Merge remote-tracking branch 'origin/master' into dev-modular

Conflicts:
	ChangeLog
	darshan-log-format.h
	darshan-runtime/Makefile.in
	darshan-runtime/configure
	darshan-runtime/configure.in
	darshan-runtime/lib/darshan-mpi-io.c
	darshan-runtime/lib/darshan-posix.c
	darshan-util/configure
	darshan-util/configure.in
	darshan-util/darshan-logutils.c

ChangeLog

@@ -5,16 +5,38 @@ Darshan Release Change Log
 Darshan-3.0.0-pre1
 =============
 
-darshan-2.3.1-pre1
+darshan-2.3.1-pre2
 =============
+* added documentation and example configuration files for using the -profile
+  or $MPICC_PROFILE hooks to add instrumentation to MPICH-based MPI
+  implementations without generating custom wrapper scripts
+* Add wrappers for mkstemp(), mkostemp(), mkstemps(), and mkostemps()
+  (reported by Tom Peterka)
 * Change OPEN_TIMESTAMP field to report timestamp right before open() is
-  invoked rather than after timestamp after open is completed
+  invoked rather than after timestamp after open is completed.
+  NOTE: updated log format version to 2.06 to reflect this change.
 * Change start_time and end_time fields in job record to use min and max
   (respectively) across all ranks
 * Fix bug in write volume data reported in file system table in
   darshan-job-summary.pl (reported by Matthieu Dorier)
-
-TODO: bump log version number and add warnings about semantic changes  
+* Clean up autoconf test for zlib and make zlib mandatory (reported by Kalyana
+  Chadalavada)
+* add --start-group and --end-group notation to Darshan libraries for Cray PE
+  2.x environment to fix link-time corner cases (Yushu Yao)
+* improve y axis labels on time interval graphs in darshan-job-summary.pl
+  (reported by Tom Peterka)
+* misc. improvements to darshan-parser --perf output (reported by Shane
+  Snyder)
+  - indicate which rank was slowest in unique file results
+  - label I/O vs. meta time more clearly
+  - include unique file meta time in agg_perf_by_slowest calculation
+* added regression test script framework in darshan-test/regression/
+  - workstation-static and workstation-dynamic test environments supported
+* update darshan-gen-fortran.pl and darshan-gen-cxx.pl to support new library
+  naming conventions in MPICH 3.1.1 and higher
+* update documentation to reflect known issues with some versions of MPICH
+* modify darshan-runtime so that link-time instrumentation options are only used
+  when statically linking via Libs.private.  (reported by Kalyana Chadalavada)
 
 darshan-2.3.0
 =============

darshan-runtime/Makefile.in

@@ -82,6 +82,10 @@ install:: all
 #	install -m 755 share/craype-1.x/darshan-module $(datarootdir)/craype-1.x/modulefiles/darshan/$(DARSHAN_VERSION)
 #	install -d $(datarootdir)/craype-2.x/modulefiles/darshan
 #	install -m 755 share/craype-2.x/darshan-module $(datarootdir)/craype-2.x/modulefiles/darshan/$(DARSHAN_VERSION)
+#	install -d $(datarootdir)/mpi-profile
+#	install -m 755 share/mpi-profile/darshan-cc.conf $(datarootdir)/mpi-profile/darshan-cc.conf
+#	install -m 755 share/mpi-profile/darshan-cxx.conf $(datarootdir)/mpi-profile/darshan-cxx.conf
+#	install -m 755 share/mpi-profile/darshan-f.conf $(datarootdir)/mpi-profile/darshan-f.conf
 #	install -d $(libdir)/pkgconfig
 #	install -m 644 lib/pkgconfig/darshan-runtime.pc $(libdir)/pkgconfig/darshan-runtime.pc
 

darshan-runtime/configure.in

@@ -188,7 +188,7 @@ CFLAGS="$old_cflags"
 AC_CHECK_HEADERS(mntent.h sys/mount.h)
 
 # libc functions wrapped by darshan
-#CP_WRAPPERS="-Wl,-u,MPI_Init,-u,MPI_Wtime,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64"
+#CP_WRAPPERS="-Wl,-u,MPI_Init,-u,MPI_Wtime,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64,-wrap,mkstemp,-wrap,mkostemp,-wrap,mkstemps,-wrap,mkostemps"
 
 CP_WRAPPERS="-Wl,-u,MPI_Init,-u,MPI_Wtime,-wrap,open,-wrap,open64,-wrap,close"
 
@@ -287,6 +287,14 @@ AC_CHECK_TYPE([MPIO_Request],
 		AC_DEFINE(__D_MPI_REQUEST, MPI_Request, Generalized request type for MPI-IO)
 	,[#include <mpi.h>])
 
+# attempt to detect librarly naming convention in mpi compiler script
+AC_MSG_CHECKING(for old (pre-3.1.1) style MPICH library naming convention)
+AS_IF([$CC -show foo.c -o foo |grep lmpich >& /dev/null], 
+    AC_MSG_RESULT(yes)
+    MPICH_LIB_OLD=1,
+    AC_MSG_RESULT(no)
+    MPICH_LIB_OLD=0)
+
 DARSHAN_VERSION="AC_PACKAGE_VERSION"
 
 AC_SUBST(darshan_lib_path)
@@ -296,6 +304,7 @@ AC_SUBST(__CP_LOG_PATH)
 AC_SUBST(CP_WRAPPERS)
 AC_SUBST(DISABLE_LDPRELOAD)
 AC_SUBST(DARSHAN_VERSION)
+AC_SUBST(MPICH_LIB_OLD)
 AC_OUTPUT(Makefile
 darshan-mk-log-dirs.pl
 darshan-gen-cc.pl
@@ -305,4 +314,7 @@ darshan-config
 share/craype-1.x/darshan-module
 share/craype-2.x/darshan-module
 lib/pkgconfig/darshan-runtime.pc
+share/mpi-profile/darshan-cc.conf
+share/mpi-profile/darshan-cxx.conf
+share/mpi-profile/darshan-f.conf
 )

darshan-runtime/darshan-gen-cxx.pl.in

@@ -274,10 +274,14 @@ print OUTPUT<<"EOF";
     if [ \$? -eq 0 ] ; then
         CXXMPICH=-lcxxmpich
     fi
-    grep -E cxxmpich\\.cnk.a \$tmpfile >& /dev/null
+    grep -E cxxmpich\\.cnk\\.a \$tmpfile >& /dev/null
     if [ \$? -eq 0 ] ; then
         CXXMPICH=-lcxxmpich.cnk
     fi
+    grep -E mpicxx\\.a \$tmpfile >& /dev/null
+    if [ \$? -eq 0 ] ; then
+        CXXMPICH=-lmpicxx
+    fi
 
     rm \$tmpfile >& /dev/null
 

darshan-runtime/darshan-gen-fortran.pl.in

@@ -275,13 +275,20 @@ print OUTPUT<<"EOF";
     grep -E \\(PMPI_File_\\)\\|\\(PMPI_Init\\)\\|\\(PMPI_Finalize\\) \$tmpfile | grep -v -E \\(mpich.*\\.a\\) |grep \\(PMPI >& /dev/null
     rc_pmpi=\$?
 
-    # normal or cnk libraries?
-    grep -E mpich\\.cnk \$tmpfile >& /dev/null
+
+    # find appropriate fortran library name for profiling
+    grep -E libmpifort \$tmpfile >& /dev/null
     rc_cnk_check=\$?
     if [ \$rc_cnk_check -eq 0 ] ; then
-        FMPICH=-lfmpich.cnk
+        FMPICH=-lmpifort
     else
-        FMPICH=-lfmpich
+        grep -E mpich\\.cnk \$tmpfile >& /dev/null
+        rc_cnk_check=\$?
+        if [ \$rc_cnk_check -eq 0 ] ; then
+            FMPICH=-lfmpich.cnk
+        else
+            FMPICH=-lfmpich
+        fi
     fi
 
     rm \$tmpfile >& /dev/null

darshan-runtime/doc/darshan-runtime.txt

@@ -143,13 +143,17 @@ for details if you intend to force one mode or the other.
 
 == Instrumenting statically-linked applications
 
-Statically linked executables must be instrumented at compile time.  The
-simplest way to do this is to generate an MPI compiler script (e.g. `mpicc`)
-that includes the link options and libraries needed by Darshan.  Once this
-is done, Darshan instrumentation is transparent; you simply compile
-applications using the darshan-enabled MPI compiler scripts.
+Statically linked executables must be instrumented at compile time.
+The simplest methods to do this are to either generate a customized
+MPI compiler script (e.g. `mpicc`) that includes the link options and
+libraries needed by Darshan, or to use existing profiling configuration
+hooks for existing MPI compiler scripts.  Once this is done, Darshan
+instrumentation is transparent; you simply compile applications using
+the darshan-enabled MPI compiler scripts.
 
-For MPICH-based MPI libraries, such as MPICH1, MPICH2, or MVAPICH, these
+=== Using customized compiler wrapper scripts
+
+For MPICH-based MPI libraries, such as MPICH1, MPICH2, or MVAPICH, custom
 wrapper scripts can be generated automatically.  The following example
 illustrates how to produce wrappers for C, C++, and Fortran compilers:
 
@@ -160,6 +164,40 @@ darshan-gen-fortran.pl `which mpif77` --output mpif77.darshan
 darshan-gen-fortran.pl `which mpif90` --output mpif90.darshan
 -----
 
+=== Using a profile configuration 
+
+The MPICH MPI implementation supports the specification of a profiling library
+configuration, then it can be used to insert Darshan instrumentation without
+modifying the existing MPI compiler script.  Example profiling configuration
+files are installed with Darshan 2.3.1 and later.  You can enable a profiling
+configuration using environment variables or command line arguments to the
+compiler scripts:
+
+Example for MPICH 3.1.1 or newer:
+----
+export MPICC_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-cc
+export MPICXX_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-cxx
+export MPIFORT_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-f
+----
+
+Example for MPICH 3.1 or earlier:
+----
+export MPICC_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-cc
+export MPICXX_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-cxx
+export MPICF77_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-f
+export MPICF90_PROFILE=$DARSHAN_PREFIX/share/mpi-profile/darshan-f
+----
+
+Examples for command line use:
+----
+mpicc -profile=$DARSHAN_PREFIX/share/mpi-profile/darshan-c <args>
+mpicxx -profile=$DARSHAN_PREFIX/share/mpi-profile/darshan-cxx <args>
+mpif77 -profile=$DARSHAN_PREFIX/share/mpi-profile/darshan-f <args>
+mpif90 -profile=$DARSHAN_PREFIX/share/mpi-profile/darshan-f <args>
+----
+
+=== Other configurations
+
 Please see the Cray recipe in this document for instructions on
 instrumenting statically-linked applications on that platform.
 
@@ -379,12 +417,30 @@ http://software.intel.com/en-us/forums/showthread.php?t=103447&o=a&s=lr
 
 === Linux clusters using MPICH 
 
-Follow the generic instructions provided at the top of this document.  The
-only modification is to make sure that the `CC` used for compilation is
+Follow the generic instructions provided at the top of this document.  For MPICH versions 3.1 and
+later, MPICH uses shared libraries by default, so you may need to consider the dynamic linking
+instrumentation approach.  
+
+The static linking method can be used if MPICH is configured to use static
+linking by default, or if you are using a version prior to 3.1.
+The only modification is to make sure that the `CC` used for compilation is
 based on a GNU compiler.  Once Darshan has been installed, it should be
 capable of instrumenting executables built with GNU, Intel, and PGI
 compilers.
 
+[NOTE]
+Darshan is not capable of instrumenting Fortran applications build with MPICH versions 3.1.1, 3.1.2,
+or 3.1.3 due to a library symbol name compatibility issue.  Consider using a newer version of
+MPICH if you wish to instrument Fortran applications.  Please see
+http://trac.mpich.org/projects/mpich/ticket/2209 for more details.
+
+[NOTE]
+MPICH versions 3.1, 3.1.1, 3.1.2, and 3.1.3 may produce link-time errors when building static
+executables (i.e. using the -static option) if MPICH is built with shared library support.
+Please see http://trac.mpich.org/projects/mpich/ticket/2190 for more details.  The workaround if you
+wish to use static linking is to configure MPICH with `--enable-shared=no --enable-static=yes` to
+force it to use static MPI libraries with correct dependencies.
+
 === Linux clusters using Open MPI
 
 Follow the generic instructions provided at the top of this document for
@@ -413,4 +469,5 @@ behavior at runtime:
 in which files that were accessed by all ranks are collapsed into a single
 cumulative file record at rank 0.  This option retains more per-process
 information at the expense of creating larger log files.
-
+* DARSHAN_LOGPATH: specifies the path to write Darshan log files to. Note that this directory needs to be formatted using the darshan-mk-log-dirs script.
+* DARSHAN_LOGFILE: specifies the path (directory + Darshan log file name) to write the output Darshan log to. This overrides the default Darshan behavior of automatically generating a log file name and adding to a log file directory formatted using darshan-mk-log-dirs script.

darshan-runtime/lib/pkgconfig/darshan-runtime.pc.in

@@ -11,8 +11,8 @@ Requires.private:
 darshan_prefix=@prefix@
 darshan_includedir=
 darshan_libdir= -L${darshan_prefix}/lib
-darshan_linkopts="-Wl,-u,MPI_Init,-u,MPI_Wtime,-u,__wrap_H5Fcreate,-u,__wrap_ncmpi_create,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64"
+darshan_linkopts="-Wl,-u,MPI_Init,-u,MPI_Wtime,-u,__wrap_H5Fcreate,-u,__wrap_ncmpi_create,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64,-wrap,mkstemp,-wrap,mkostemp,-wrap,mkstemps,-wrap,mkostemps"
 
 Cflags:
-Libs: ${darshan_linkopts} ${darshan_libdir} -lfmpich -lmpichcxx -ldarshan-mpi-io -ldarshan-posix -ldarshan-stubs
-Libs.private:
+Libs:
+Libs.private: ${darshan_linkopts} ${darshan_libdir} -lfmpich -lmpichcxx -Wl,--start-group -ldarshan-mpi-io -ldarshan-posix -ldarshan-stubs -Wl,--end-group

darshan-runtime/share/craype-1.x/darshan-module.in

@@ -55,7 +55,7 @@ prepend-path CRAY_LD_LIBRARY_PATH           $root/lib
 
 
 # initial link options for Darshan
-setenv DARSHAN_POST_LINK_OPTS " -L$root/lib -ldarshan-mpi-io -lz -Wl,-u,__wrap_fopen,-u,MPI_Init,-u,MPI_Wtime,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64  -lfmpich -lmpichcxx -ldarshan-posix -ldarshan-mpi-io -lz "
+setenv DARSHAN_POST_LINK_OPTS " -L$root/lib -ldarshan-mpi-io -lz -Wl,-u,__wrap_fopen,-u,MPI_Init,-u,MPI_Wtime,-wrap,write,-wrap,open,-wrap,creat,-wrap,creat64,-wrap,open64,-wrap,close,-wrap,read,-wrap,lseek,-wrap,lseek64,-wrap,pread,-wrap,pwrite,-wrap,readv,-wrap,writev,-wrap,__xstat,-wrap,__lxstat,-wrap,__fxstat,-wrap,__xstat64,-wrap,__lxstat64,-wrap,__fxstat64,-wrap,mmap,-wrap,mmap64,-wrap,fopen,-wrap,fclose,-wrap,fread,-wrap,fwrite,-wrap,fseek,-wrap,fopen64,-wrap,pread64,-wrap,pwrite64,-wrap,fsync,-wrap,fdatasync,-wrap,ncmpi_create,-wrap,ncmpi_open,-wrap,ncmpi_close,-wrap,H5Fcreate,-wrap,H5Fopen,-wrap,H5Fclose,-wrap,aio_write,-wrap,aio_write64,-wrap,aio_read,-wrap,aio_read64,-wrap,lio_listio,-wrap,lio_listio64,-wrap,aio_return,-wrap,aio_return64,-wrap,mkstemp,-wrap,mkostemp,-wrap,mkstemps,-wrap,mkostemps  -lfmpich -lmpichcxx -ldarshan-posix -ldarshan-mpi-io -lz "
 
 # Add Darshan to the PE_PRODUCT_LIST variable.  This will cause the
 # compiler scripts to insert DARSHAN_POST_LINK_OPTS into the link command

darshan-runtime/share/mpi-profile/darshan-cc.conf.in

+#!/bin/bash
+
+# Example Darshan profiling configuration file for MPICH.
+
+
+DARSHAN_PREFIX=@prefix@
+
+# Libraries (and paths) to include before the MPI library 
+export PROFILE_PRELIB=`$DARSHAN_PREFIX/bin/darshan-config --pre-ld-flags`
+
+# Libraries to include after the MPI library 
+export PROFILE_POSTLIB=`$DARSHAN_PREFIX/bin/darshan-config --post-ld-flags`
+
+# C preprocessor arguments for any include files For example, to add
+# /usr/local/myprof/include to the include path and the library libmyprof.a in
+# /usr/local/myprof/lib to the link step, you could create the file myprof.conf with the
+# lines 
+# PROFILE_INCPATHS

darshan-runtime/share/mpi-profile/darshan-cxx.conf.in

+#!/bin/bash
+
+# Example Darshan profiling configuration file for MPICH.
+
+
+DARSHAN_PREFIX=@prefix@
+MPICH_LIB_OLD=@MPICH_LIB_OLD@
+
+# Libraries (and paths) to include before the MPI library 
+if [ $MPICH_LIB_OLD -eq 1 ]; then
+    export PROFILE_PRELIB="-lmpichcxx `$DARSHAN_PREFIX/bin/darshan-config --pre-ld-flags`"
+else
+    export PROFILE_PRELIB="-lmpicxx `$DARSHAN_PREFIX/bin/darshan-config --pre-ld-flags`"
+fi
+
+# Libraries to include after the MPI library 
+export PROFILE_POSTLIB=`$DARSHAN_PREFIX/bin/darshan-config --post-ld-flags`
+
+# C preprocessor arguments for any include files For example, to add
+# /usr/local/myprof/include to the include path and the library libmyprof.a in
+# /usr/local/myprof/lib to the link step, you could create the file myprof.conf with the
+# lines 
+# PROFILE_INCPATHS

darshan-runtime/share/mpi-profile/darshan-f.conf.in

+#!/bin/bash
+
+# Example Darshan profiling configuration file for MPICH.
+
+
+DARSHAN_PREFIX=@prefix@
+MPICH_LIB_OLD=@MPICH_LIB_OLD@
+
+# Libraries (and paths) to include before the MPI library 
+if [ $MPICH_LIB_OLD -eq 1 ]; then
+    export PROFILE_PRELIB="-lfmpich `$DARSHAN_PREFIX/bin/darshan-config --pre-ld-flags`"
+else
+    export PROFILE_PRELIB="-lmpifort `$DARSHAN_PREFIX/bin/darshan-config --pre-ld-flags`"
+fi
+
+# Libraries to include after the MPI library 
+export PROFILE_POSTLIB=`$DARSHAN_PREFIX/bin/darshan-config --post-ld-flags`
+
+# C preprocessor arguments for any include files For example, to add
+# /usr/local/myprof/include to the include path and the library libmyprof.a in
+# /usr/local/myprof/lib to the link step, you could create the file myprof.conf with the
+# lines 
+# PROFILE_INCPATHS

darshan-test/RELEASE-CHECKLIST.txt

@@ -20,8 +20,13 @@ Notes on how to release a new version of Darshan
   pushed to origin/master
 - make a tag for the release according to instructions at
   http://git-scm.com/book/en/Git-Basics-Tagging
+  - example (annotated tag, pushed to repo):
+    git tag -a darshan-2.3.1-pre2 -m 'Darshan 2.3.1-pre2'
+    git push origin darshan-2.3.1-pre2
 - TESTING
-- export the tag (TODO: document recommended method) and tar gzip it
+- export the tag and tar gzip it
+  - easiest method is to do a fresh checkout and remove the .git
+    subdirectory
   - upload .tar.gz file to /mcs/ftp/pub/darshan/releases
 - generate web documentation from asciidoc by running make in
   darshan-util/doc/ and darshan-runtime/doc/ directories

darshan-test/regression/README.txt

+This directory contains regression tests for both the runtime and util
+components of Darshan, assuming that Darshan is already compiled and
+installed in a known path.
+
+The master script must be executed with three arguments:
+
+1) path to darshan installation
+2) path to temporary directory (for building executables, collecting logs, 
+   etc. during test)
+3) platform type; options include:
+   - ws (for a standard workstation)
+
+The platform type should map to a subdirectory containing scripts
+that describe how to perform platform-specific tasks (like loading or
+generating darshan wrappers and executing jobs).
+

darshan-test/regression/run-all.sh

+#!/bin/bash
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: run-all.sh <darshan_install_path> <tmp_path> <platform>" 1>&2
+    echo "Example: ./run-all.sh ~/darshan-install /tmp/test ws" 1>&2
+    exit 1
+fi
+
+# set variables for use by other sub-scripts
+export DARSHAN_PATH=$1
+export DARSHAN_TMP=$2
+export DARSHAN_PLATFORM=$3
+# number of procs that most test jobs will use
+export DARSHAN_DEFAULT_NPROCS=4
+
+DARSHAN_TESTDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+export DARSHAN_TESTDIR
+
+# check darshan path
+if [ ! -x $DARSHAN_PATH/bin/darshan-parser ]; then
+    echo "Error: $DARSHAN_PATH doesn't contain a valid Darshan install." 1>&2
+    exit 1
+fi
+
+# check and/or create tmp path
+if [ ! -d $DARSHAN_TMP ]; then
+    mkdir -p $DARSHAN_TMP
+fi
+
+if [ ! -d $DARSHAN_TMP ]; then
+    echo "Error: unable to find or create $DARSHAN_TMP" 1>&2
+    exit 1
+fi
+if [ ! -w $DARSHAN_TMP ]; then
+    echo "Error: unable to write to $DARSHAN_TMP" 1>&2
+    exit 1
+fi
+
+# make sure that we have sub-scripts for the specified platform
+if [ ! -d $DARSHAN_TESTDIR/$DARSHAN_PLATFORM ]; then
+    echo "Error: unable to find scripts for platform $DARSHAN_PLATFORM" 1>&2
+    exit 1
+fi
+
+# set up environment for tests according to platform
+source $DARSHAN_TESTDIR/$DARSHAN_PLATFORM/env.sh
+
+for i in `ls $DARSHAN_TESTDIR/test-cases/*.sh`; do
+    echo Running ${i}...
+    $i
+    if [ $? -ne 0 ]; then
+        echo "Error: failed to execute test case $i"
+        exit 1
+    fi
+    echo Done.
+done
+
+exit 0

darshan-test/regression/test-cases/cxxpi.sh

+#!/bin/bash
+
+PROG=cxxpi
+
+# set log file path; remove previous log if present
+export DARSHAN_LOGFILE=$DARSHAN_TMP/${PROG}.darshan.gz
+rm -f ${DARSHAN_LOGFILE}
+
+# compile
+$DARSHAN_CXX $DARSHAN_TESTDIR/test-cases/src/${PROG}.cxx -o $DARSHAN_TMP/${PROG}
+if [ $? -ne 0 ]; then
+    echo "Error: failed to compile ${PROG}" 1>&2
+    exit 1
+fi
+
+# execute
+$DARSHAN_RUNJOB $DARSHAN_TMP/${PROG} -f $DARSHAN_TMP/${PROG}.tmp.dat
+if [ $? -ne 0 ]; then
+    echo "Error: failed to execute ${PROG}" 1>&2
+    exit 1
+fi
+
+# parse log
+$DARSHAN_PATH/bin/darshan-parser $DARSHAN_LOGFILE > $DARSHAN_TMP/${PROG}.darshan.txt
+if [ $? -ne 0 ]; then
+    echo "Error: failed to parse ${DARSHAN_LOGFILE}" 1>&2
+    exit 1
+fi
+
+# check results
+# in this case we want to confirm that the open counts are zero; cxxpi does not do any IO
+POSIX_OPENS=`grep CP_POSIX_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ "$POSIX_OPENS"x != ""x ]; then
+    echo "Error: Found unexpected POSIX open count of $POSIX_OPENS" 1>&2
+    exit 1
+fi
+
+
+exit 0

darshan-test/regression/test-cases/fperf-f77.sh

+#!/bin/bash
+
+PROG=fperf-f77
+
+# set log file path; remove previous log if present
+export DARSHAN_LOGFILE=$DARSHAN_TMP/${PROG}.darshan.gz
+rm -f ${DARSHAN_LOGFILE}
+
+# compile
+$DARSHAN_F77 $DARSHAN_TESTDIR/test-cases/src/fperf.f -o $DARSHAN_TMP/${PROG}
+if [ $? -ne 0 ]; then
+    echo "Error: failed to compile ${PROG}" 1>&2
+    exit 1
+fi
+
+# execute
+$DARSHAN_RUNJOB $DARSHAN_TMP/${PROG} -fname $DARSHAN_TMP/${PROG}.tmp.dat
+if [ $? -ne 0 ]; then
+    echo "Error: failed to execute ${PROG}" 1>&2
+    exit 1
+fi
+
+# parse log
+$DARSHAN_PATH/bin/darshan-parser $DARSHAN_LOGFILE > $DARSHAN_TMP/${PROG}.darshan.txt
+if [ $? -ne 0 ]; then
+    echo "Error: failed to parse ${DARSHAN_LOGFILE}" 1>&2
+    exit 1
+fi
+
+# check results
+# in this case we want to confirm that both the MPI and POSIX open counters were triggered
+MPI_OPENS=`grep CP_COLL_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $MPI_OPENS -gt 0 ]; then
+    echo "Error: MPI open count of $MPI_OPENS is incorrect" 1>&2
+    exit 1
+fi
+POSIX_OPENS=`grep CP_POSIX_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $POSIX_OPENS -gt 0 ]; then
+    echo "Error: POSIX open count of $POSIX_OPENS is incorrect" 1>&2
+    exit 1
+fi
+
+exit 0

darshan-test/regression/test-cases/fperf-f90.sh

+#!/bin/bash
+
+PROG=fperf-f90
+
+# set log file path; remove previous log if present
+export DARSHAN_LOGFILE=$DARSHAN_TMP/${PROG}.darshan.gz
+rm -f ${DARSHAN_LOGFILE}
+
+# compile
+$DARSHAN_F90 $DARSHAN_TESTDIR/test-cases/src/fperf.f -o $DARSHAN_TMP/${PROG}
+if [ $? -ne 0 ]; then
+    echo "Error: failed to compile ${PROG}" 1>&2
+    exit 1
+fi
+
+# execute
+$DARSHAN_RUNJOB $DARSHAN_TMP/${PROG} -fname $DARSHAN_TMP/${PROG}.tmp.dat
+if [ $? -ne 0 ]; then
+    echo "Error: failed to execute ${PROG}" 1>&2
+    exit 1
+fi
+
+# parse log
+$DARSHAN_PATH/bin/darshan-parser $DARSHAN_LOGFILE > $DARSHAN_TMP/${PROG}.darshan.txt
+if [ $? -ne 0 ]; then
+    echo "Error: failed to parse ${DARSHAN_LOGFILE}" 1>&2
+    exit 1
+fi
+
+# check results
+# in this case we want to confirm that both the MPI and POSIX open counters were triggered
+MPI_OPENS=`grep CP_COLL_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $MPI_OPENS -gt 0 ]; then
+    echo "Error: MPI open count of $MPI_OPENS is incorrect" 1>&2
+    exit 1
+fi
+POSIX_OPENS=`grep CP_POSIX_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $POSIX_OPENS -gt 0 ]; then
+    echo "Error: POSIX open count of $POSIX_OPENS is incorrect" 1>&2
+    exit 1
+fi
+
+exit 0

darshan-test/regression/test-cases/mpi-io-test.sh

+#!/bin/bash
+
+PROG=mpi-io-test
+
+# set log file path; remove previous log if present
+export DARSHAN_LOGFILE=$DARSHAN_TMP/${PROG}.darshan.gz
+rm -f ${DARSHAN_LOGFILE}
+
+# compile
+$DARSHAN_CC $DARSHAN_TESTDIR/test-cases/src/${PROG}.c -o $DARSHAN_TMP/${PROG}
+if [ $? -ne 0 ]; then
+    echo "Error: failed to compile ${PROG}" 1>&2
+    exit 1
+fi
+
+# execute
+$DARSHAN_RUNJOB $DARSHAN_TMP/${PROG} -f $DARSHAN_TMP/${PROG}.tmp.dat
+if [ $? -ne 0 ]; then
+    echo "Error: failed to execute ${PROG}" 1>&2
+    exit 1
+fi
+
+# parse log
+$DARSHAN_PATH/bin/darshan-parser $DARSHAN_LOGFILE > $DARSHAN_TMP/${PROG}.darshan.txt
+if [ $? -ne 0 ]; then
+    echo "Error: failed to parse ${DARSHAN_LOGFILE}" 1>&2
+    exit 1
+fi
+
+# check results
+# in this case we want to confirm that both the MPI and POSIX open counters were triggered
+MPI_OPENS=`grep CP_INDEP_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $MPI_OPENS -gt 0 ]; then
+    echo "Error: MPI open count of $MPI_OPENS is incorrect" 1>&2
+    exit 1
+fi
+POSIX_OPENS=`grep CP_POSIX_OPENS $DARSHAN_TMP/${PROG}.darshan.txt |cut -f 4`
+if [ ! $POSIX_OPENS -gt 0 ]; then
+    echo "Error: POSIX open count of $POSIX_OPENS is incorrect" 1>&2
+    exit 1
+fi
+
+
+exit 0

darshan-test/regression/test-cases/src/cxxpi.cxx

+/* -*- Mode: C++; c-basic-offset:4 ; -*- */
+/*  
+ *  (C) 2004 by Argonne National Laboratory.
+ *      See COPYRIGHT in top-level directory.
+ */
+
+#include "mpi.h"
+#include <iostream>
+using namespace std;
+#include <math.h>
+
+double f(double);
+
+double f(double a)
+{
+    return (4.0 / (1.0 + a*a));
+}
+
+int main(int argc,char **argv)
+{
+    int n, myid, numprocs, i;
+    double PI25DT = 3.141592653589793238462643;
+    double mypi, pi, h, sum, x;
+    double startwtime = 0.0, endwtime;
+    int  namelen;
+    char processor_name[MPI_MAX_PROCESSOR_NAME];
+
+    MPI::Init(argc,argv);
+    numprocs = MPI::COMM_WORLD.Get_size();
+    myid     = MPI::COMM_WORLD.Get_rank();
+    MPI::Get_processor_name(processor_name,namelen);
+
+    cout << "Process " << myid << " of " << numprocs << " is on " <<
+	processor_name << endl;
+
+    n = 10000;			/* default # of rectangles */
+    if (myid == 0)
+	startwtime = MPI::Wtime();
+
+    MPI::COMM_WORLD.Bcast(&n, 1, MPI_INT, 0);
+
+    h   = 1.0 / (double) n;
+    sum = 0.0;
+    /* A slightly better approach starts from large i and works back */
+    for (i = myid + 1; i <= n; i += numprocs)
+    {
+	x = h * ((double)i - 0.5);
+	sum += f(x);
+    }
+    mypi = h * sum;
+
+    MPI::COMM_WORLD.Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0);
+
+    if (myid == 0) {
+	endwtime = MPI::Wtime();
+	cout << "pi is approximately " << pi << " Error is " <<
+	    fabs(pi - PI25DT) << endl;
+	cout << "wall clock time = " << endwtime-startwtime << endl;
+    }
+
+    MPI::Finalize();
+    return 0;
+}

darshan-test/regression/test-cases/src/fperf.f

+! -*- Mode: Fortran; -*- 
+!  
+!  (C) 2001 by Argonne National Laboratory.
+!      See COPYRIGHT in top-level directory.
+!
+      program main
+      implicit none
+
+      include 'mpif.h'
+      
+
+!     Fortran equivalent of perf.c
+
+      integer SIZE 
+      parameter (SIZE=1048576*4)
+!     read/write size per node in bytes
+
+      integer buf(SIZE/4), j, mynod, nprocs, ntimes, flag, foo
+      double precision stim, read_tim, write_tim, new_read_tim
+      double precision new_write_tim, min_read_tim, min_write_tim
+      double precision read_bw, write_bw
+      integer fh, status(MPI_STATUS_SIZE), ierr, argc, iargc, i
+      character*1024 str    ! used to store the filename
+      integer*8 offset
+      
+
+      ntimes = 5
+      min_read_tim = 10000000.0D0
+      min_write_tim = 10000000.0D0
+
+      call MPI_INIT(ierr)
+      call MPI_COMM_SIZE(MPI_COMM_WORLD, nprocs, foo, ierr)
+      call MPI_COMM_RANK(MPI_COMM_WORLD, mynod, ierr)
+
+!     process 0 takes the file name as a command-line argument and 
+!     broadcasts it to other processes
+
+      if (mynod .eq. 0) then
+         argc = iargc()
+         i = 0
+         call getarg(i,str)
+         do while ((i .lt. argc) .and. (str .ne. '-fname'))
+            i = i + 1
+            call getarg(i,str)
+         end do
+         if (i .ge. argc) then
+            print *
+            print *, '*#  Usage: fperf -fname filename'
+            print *
+            call MPI_ABORT(MPI_COMM_WORLD, 1, ierr)
+         end if
+
+         i = i + 1
+         call getarg(i,str)
+         call MPI_BCAST(str, 1024, MPI_CHARACTER, 0,                    &  
+     &        MPI_COMM_WORLD, ierr)
+         print *, 'Access size per process = ', SIZE, ' bytes',         &
+     &        ', ntimes = ', ntimes
+      else 
+         call MPI_BCAST(str, 1024, MPI_CHARACTER, 0,                    &