.0
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
 # base path where the generated documentation will be put. 
@@ -459,7 +459,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = src/STAT_FrontEnd.h src/STAT_FrontEnd.C src/STAT.h src/STAT_BackEnd.h src/STAT_BackEnd.C src/STAT_FilterDefinitions.C src/STAT.C src/STATD.C src/STATBench.C src/STATBenchD.C scripts/STATview.py scripts/STATGUI.py doc/src/mainpage
+INPUT                  = src/STAT_FrontEnd.h src/STAT_FrontEnd.C src/STAT.h src/STAT_BackEnd.h src/STAT_BackEnd.C src/STAT_FilterDefinitions.C src/STAT.C src/STATD.C src/STATBench.C src/STATBenchD.C src/STAT_merge.C src/STAT_GraphRoutines.h src/STAT_GraphRoutines.C scripts/STAThelper.py scripts/STATmerge.py scripts/STATview.py scripts/STATGUI.py doc/src/mainpage
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 

INSTALL

@@ -59,24 +59,32 @@ Installation
    within the stat-gui script. To disable the building of the GUI,
    use the --enable-gui=no configure option.
 
-   On BlueGene systems, also be sure to configure --with-bluegene.
-   This will enable the BGL macro for BlueGene specific
-   compilation. Similarly, to compile on Cray XT systems, specify
-   --with-cray-xt.
+   To compile on Cray systems, specify --with-cray-xt. On BlueGene
+   systems, also be sure to configure --with-bluegene. This will
+   enable the BGL macro for BlueGene specific compilation. It is
+   important to note that on BlueGene systems, you may need to use
+   an alternate hostname for the front-end node in order to get
+   MRNet to bind to the appropriate network interface that can
+   communicate with the I/O nodes. By default, STAT will append
+   "-io" to the hostname. Alternatively, you can specify the
+   hostname with the STAT_FE_HOSTNAME environment variable.
 
-   An example configure line for Cray XT:
+   An example configure line for Cray:
 
 ./configure --with-launchmon=/tmp/work/lee218/install \
 --with-mrnet=/tmp/work/lee218/install \
 --with-graphlib==/tmp/work/lee218/install \
 --with-stackwalker=/tmp/work/lee218/install \
 --with-libdwarf=/tmp/work/lee218/install \
 --prefix=/tmp/work/lee218/install --with-cray-xt \
-MPICC=cc MPICXX=CC MPIF77=ftn --enable-shared LD=/usr/bin/ld.x
+MPICC=cc MPICXX=CC MPIF77=ftn --enable-shared LD=/usr/bin/ld
 
-   Note that specifying LD=/usr/bin/ld.x is only advised on Cray
-   systems, as doing so on other systems may inhibit the abililty
-   to generate shared libraries. Next you just need to run:
+   Note that specifying LD=/usr/bin/ld may be required on Cray
+   systems to avoid using the compute node linker. It is also
+   worth noting that Cray includes a build of STAT as part of
+   their system software stack. It is typically installed in
+   /opt/cray/stat and can be loaded via modules. After running
+   configure you just need to run:
 
 make
 make install
@@ -89,4 +97,8 @@ make install
    components can, however, be overridden with the --daemon and
    --filter arguments. Further, the STAT_PREFIX environment
    variable can be defined to override the hardcoded paths in
-   STAT.
+   STAT. STAT will also, by default, add rpaths to dependent
+   libraries. This behavior can be disabled by specifying
+   "--with-rpath=no". However, when doing so, you must be sure to
+   set LD_LIBRARY_PATH to point to the directories containing the
+   dependent libraries.

config/x_ac_debuglibs.m4

@@ -1,4 +1,18 @@
 AC_DEFUN([X_AC_DEBUGLIBS], [
+
+  AC_ARG_ENABLE(stackwalker-rpm,
+    [AS_HELP_STRING([--enable-stackwalker-rpm],[Enable the use of rpm-installed stackwalker, default=no])],
+    [CXXFLAGS="$CXXFLAGS -I/usr/include/dyninst"
+     LDFLAGS="$LDFLAGS -L/usr/lib64/dyninst"
+     RPATH_FLAGS="$RPATH_FLAGS -Wl,-rpath=/usr/lib64/dyninst"],
+    [CXXFLAGS="$CXXFLAGS"]
+  )  
+  AC_ARG_ENABLE(libdwarf-rpm,
+    [AS_HELP_STRING([--enable-libdwarf-rpm],[Enable the use of rpm-installed libdwarf, default=no])],
+    [CXXFLAGS="$CXXFLAGS -I/usr/include/libdwarf"],
+    [CXXFLAGS="$CXXFLAGS"]
+  )  
+
   AC_ARG_WITH(stackwalker,
     [AS_HELP_STRING([--with-stackwalker=prefix],
       [Add the compile and link search paths for stackwalker]

configure

@@ -953,6 +953,8 @@ with_python
 with_graphviz
 with_bluegene
 with_cray_xt
+enable_stackwalker_rpm
+enable_libdwarf_rpm
 with_stackwalker
 with_libdwarf
 with_graphlib
@@ -1623,6 +1625,10 @@ Optional Features:
                           optimize for fast installation [default=yes]
   --disable-libtool-lock  avoid locking (might break parallel builds)
   --enable-gui            Enable the compilation of the STAT GUI.
+  --enable-stackwalker-rpm
+                          Enable the use of rpm-installed stackwalker,
+                          default=no
+  --enable-libdwarf-rpm   Enable the use of rpm-installed libdwarf, default=no
   --enable-debug          enable debug build
   --enable-rpath          Enable the use of rpaths, default=yes
   --enable-statbench      Enable the compilation of STATBench, the STAT
@@ -5096,13 +5102,13 @@ if test "${lt_cv_nm_interface+set}" = set; then
 else
   lt_cv_nm_interface="BSD nm"
   echo "int some_variable = 0;" > conftest.$ac_ext
-  (eval echo "\"\$as_me:5099: $ac_compile\"" >&5)
+  (eval echo "\"\$as_me:5105: $ac_compile\"" >&5)
   (eval "$ac_compile" 2>conftest.err)
   cat conftest.err >&5
-  (eval echo "\"\$as_me:5102: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+  (eval echo "\"\$as_me:5108: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
   (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
   cat conftest.err >&5
-  (eval echo "\"\$as_me:5105: output\"" >&5)
+  (eval echo "\"\$as_me:5111: output\"" >&5)
   cat conftest.out >&5
   if $GREP 'External.*some_variable' conftest.out > /dev/null; then
     lt_cv_nm_interface="MS dumpbin"
@@ -6308,7 +6314,7 @@ ia64-*-hpux*)
   ;;
 *-*-irix6*)
   # Find out which ABI we are using.
-  echo '#line 6311 "configure"' > conftest.$ac_ext
+  echo '#line 6317 "configure"' > conftest.$ac_ext
   if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -8869,11 +8875,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:8872: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:8878: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:8876: \$? = $ac_status" >&5
+   echo "$as_me:8882: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -9208,11 +9214,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:9211: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:9217: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:9215: \$? = $ac_status" >&5
+   echo "$as_me:9221: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -9313,11 +9319,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:9316: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:9322: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:9320: \$? = $ac_status" >&5
+   echo "$as_me:9326: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -9368,11 +9374,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:9371: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:9377: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:9375: \$? = $ac_status" >&5
+   echo "$as_me:9381: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -12171,7 +12177,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<_LT_EOF
-#line 12174 "configure"
+#line 12180 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -12267,7 +12273,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<_LT_EOF
-#line 12270 "configure"
+#line 12276 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -14287,11 +14293,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:14290: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:14296: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:14294: \$? = $ac_status" >&5
+   echo "$as_me:14300: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -14386,11 +14392,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:14389: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:14395: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:14393: \$? = $ac_status" >&5
+   echo "$as_me:14399: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -14438,11 +14444,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:14441: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:14447: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:14445: \$? = $ac_status" >&5
+   echo "$as_me:14451: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -16031,6 +16037,26 @@ fi
 
 
 
+  # Check whether --enable-stackwalker-rpm was given.
+if test "${enable_stackwalker_rpm+set}" = set; then
+  enableval=$enable_stackwalker_rpm; CXXFLAGS="$CXXFLAGS -I/usr/include/dyninst"
+     LDFLAGS="$LDFLAGS -L/usr/lib64/dyninst"
+     RPATH_FLAGS="$RPATH_FLAGS -Wl,-rpath=/usr/lib64/dyninst"
+else
+  CXXFLAGS="$CXXFLAGS"
+
+fi
+
+  # Check whether --enable-libdwarf-rpm was given.
+if test "${enable_libdwarf_rpm+set}" = set; then
+  enableval=$enable_libdwarf_rpm; CXXFLAGS="$CXXFLAGS -I/usr/include/libdwarf"
+else
+  CXXFLAGS="$CXXFLAGS"
+
+fi
+
+
+
 # Check whether --with-stackwalker was given.
 if test "${with_stackwalker+set}" = set; then
   withval=$with_stackwalker; CXXFLAGS="$CXXFLAGS -I${withval}/include"

doc/quickstart/stat_quickstart.pdf

@@ -17,5 +17,5 @@ You will then need to run your application with the --io-watchdog <command>srun<
     </screen>
 </informalexample>
 <para>
-When STAT is invoked, it will create a STAT_results directory in the current working directory, as it would in a typical STAT run.  The outputted .dot files can then be viewed with <command>STATview</command>.  For more details about using IO Watchdog, refer to the IO Watchdog README file in /usr/local/tools/io-watchdog/README.
+When STAT is invoked, it will create a stat_results directory in the current working directory, as it would in a typical STAT run.  The outputted .dot files can then be viewed with <command>stat-view</command>.  For more details about using IO Watchdog, refer to the IO Watchdog README file in /usr/local/tools/io-watchdog/README.
 </para>

doc/src/io_watchdog.sgml

@@ -1,4 +1,4 @@
 <para>
-STAT (the Stack Trace Analysis Tool) is a highly scalable, lightweight tool that gathers and merges stack traces from all of the processes of a parallel application.  After running the STAT command, STAT will create a STAT_results directory in your current working directory.  This directory will contain a subdirectory, based on your parallel application's executable name, with the merged stack traces in DOT format.
+STAT (the Stack Trace Analysis Tool) is a highly scalable, lightweight tool that gathers and merges stack traces from all of the processes of a parallel application.  After running the STAT command, STAT will create a stat_results directory in your current working directory.  This directory will contain a subdirectory, based on your parallel application's executable name, with the merged stack traces in DOT format.
 </para>
 

doc/src/stat_description.sgml

@@ -122,6 +122,14 @@ Several environment variables influence STAT and its dependent packages.  Note t
         </para>
     </listitem>
 </varlistentry>
+<varlistentry>
+    <term>STAT_FE_HOSTNAME=<replaceable class="parameter">value</replaceable></term>
+    <listitem>
+        <para>
+        Set the STAT Front End hostname to <replaceable class="parameter">value</replaceable>.  This may be necessary for example on BlueGene systems to use the proper network interface for the I/O nodes to connect back to.
+        </para>
+    </listitem>
+</varlistentry>
 <varlistentry>
     <term>STAT_CHECK_NODE_ACCESS=<replaceable class="parameter">value</replaceable></term>
     <listitem>

doc/src/stat_environment_variables.sgml

@@ -32,11 +32,11 @@ With the -a option (or when automatic topology is set as default), STAT will try
     </screen>
 </informalexample>
 <para>
-Upon successful completion, STAT will write its output to a STAT_results directory within the current working directory.  Each run creates a subdirectory named after the application with a unique integer ID.  STAT's output indicates the directory created with a message such as:
+Upon successful completion, STAT will write its output to a stat_results directory within the current working directory.  Each run creates a subdirectory named after the application with a unique integer ID.  STAT's output indicates the directory created with a message such as:
 </para>
 <informalexample>
     <screen>
-  Results written to /home/user/bin/STAT_results/mpi_application.6
+  Results written to /home/user/bin/stat_results/mpi_application.6
     </screen>
 </informalexample>
 <para>

doc/src/stat_example.sgml

@@ -8,10 +8,10 @@ STAT creates wrapper scripts for the stat-cl command line and stat-gui commands.
 STAT will try to build the GUI by default.  If you need to modify your PYTHONPATH envirnment variable to search for side installed site-packages, you can do this by specifying STAT_PYTHONPATH=path during configure.  This will add the appropriate directory to the $PYTHONPATH environment variable within the stat-gui script.  To disable the building of the GUI, use the --enable-gui=no configure option.
 </para>
 <para>
-On BlueGene systems, also be sure to configure --with-bluegene.  This will enable the BGL macro for BlueGene specific compilation.  Similarly, to compile on Cray XT systems, specify --with-cray-xt.
+To compile on Cray systems, specify --with-cray-xt.  On BlueGene systems, also be sure to configure --with-bluegene.  This will enable the BGL macro for BlueGene specific compilation.  It is important to note that on BlueGene systems, you may need to use an alternate hostname for the front-end node in order to get MRNet to bind to the appropriate network interface that can communicate with the I/O nodes.  By default, STAT will append "-io" to the hostname.  Alternatively, you can specify the hostname with the STAT_FE_HOSTNAME environment variable.  
 </para>
 <para>
-An example configure line for Cray XT:
+An example configure line for Cray:
 </para>
 <informalexample>
     <screen>
@@ -21,11 +21,11 @@ An example configure line for Cray XT:
 --with-stackwalker=/tmp/work/lee218/install \
 --with-libdwarf=/tmp/work/lee218/install \
 --prefix=/tmp/work/lee218/install --with-cray-xt \
-MPICC=cc MPICXX=CC MPIF77=ftn --enable-shared LD=/usr/bin/ld.x    
+MPICC=cc MPICXX=CC MPIF77=ftn --enable-shared LD=/usr/bin/ld   
     </screen>
 </informalexample>
 <para>
-Note that specifying LD=/usr/bin/ld.x is only advised on Cray systems, as doing so on other systems may inhibit the abililty to generate shared libraries.  Next you just need to run:
+Note that specifying LD=/usr/bin/ld may be required on Cray systems to avoid using the compute node linker.  It is also worth noting that Cray includes a build of STAT as part of their system software stack.  It is typically installed in /opt/cray/stat and can be loaded via modules.  After running configure you just need to run:
 </para>
 <informalexample>
     <screen>
@@ -35,4 +35,6 @@ make install
 </informalexample>
 <para>
 Note that STAT hardcodes the paths to its daemon and filter shared object, assuming that they are in $prefix/bin and $prefix/lib respectively, thus testing should be done in the install prefix after running "make install" and the installation directory should not be moved.  The path to these components can, however, be overridden with the --daemon and --filter arguments.  Further, the STAT_PREFIX environment variable can be defined to override the hardcoded paths in STAT.
+
+STAT will also, by default, add rpaths to dependent libraries.  This behavior can be disabled by specifying "--with-rpath=no".  However, when doing so, you must be sure to set LD_LIBRARY_PATH to point to the directories containing the dependent libraries.
 </para>