CRAY XC40 Tools

Cray provided tools

Cray does provide several official tools. Below is a list of some of the tools, you can get more information about them in the online manual (man atp for example).

Jump to ATP, STAT and IOBUF

At HLRS Cray also supports some tools with limited or no support. Currently available is the Cray Profiler

ATP : Abnormal Termination Processing

Abnormal Termination Processing (ATP) is a system that monitors Cray system user applications. If an application takes a system trap, ATP performs analysis on the dying application. All stack backtraces of the application processes are gathered into a merged stack backtrace tree and written to disk as the file, atpMergedBT.dot. The stack backtrace tree for the first process to die is sent to stderr as is the number of the signal that caused the application to fail. If Linux core dumping is enabled (see ulimit or limit in your shell documentation), a heuristically selected set of processes also dump their cores.

The atpMergedBT.dot file can be viewed with statview, (the Stack Trace Analysis Tool viewer), which is included in the Cray Debugger Support Tools (module load stat), or alternatively with the file viewer dotty, which can be found on most Linux systems. The merged stack backtrace tree provides a concise yet comprehensive view of what the application was doing at the time of its termination.

At HLRS ATP module is loaded by default. To use it you have to set ATP_ENABLED=1 in your batch script.

STAT : Stack Trace Analysis Tool

Stack Trace Analysis Tool (STAT) is a cross-platform tool from the University of Wisconsin-Madison. It gathers and merges stack traces from a running application’s parallel processes. It creates call graph prefix tree, which are a compressed representation, with scalable visualization and scalable analysis It is very useful when application seems to be stuck/hung. Full information including use cases is available at {http://www.paradyn.org/STAT/STAT.html paradyn}. STAT scales to many thousands of concurrent process.

To use it, you simply load the module and attach it to your running/hanging application.

$> module load stat
$> qsub  job.pbs
	#start the application e.g. using a batch script
	#Wait until application reaches the suspicious state
$> STATGUI <JOBID> 
	#Launches the graphical interface
	#Attach to the job
	#Shows the calltree
$> qdel <JOBID>
	#Terminate the running application

IOBUF - I/O buffering library

IOBUF is an I/O buffering library that can reduce the I/O wait time for programs that read or write large files sequentially. IOBUF intercepts I/O system calls such as read and open and adds a layer of buffering, thus improving program performance by enabling asynchronous prefetching and caching of file data.

IOBUF can also gather runtime statistics and print a summary report of I/O activity for each file.

In general, no program source changes are needed in order to take advantage of IOBUF. Instead, IOBUF is implemented by following these steps:

Load the IOBUF module:

% module load iobuf

Relink the program. Set the IOBUF_PARAMS environment variable as needed.

% export IOBUF_PARAMS='*:verbose'

Execute the program.

If a memory allocation error occurs, buffering is reduced or disabled for that file and a diagnostic is printed to stderr. When the file is opened, a single buffer is allocated if buffering is enabled. The allocation of additional buffers is done when a buffer is needed. When a file is closed, its buffers are freed (unless asynchronous I/O is pending on the buffer and lazyclose is specified).

Please check the complete manual and all environment variables available by reading the man page (man iobuf, after loading the iobuf module)

 IMPORTANT NOTICE : As iobuf is written for serial IO, its behavior is undefined 
 when used for parallel I/O into a single file. 

You should never use IOBUF in the case when several parallel processes operates on a single file.

Perftools : Performance Analysis Tool Kit

Description

The Cray Performance Measurement and Analysis Tools (or CrayPat) are a suite of optional utilities that enable you to capture and analyze performance data generated during the execution of your program on a Cray system. The information collected and analysis produced by use of these tools can help you to find answers to two fundamental programming questions: How fast is my program running? and How can I make it run faster? A detailed documantation about CrayPAT can be found in document S-2376-622. Here a short summary is presented, concentrating on the usage.

Profiling is mainly distinguished between two main run cases, sampling and tracing:

Sampling	Tracing
Advantages Only need to instrument main routine Low Overhead – depends only on sampling frequency Smaller volumes of data produced	Advantages More accurate and more detailed information Data collected from every traced function call not statistical averages
Disadvantages Only statistical averages available Limited information from performance counters	Disadvantages Increased overheads as number of function calls increases Huge volumes of data generated

Using the fully adjustable CrayPAT, Automatic Profiling Analysis (APA) is a guided tracing combining the advantages of Sampling and tracing. Furthermore, the event tracing can be enhanced by using loop profiling.

Usage

Starting with perftools version 6.3.0 as a basis the module perftools-base should be loaded. This provides access to man pages, Reveal, Cray Apprentice2, and the new instrumentation modules. This module can be kept loaded without impact to applications. As instrumentation modules following is available:

• perftools-lite (sampling experiments)
• perftools-lite-events (tracing experimants)
• perftools-lite-loops (collect data for auto-parallelization / loop estimates in Reveal)
• perftools-lite-gpu (gpu kernel and data movemnets)
• perftools (fully adjustable CrayPAT, using pat_build and pat_report)

CrayPAT

The perftools-lite modules provide a user-friendly way to auto-instrument your application for various profiling cases. The perftools module provide CrayPATs full functionality. As described below instrumentation and report generation can be triggered manually specifying various options. In the following descriptions we assume using a simple batch job script:

$> cat job.pbs
#!/bin/bash
#PBS –l nodes=1:ppn=24
#PBS –l walltime=00:10:00
#PBS –j oe
#PBS -o job.out

cd $PBS_O_WORKDIR
aprun –n 384 –N 24 <exe>

An application is instrumented and run using the following commands:

$> module load perftools-base
$> module load <CrayPAT-lite-module>
$> make clean; make
$> qsub job.pbs   <span style="color:#808080"># no changes needed: aprun –n 24 app.exe >& job.out </span>
$> less job.out

As a result a *.rpt and a *.ap2 file are created and the report is additionally printed to stdout.

Additional information and representation can be gathered using pat_report with the produced *.ap2 file.

$> pat_report <option> *.ap2 

Descriptions of the available option can be obtained using man pat_report

REMEMBER: After the experiment is complete, unload perftools-lite-XXX module to prevent further program instrumentation. The perftools-base module can be kept loaded.

perftools-lite

This module is default CrayPat-lite profiling. It enables sampling of the application.

Beside other information the Profiling by Function Group and Function is presented in the report:

Table 1:  Profile by Function Group and Function (top 8 functions shown)

  Samp% |  Samp |  Imb. |  Imb. |Group
        |       |  Samp | Samp% | Function
        |       |       |       |  PE=HIDE
       
 100.0% | 263.4 |    -- |    -- |Total
|----------------------------------------------------------------------
|  78.0% | 205.3 |    -- |    -- |MPI
||---------------------------------------------------------------------
||  62.4% | 164.4 | 115.6 | 42.2% |mpi_bcast
||  10.4% |  27.4 | 186.6 | 89.1% |MPI_ALLREDUCE
||   4.7% |  12.4 |  86.6 | 89.3% |MPI_IPROBE
||=====================================================================
|  13.1% |  34.5 |    -- |    -- |USER
||---------------------------------------------------------------------
...
|======================================================================

Where the stack trace of all processes are merged and the combined information is presented as relative and absolute values of the counted samples in the group/function and imbalances between processes.

perftools-lite-events

This module enables CrayPATs event tracing of applications. After loading the modules, re-compiled/linked the application and submitting the job as usual, the report is written in the above described way. In contrast to sampling, event tracing reports out real time in groups / functions.

perftools-lite-loops

This module enables CrayPat-lite loop work estimates. It must be used with Cray compiler. After proceeding in the above described way, loop work estimates are sent to stdout and to .ap2 file. Performance data can be combined with source code information and compiler annotation using the .ap2 file with Reveal. The module modify the compile and link steps to include CCE’s –h profile_generate option and instrumenting the program for tracing (pat_build -w). Remember that –h profile_generate reduces compiler optimization levels. After experiment is complete, unload perftools-lite-loops to prevent further program instrumentation.

Table 1:  Inclusive and Exclusive Time in Loops (from -hprofile_generate)
  Loop | Loop Incl |      Time |    Loop |  Loop |  Loop |  Loop |Function=/.LOOP[.]
  Incl |      Time |     (Loop |     Hit | Trips | Trips | Trips | PE=HIDE
 Time% |           |     Adj.) |         |   Avg |   Min |   Max |
|-----------------------------------------------------------------------------
| 93.0% | 19.232051 |  0.000849 |       2 |  26.5 |     3 |    50 |jacobi.LOOP.1.li.236 
| 77.8% | 16.092021 |  0.001350 |      53 | 255.0 |   255 |   255 |jacobi.LOOP.2.li.240 
| 77.8% | 16.090671 |  0.110827 |   13515 | 255.0 |   255 |   255 |jacobi.LOOP.3.li.241 
| 77.3% | 15.979844 | 15.979844 | 3446325 | 511.0 |   511 |   511 |jacobi.LOOP.4.li.242 
| 14.1% |  2.906115 |  0.001238 |      53 | 255.0 |   255 |   255 |jacobi.LOOP.5.li.263

perftools

In contrast to the perftools-lite module, which automatically instrument and report, the perftools module require a manually instrumentation and report generation:

$> module load perftools-base
$> module load perftools
$> make clean; make	# If your application is already built with perftools loaded you do not have to rebuild when switching the experiment.
$> pat_build <pat_options> app.exe	# pat_options are described below; Creates instrumented binary app.exe+pat
$> qsub job.pbs       # ATTENTION: now you have to use the new instrumented binary "aprun <options> ./app.exe+pat"
$> pat_report –o myrep.txt app.exe+pat+*  

Running the “+pat” binary creates a data file or directory. pat_report reads that data file and prints lots of human-readable performance data. It also creates an *.ap2 file which contains all profiling data. (The app.exe+pat+* file/directory can be deleted after the creation of the .ap2 file)

The instrumentation can be adjusted using pat_build options, which are listed in man pat_build, some few commonly used options are:

Option	Description
	Sampling profile
-u	tracing of functions in source file owned by the user
-w	Tracing is default experiment
-T <func>	Specifies a function which will be traced
-t <file>	All functions in the specified file will be traces
-g <group>	Instrument all functions belonging to the specified trace function group, e.g. blas, io, mpi, netcdf, syscall

It should be noted, that only true function calls can be traced. Functions that are inlined by the compiler or that have local scope in a compilation unit cannot be traced.

Cray Profiler

The Cray profiler library is deprecated, but still available on the system. A description can be found here

Third party tools

Gnu-Tools

The module gnu-tools collects more recent versions of basic functionalities, including the GNU building system (autoconf, automake, libtool, m4), as well as bash, cmake, gperf, git, gwak, swig, and bison. The actual versions can be listed using

% module whatis tools/gnu-tools

To use the actual version of bash with full support of the module environment you can simply call

% bash -l myScript.sh

or define the absolute path in the first line of your script

#!/opt/hlrs/tools/gnu-tools/generic/bin/bash -l

Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. GNU Octave is normally used through its interactive interface (CLI and GUI), but it can also be used to write non-interactive programs. The GNU Octave language is quite similar to Matlab so that most programs are easily portable.

Octave is compiled to run on the compute nodes and can be launched e.g. in an interactive session:

% qsub -I [options]
% module load tools/octave 
% aprun -n 1 -N 1 octave octave.script

PARPACK

With the module hlrs_PARPACK the collections of f77 routines designed to solve large scale eigenvalue problems (ARPACK) and the parallel version (PARPACK) are provided. To link these libraries you only have to load the module

 numlib/hlrs_PARPACK 

Important Features of ARPACK:

• Reverse Communication Interface.
• Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric,
• Standard or Generalized Problems.
• Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems.
• Routines for Banded Matrices - Standard or Generalized Problems.
• Routines for The Singular Value Decomposition.
• Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision.

Warning: after swapping the PrgEnv this module has to be (re)loaded again (module load numlib/hlrs_PARPACK).

Python

Actual versions of Python can be used loading the module tools/python.

SLEPc

The SLEPc (Scalable Library for Eigenvalue Problem Computations) is an extantion of PETSc for solving linear eigenvalue problems in either standard or generalized form. Furthermore, SLEPc can compute partial SVD of a large, sparse, rectangular matrix, and solve nonlinear eigenvalue problems (polynomial or general). Additionally, SLEPc provides solvers for the computation of the action of a matrix function on a vector. SLEPc can be used for real (default) and complex arithmetics, therefore two different modules are provided:

  module load numlib/hlrs_SLEPc    # deafault version

OR

  module load numlib/hlrs_SLEPc/3.5.3-complex 

As usual the modules provides all compiler and linker flags, thus ex1.c (containing SLEPc calls) can be simply compiled by

 
  cc ex1.c -o ex1.exe

Warning: Please select first the desired PrgEnv or after swapping the PrgEnv (re)loaded this module again (module load numlib/hlrs_SLEPc). Supported programming environments are PrgEnv-cray, PrgEnv-gnu, and PrgEnv-intel.

SVN

Subversion is installed with the following repository access (RA) modules: ra_svn, ra_local, ra_serf. Plaintext and GPG-Agent authentication credential caches are avaiable.

  module load tools/svn

Utilities for processing netcdf files

The module tools/netcdf_utils contains the follwing tools:

• nco (see http://nco.sourceforge.net/)
• ncview (see http://meteora.ucsd.edu/~pierce/ncview_home_page.html)
• cdo (see https://code.zmaw.de/projects/cdo)

Third party scientific software

CP2K

CP2K is a freely available (GPL) program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. It is very well and consistently written, standards-conforming Fortran 95, parallelized with MPI and in some parts with hybrid OpenMP+MPI as an option.

CP2K provides state-of-the-art methods for efficient and accurate atomistic simulations, sources are freely available and actively improved. It has an active international development team, with the unofficial head quarters in the University of Zürich.

The molecular simulation package is installed, optimized for the present architecture, compiled with gfortran using optimized versions of libxc, libint and libsmm.

 module load chem/cp2k 

provide four versions of different kind of parallelizations:

 cp2k.ssmp  - only OpenMP
 cp2k.popt  - only MPI 
 cp2k.psmp  - hybrid MPI + OpenMP
 cp2k.pdbg  - only MPI compiled with debug flags

After loading the related module (chem/cp2k), the binary can be directly called in the job submission script, e.g.:

aprun -n 24 -N 24 cp2k.psmp myCp2kInputFile.inp > myOutput.out

Some examples for CP2K input files are provided on the CP2K homepage and there also exist the input reference.

Gromacs

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package which can be used by

 module load chem/gromacs 

LAMMPS

LAMMPS "LAMMPS Molecular Dynamics Simulator" is a molecular dynamics package which can be used by

 module load chem/lammps 

The executable is named lmp_CrayXC.

NAMD

NAMD (Scalable Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems, based on Charm++ parallel objects. The package can be loaded using

 module load chem/namd 

A tutorial can be found here.

OpenFOAM

OpenFOAM (Open Field Operation and Manipulation) is an open source CFD software package. Multiple versions of OpenFOAM are available compiled with gnu and intel. Available versions can be listed using

 module avail cae/openfoam 

OpenFOAM can be used with PrgEnv-gnu and PrgEnv-intel, e.g.

 
module swap PrgEnv-cray PrgEnv-gnu
module load cae/openfoam

Furthermore, Foam-extend is available but only for PrgEnv-gnu

 
module swap PrgEnv-cray PrgEnv-gnu
module load cae/openfoam/3.0-extend

As a first example a test case of incompressible laminar flow in a cavity using blockMesh and icoFoam is provided, which can be found in the directory

 /opt/hlrs/cae/fluid/OPENFOAM/ESM/CRAY-Versionen/hornet-example 

To run this example you have to copy the directory and submit the prepareOF and runOF jobs.

It is also possible to use CrayPAT profiling for certain version of OpenFOAM. Therefore, specialized module exist providing relevant versions cae/openfoam/xxx-perftools, where xxx are version numbers. The related binaries still has to be instrumented using

 
pat_build $FOAM_APPBIN/icoFoam

As a result a binary icoFoam+pat is generated in the current directory. Using these binary in the batch script the profiling will be performed. To analyze the resulting profiling data pat_report and further tools can be used (Cray Performance Tools). If during the execution of your instrumented binary you notice that the MPI is not recognized, i.e. you see replicated output or several *.xf files not collected in a single directory in your workspace, you cat export PAT_BUILD_PROG_MODELS="0x1" in your shell and run the pat_build command again after removing the instrumented binary. Please file a ticket if this did not work for you.