(K)TAU
THIS SECTION UNDER CONSTRUCTION, PLEASE RETURN LATER
Both TAU (Tuning and Analysis Utilities) and its Linux kernel counterpart, KTAU have been ported to ZeptoOS. In addition the build system of the ZeptoOS kernel has been modified to simplify the integration of KTAU patches. The following sections describe how to acquire, configure, build and use TAU and KTAU under ZeptoOS, with Surveyor at ANL as the test platform. The KTAU section appears first as the TAU section has some dependencies on that information.
KTAU
Acquiring KTAU
You can download a gzipped tarball of KTAU (version: 1.7.15-bgpzepto) from http://www.cs.uoregon.edu/research/ktau/downloads.php .
Integrating KTAU into ZeptoOS
For the below examples showing the configuration and build steps, it is assumed that the KTAU tarball has been expanded into the location /home/anataraj/ktau-1.7.15-bgpzepto and that the ZeptoOS tarball has been expanded into /home/anataraj/BGP.
Configure ZeptoOS to point to KTAU path and patch
Begin by configuring the ZeptoOS by pointing it to the correct KTAU path and the name of the patch to be used.
[email protected]:~/BGP> ./configure --edit
Once this is done, the changes will be saved to the Make.rules file as can be checked.
[email protected]:~/BGP> cat Make.rules # # Automatically generated make config: don't edit # # # BG/P DIST_DIR # DRV_DIR="/bgsys/drivers/ppcfloor/" BGP_CROSS="$(DRV_DIR)/gnu-linux/bin/powerpc-bgp-linux-" BGCNS_H_PATH="$(DRV_DIR)/mcp-2.6.16.46/include/" BGCNS_H="$(BGCNS_H_PATH)/bgcns.h" OS_DIR="/bgsys/linux/1.3.020081029" # # KTAU # KTAU_DIR="/home/anataraj/ktau-1.7.15-bgpzepto" KTAU_PATCH="patch-2.6.19.2-ktau-1.7.15-bgpzepto"
Patching ZeptoOS with KTAU
Step down into the "kernel" directory of ZeptoOS next. Issuing a 'make help' will show all the targets, including the KTAU specific ones.
[email protected]:~/BGP> cd kernel/ [email protected]:~/BGP/kernel> make help [menu] bgp-ion-linux : Simply use recent built or prebuilt ION kernel (no kernel rebuild) bgp-ion-linux-prebuilt : Use prebuilt ION kernel bgp-ion-linux-menuconfig : Invoke ION kernel menuconfig bgp-ion-linux-build : Rebuild ION kernel and copy bgp-ion-linux-try-patching : Try to apply new patch to ION kernel bgp-ion-linux-update-prebuilt : Copy ION kernel from tmp dir to prebuilt dir (no rebuild) bgp-cn-linux : Rebuild CN ramdisk and merge with recent built or prebuilt CN kernel objs bgp-cn-linux-prebuilt : Use prebuilt CN kernel bgp-cn-linux-menuconfig : Invoke CN kernel menuconfig bgp-cn-linux-build : Rebuild CN kernel objs and CN ramdisk, then merge them into CN Kernel bgp-cn-linux-try-patching : Try to apply new patch to CN kernel bgp-cn-linux-update-prebuilt : Copy CN kernel objs from tmp dir to prebuilt dir (no build) bgp-cn-linux-add-ktau : Patch CN kernel with KTAU and link in KTAU headers & sources bgp-cn-linux-del-ktau : Remove KTAU patch and links from CN kernel NOTE: - The following targets copy prebuilt or newly built kernel image to the top dir bgp-ion-linux, bgp-ion-linux-build, bgp-cn-linux, bgp-cn-linux-build and bgp-cn-linux-ramdisk - 'make GIT=1 ...' clone repo from public git repo via http and use them as target source tree - By default, kernel tarballs are extracted and use them as target source tree
Issuing 'make bgp-cn-linux-add-ktau' target patches the ZeptoOS compute node Linux kernel with KTAU the configured patch and then links to headers and sources from the KTAU path.
[email protected]:~/BGP/kernel> make bgp-cn-linux-add-ktau [ -d work ] || mkdir work tar xfj tarball/linux-2.6.19.2-BGP-V1R3.tar.bz2 -C work if [ -f tarball/linux-2.6.19.2-BGP-V1R3.patch ] ; then \ ( cd work/linux-2.6.19.2-BGP-V1R3 ; patch -p1 < ../../tarball/linux-2.6.19.2-BGP-V1R3.patch ) ; \ cp tarball/linux-2.6.19.2-BGP-V1R3.patch work/linux-2.6.19.2-BGP-V1R3.patch.applied ; \ fi patching file Makefile patching file arch/ppc/Kconfig patching file arch/ppc/kernel/head_44x.S patching file arch/ppc/kernel/vmlinux.lds.S patching file arch/ppc/mm/zepto_flatmem.c patching file arch/ppc/syslib/bgdd/bluegene_console.c patching file arch/ppc/syslib/bgdd/bluegene_dma.c patching file bgp-cn-2.6.19.2-dot-config patching file bgp-ion-flatmem-2.6.19.2-dot-config patching file fs/Kconfig patching file include/asm-ppc/page.h patching file include/asm-ppc/pgtable.h patching file include/linux/mmzone.h patching file kernel/exit.c touch work/.cn_kernel_prepared Linking to KTAU headers... Linking to KTAU sources... Linking to KTAU make... Applying KTAU patch... patching file arch/powerpc/kernel/irq.c patching file arch/powerpc/oprofile/Kconfig patching file arch/ppc/kernel/entry.S Hunk #4 succeeded at 306 (offset -6 lines). patching file arch/ppc/kernel/smp.c patching file arch/ppc/kernel/time.c patching file arch/ppc/kernel/traps.c Hunk #1 succeeded at 69 (offset -7 lines). patching file arch/ppc/syslib/bgdd/bluegene_network.c Hunk #2 succeeded at 496 (offset -34 lines). Hunk #3 succeeded at 513 (offset -34 lines). patching file include/linux/sched.h patching file init/main.c patching file kernel/fork.c patching file kernel/irq/handle.c patching file kernel/Makefile patching file kernel/sched.c patching file kernel/softirq.c patching file kernel/timer.c patching file kernel/workqueue.c patching file Makefile NOTE: Integration of KTAU into ZeptoOS is complete. Next, please configure KTAU kernel options using "make bgp-cn-linux-menuconfig". After that, please follow the standard ZeptoOS build steps (e.g. "make bgp-cn-linux-build").
Configuring KTAU parameters of the patched ZeptoOS CN Linux
Next the KTAU parameters of the kernel configuration need to be set. This can be done by issuing a 'make bgp-cn-linux-menuconfig'.
[email protected]:~/BGP/kernel> make bgp-cn-linux-menuconfig
Building ZeptoOS with KTAU
After configuration is performed and saved, the kernel needs to be built.
[email protected]:~/BGP/kernel> make bgp-cn-linux-build
Do not forget to update the prebuilt binaries with the kernel image you just built.
[email protected]:~/BGP/kernel> make bgp-cn-linux-update-prebuilt Copying kernel objs from tmp/cnkernelobjs to prebuilt/2.6.19/objs/ ... done CN kernel prebuilt objs and kernel image has been updated
Lastly, go back up to the root-level ZeptoOS directory and perform a 'make' to set / update / build any other targets.
[email protected]:~/BGP/kernel> cd .. [email protected]:~/BGP> pwd /home/anataraj/BGP [email protected]:~/BGP> make Create root password for I/O Node Leave the password field empty if you want to disable root login New password: Retype new password: <snipped out> Zepto Kernel and ramdisk images are ready: BGP-CN-zImage-with-initrd.elf BGP-ION-ramdisk.elf BGP-ION-ramdisk-for-CNL.elf BGP-ION-zImage.elf
You should now have a KTAU-patched and configured ZeptoOS Compute Node Linux kernel ready for use.
Removing KTAU from ZeptoOS
If you wish to revert back to the original version of ZeptoOS without KTAU integration, please perform the below steps.
[email protected]:~/BGP> pwd /home/anataraj/BGP [email protected]:~/BGP> cd kernel/ [email protected]:~/BGP/kernel> make bgp-cn-linux-del-ktau Reversing the KTAU patch (using a local copy of the applied patch)... patching file arch/powerpc/kernel/irq.c patching file arch/powerpc/oprofile/Kconfig patching file arch/ppc/kernel/entry.S Hunk #4 succeeded at 287 (offset -6 lines). patching file arch/ppc/kernel/smp.c patching file arch/ppc/kernel/time.c patching file arch/ppc/kernel/traps.c Hunk #1 succeeded at 69 (offset -7 lines). patching file arch/ppc/syslib/bgdd/bluegene_network.c Hunk #2 succeeded at 493 (offset -34 lines). Hunk #3 succeeded at 505 (offset -34 lines). patching file include/linux/sched.h patching file init/main.c patching file kernel/fork.c patching file kernel/irq/handle.c patching file kernel/Makefile patching file kernel/sched.c patching file kernel/softirq.c patching file kernel/timer.c patching file kernel/workqueue.c patching file Makefile NOTE: KTAU integration has been undone (patch reversed and all links removed). Next, please reconfigure and build the ZeptoOS CN Linux following standard steps. You can "make bgp-cn-linux-menuconfig" and "make bgp-cn-linux-build".
Please remember to reconfigure and rebuild ZeptoOS after undoing the KTAU integration.
TAU
Acquiring TAU
You can get TAU from the downloads page.
Configuration under ZeptoOS on BG/P
Before proceeding we assume that ZeptoOS has been downloaded, configured and installed. For the purpose of this how-to, the ZeptoOS install location is assumed to be "/home/anataraj/ZeptoReleases/install-BGP". You may have a different location or may opt to use the default ZeptoOS install location on your machine. Installing your own ZeptoOS can done by issuing 'python install.py /path/to/install' at the root-directory of the ZeptoOS release (but please refer to the detailed ZetpoOS documentation).
TAU needs to be told where the ZeptoOS install location is using the '-zeptodir' configure option.
[email protected]:~/tau-2.18.1p2> pwd /home/anataraj/tau-2.18.1p2 [email protected]:~/tau-2.18.1p2> ./configure -fullhelp | grep Zepto -zeptodir=<dir> ............................. ZeptoOS install location.
A simple example configuration is shown below that includes the -mpi option. It is important to note that the TAU configuration under ZeptoOS on BGP is different from the standard TAU configuration on BGP when using the default IBM OS suite.
In this case the architecture needs to be specified as 'ppc' in addition to the ZeptoOS install location.
[email protected]:~/tau-2.18.1p2> ./configure -arch=ppc -zeptodir=/home/anataraj/ZeptoReleases/install-BGP -mpi -------------------- TAU configure script --------------- The TAU source code has just been configured to use the tau root directory /home/anataraj/tau-2.18.1p2. If you move the Tau distribution, you must either * set an environment variable TAUROOT containing the new location before running any TAU tools or * run configure again and recompile ----------------------------------------------------------------- WARNING!! Auto-detect:ppc64 overridden with ppc -PROFILE and/or -TRACE should be specified. Choosing -PROFILE as the default Default C++ compiler will be g++ version 4.1.2 20070115 (prerelease) (SUSE Linux) Thread-safe MPI interface is defined... MPI-2 Interface is defined... MPI-2 Grequest Interface is defined... MPI-2 MPI_Datarep_conversion_function Interface is defined... MPI-2 Comm_create_errhandler Interface is defined... MPI-2 MPI*attr_functions are defined... MPI-2 MPI_File functions are defined... MPI-2 MPI_Type_dup and MPI_Exscan are defined... MPI-2 MPI_Add_error* functions are defined... MPI_Status f2c/c2f found... NOTE: MPI library does not have a threaded _r suffix Default C compiler will be /bgsys/drivers/ppcfloor/gnu-linux/bin/powerpc-bgp-linux-gcc Checking if open takes O_LARGEFILE... yes Checking for weak symbols... yes C++ compiler supports Std Runtime Type Information (default) Testing for Standard C++ Library support for string class Found support for Standard C++ Library string NOTE: Compiling Profiling Library and Applications with -DTAU_STDCXXLIB *********************************************************************** No special modifications found for architecture "ppc" Checking for bfd.h... no Checking for shared library compatible libbfd... no TAU: installing TAU's ParaProf profile browser jdk version 1.4 or better found TAU: installed tau_compiler.sh in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed tau_load.sh in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed Java trace reader/writer api in /home/anataraj/tau-2.18.1p2/ppc/lib TAU: installed tau2slog2, slog2print and jumpshot in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed required slog2sdk jars in /home/anataraj/tau-2.18.1p2/ppc/lib TAU: installed tauinc.pl in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed TAU's PerfDMF database utilities in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed ParaProf, PerfDMF, PerfExplorer and supporting jars in: /home/anataraj/tau-2.18.1p2/ppc/lib Platform does not support JOGL, no 3d displays will be available in ParaProf TAU: installed tau_analyze in /home/anataraj/tau-2.18.1p2/ppc/bin TAU: installed Makefile.inc in /home/anataraj/tau-2.18.1p2/tools/src/TauIL TAU: installed TauIL and supporting jars in /home/anataraj/tau-2.18.1p2/ppc/lib TAU: installed tau_throttle script TAU: installing tools in /home/anataraj/tau-2.18.1p2/ppc/bin NOTE: *** Using ZeptoOS BGP gfortran. *** NOTE: Enabled Profiling. Compiling with -DPROFILING_ON NOTE: Using the TAU MPI Profiling Interface NOTE: Using the TAU MPI_Init_thread Profiling Interface Wrapper NOTE: Using TAU's MPI-2 extensions NOTE: Using TAU's MPI-2 Grequest extensions NOTE: Using TAU's MPI-2 Datarep_conversion extensions NOTE: Using TAU's MPI-2 Error handler extensions NOTE: Using TAU's MPI-2 Attr extensions NOTE: Using TAU's MPI-2 File extensions NOTE: Using TAU's MPI-2 Type and Exscan extensions NOTE: Using TAU's MPI-2 Add_error extensions NOTE: Using default cc compiler. NOTE: Using the O_LARGEFILE flag to open NOTE: Using Weak Symbol support NOTE: Using Standard C++ Library NOTE: Disabling building of shared objects Script to modify Makefiles created. Applying script to all Makefiles, please wait, this may take a while... ......................................................................................................................................................... Configuring TAU Build scripts... Modifying Makefiles in the examples subdirectory... ........... Configuration complete!
Configuring with PDT under ZeptoOS on BG/P
The Program Database Toolkit(PDT) provides TAU with automatic source instrumentation capability. This allows routines, particularly in large projects, to be instrumented without tedious manual intervention.
First download and untar PDT. Then configure and build it:
[email protected]:~/pdtoolkit-3.14> pwd /home/anataraj/pdtoolkit-3.14 [email protected]:~/pdtoolkit-3.14> ./configure [email protected]:~/pdtoolkit-3.14> make [email protected]:~/pdtoolkit-3.14> make install
Next configure TAU with the above PDT:
[email protected]:~/tau-2.18.1p2> ./configure -arch=ppc \ -zeptodir=/home/anataraj/ZeptoReleases/install-BGP -mpi -pdt=/home/anataraj/pdtoolkit-3.14 \ -pdtarchdir=ppc64 -pdt_c++=xlC
Please pay close attention to the '-pdtarchdir=' and the '-pdt_c++=' options as they are important to it working on the ZeptoOS/BGP platform.
Please refer to the TAU documentation for various other TAU configuration options that may be used.
Building TAU
Lastly, build TAU in-place by issuing a 'make install'.
[email protected]:~/tau-2.18.1p2> make install
This should provide a TAU built for ZeptoOS with MPI profiling and automatic instrumentation capabilities.
Using TAU with KTAU : Integrated Profiles
TAU can be used in a tightly coupled fashion with KTAU to provide integrated profiles that show both user and kernel performance data under certain configurations. The following subsection describes such a configuration.
Configuring under ZeptoOS
Use all the previously described configuration options, but in addition add the -MULTIPLECOUNTERS and -ktau* options to the configure line. As follows:
./configure -arch=ppc \ -zeptodir=/home/anataraj/ZeptoReleases/install-BGP -mpi \ -pdt=/home/anataraj/pdtoolkit-3.14 -pdtarchdir=ppc64 -pdt_c++=xlC \ -ktau -ktauinc=/home/anataraj/BGP/kernel/work/linux-2.6.19.2-BGP-V1R3/include \ -ktauincuser=/home/anataraj/ktau-1.7.15-bgpzepto/user-src/include \ -ktaulib=/home/anataraj/ktau-1.7.15-bgpzepto/user-src/lib/ \ -ktausym=/proc/kallsyms \ -ktau_shctr
Then build as usual:
make clean install
This will provide a TAU that is capable of profiling MPI applications on ZeptoOS/BGP while also providing kernel-level performance information. It is assumed, of course, that ZeptoOS has also been configured and built with KTAU.
Example Run
TAU has several example codes listed in the "tau-<version>/examples" directory. Depending on the configuration of TAU, not all of those examples can be run.
If PDT and MPI have been included in the configuration, then the sample codes in "tau-<version>/examples/pdt_mpi/" directory can be run as follows:
[email protected]:~/tau-2.18.1p2> cd examples/pdt_mpi/c [email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> ls Makefile ring.c [email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> make [email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> ls Makefile ring ring.c ring.inst.c ring.o
Once 'ring' is built it needs to be turned into a zepto-compute-binary (zcb) by turning a flag on in the elf-header of the binary. This is done using the 'zelftool' which is part of the ZeptoOS installation.
[email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> /home/anataraj/ZeptoReleases/install-BGP/bin/zelftool ./ring zcb is off [email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> /home/anataraj/ZeptoReleases/install-BGP/bin/zelftool -e ./ring [email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> /home/anataraj/ZeptoReleases/install-BGP/bin/zelftool ./ring zcb is on
Now this binary can be run on ZeptoOS/BGP by specifiying the correct kernel-profile to cqsub. In the below example, the 'anataraj' profile points to a ZeptoOS kernel patched with KTAU.
[email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> cqsub -p ZeptoOS -k anataraj -t 10 -n 64 ./ring
After the run, user and kernel profiles will be created for each MPI rank. These (user-readable ascii) profiles can be read through the Paraprof Analysis and Visualization tool in TAU.
The user profiles are named "profile.<rank>.0.0". In this example run there are 64 ranks.
[email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> ls profile.* profile.0.0.0 profile.16.0.0 profile.23.0.0 profile.30.0.0 profile.38.0.0 profile.45.0.0 profile.52.0.0 profile.6.0.0 profile.1.0.0 profile.17.0.0 profile.24.0.0 profile.31.0.0 profile.39.0.0 profile.46.0.0 profile.53.0.0 profile.60.0.0 profile.10.0.0 profile.18.0.0 profile.25.0.0 profile.32.0.0 profile.4.0.0 profile.47.0.0 profile.54.0.0 profile.61.0.0 profile.11.0.0 profile.19.0.0 profile.26.0.0 profile.33.0.0 profile.40.0.0 profile.48.0.0 profile.55.0.0 profile.62.0.0 profile.12.0.0 profile.2.0.0 profile.27.0.0 profile.34.0.0 profile.41.0.0 profile.49.0.0 profile.56.0.0 profile.63.0.0 profile.13.0.0 profile.20.0.0 profile.28.0.0 profile.35.0.0 profile.42.0.0 profile.5.0.0 profile.57.0.0 profile.7.0.0 profile.14.0.0 profile.21.0.0 profile.29.0.0 profile.36.0.0 profile.43.0.0 profile.50.0.0 profile.58.0.0 profile.8.0.0 profile.15.0.0 profile.22.0.0 profile.3.0.0 profile.37.0.0 profile.44.0.0 profile.51.0.0 profile.59.0.0 profile.9.0.0
The kernel profiles for all processes corresponding to each node are under the respective "Kprofile.<rank>.0.perprocess" directories and there are 64 of those as well in this example. The files in these directories are numbered by their process-ids.
[email protected]:~/tau-2.18.1p2/examples/pdt_mpi/c> ls Kprofile.0.0.perprocess/ profile.1.0.0 profile.12.0.0 profile.17.0.0 profile.21.0.0 profile.26.0.0 profile.30.0.0 profile.44.0.0 profile.55.0.0 profile.9.0.0 profile.10.0.0 profile.13.0.0 profile.18.0.0 profile.22.0.0 profile.27.0.0 profile.31.0.0 profile.48.0.0 profile.6.0.0 profile.11.0.0 profile.14.0.0 profile.19.0.0 profile.23.0.0 profile.28.0.0 profile.32.0.0 profile.5.0.0 profile.62.0.0 profile.115.0.0 profile.15.0.0 profile.2.0.0 profile.24.0.0 profile.29.0.0 profile.34.0.0 profile.53.0.0 profile.7.0.0 profile.116.0.1 profile.16.0.0 profile.20.0.0 profile.25.0.0 profile.3.0.0 profile.4.0.0 profile.54.0.0 profile.8.0.0
