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STAT and ATP

STAT

Note

The tool may fail to work properly without loading the cray-cti module. Until this is added automatically by the system, please load the module, too.

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. The results are then presented graphically as a call tree showing the location that each process is executing.

This is a useful tool for debugging an application that hangs because collected call backtraces can quickly tell you where each process is executing at the moment in the code, providing a hint on where to look further for more detailed analysis.

It supports distributed-memory parallel programming only such as MPI, Coarray Fortran and UPC (Unified Parallel C).

One way to collect backtraces under Slurm is explained below.

  1. Start an interactive batch job and launch an application in background. Keep the process ID (PID).

    $ salloc -N 1 -t 30:00 -q debug [...other flags...]
    ...
    $ srun -n 4 [...other flags...] ./jacobi_mpi &
    [1] 95298
    

    You can also see the PID by running the ps command:

    $ ps
       PID TTY          TIME CMD
     95018 pts/0    00:00:00 bash
     95298 pts/0    00:00:00 srun
     95302 pts/0    00:00:00 srun
     95325 pts/0    00:00:00 ps
    
  2. Load the stat module on Cori. Load cray-stat on Perlmutter:

    module load stat             # Cori
    
    module load cray-stat        # Perlmutter
    
  3. Run the stat-cl command on this process. You may want to use the -i flag to gather source line numbers, too:

    $ stat-cl -i 95298
    STAT started at 2016-11-30-07:33:37
    Attaching to job launcher (null):95298 and launching tool daemons...
    Tool daemons launched and connected!
    Attaching to application...
    Attached!
    Application already paused... ignoring request to pause
    Sampling traces...
    Traces sampled!
    ...
    Resuming the application...
    Resumed!
    Merging traces...
    Traces merged!
    Detaching from application...
    Detached!
    
    Results written to /global/cscratch1/sd/elvis/parallel_jacobi/stat_results/jacobi_mpi.0004
    

    stat-cl takes several backtrace samples after attaching to the running processes. The result file is created in the stat_results subdirectory under the current working directory. This subdirectory contains another subdirectory whose name is based on your parallel application's executable name that contains the merged stack trace file in DOT format.

  4. Then, run the GUI command, stat-view (or STATview), with the file above to visualize the generated *.dot files for stack backtrace information.

    stat-view stat_results/jacobi_mpi.0004/00_jacobi_mpi.0004.3D.dot
    

    Please note that, if you're running on Cori KNL nodes, you have to go to a login node for this step (after loading the stat module there). Otherwise, fonts will not be shown correctly.

    STAT with linenumer

    The above call tree diagram reveals that rank 0 is in the init_fields routine (line 172 of jacobi_mpi.f90), rank 3 in the set_bc routine (line 214 of the same source file), and the other ranks (1 and 2) are in the MPI_Sendrecv function. If this pattern persists, it means that the code hangs in these locations. With this information, you may want to use a full-fledged parallel debugger such as DDT or TotalView to find out why your code is stuck in these places.

ATP

Note

The tool may fail to work properly without loading the cray-cti module. Until this is added automatically by the system, please load the module, too.

Note

ATP is not currently working on Perlmutter, we are working with Cray on a solution.

Another useful tool in the same vein is ATP (Abnormal Termination Processing) that Cray has developed. ATP gathers stack backtraces when the code crashes, by running STAT before it exits.

The atp module is load by default on Cori. However, it is not on Perlmutter. Ensure that the target application is built with debug symbols (usually -g) after loading the module. Note also that, when the module is loaded, applications built with the Cray or GNU compilers are automatically linked against the ATP signal handler.

To enable it at runtime so that it generates stack backtrace info upon a failure, set the following environment variable before your srun command in your batch script:

setenv ATP_ENABLED 1          # for csh/tcsh

export ATP_ENABLED=1          # for bash/sh/ksh

Intel Fortran and GNU Fortran have their own abnormal termination handling enabled by default. If ATP processing is desired instead, you need to set the FOR_IGNORE_EXCEPTIONS environment variable if you're using Fortran and you have built with the Intel compiler:

setenv FOR_IGNORE_EXCEPTIONS true   # for csh/tcsh

export FOR_IGNORE_EXCEPTIONS=true   # for bash/sh/ksh

If your Fortran code is built with the GNU compiler, you will need to link with the -fno-backtrace option.

When atp is loaded no core file will be generated. However, you can get core dumps (core.atp.<apid>.<rank>) if you set coredumpsize to unlimited:

unlimit coredumpsize   # for csh/tcsh

ulimit -c unlimited    # for bash/sh/ksh

Even if Linux core dumping is enabled, ATP-specific core dumping can be disabled by setting the environment variable ATP_MAX_CORES to 0.

More information can be found in the man page: type man intro_atp or, simply, man atp.

The following is to test ATP using an example code available in the ATP distribution package on Cori.

$ cp $ATP_HOME/demos/testMPIApp.c .
$ cc -o testMPIApp testMPIApp.c

$ cat runit
#!/bin/bash
#SBATCH -N 1
#SBATCH -t 5:00
#SBATCH -q debug

export ATP_ENABLED=1
srun -n 8 ./testMPIApp 1 4

$ sbatch runit
Submitted batch job 3044170

$ cat slurm-3044710.out
[snip]
testApp: (31929) starting up...
testApp: (31932) starting up...
testApp: (31930) starting up...
testApp: (31933) starting up...
Application 3044170 is crashing. ATP analysis proceeding...

ATP Stack walkback for Rank 3 starting:
  _start@start.S:122
  __libc_start_main@libc-start.c:285
  main@testMPIApp.c:76
  raise@pt-raise.c:37
ATP Stack walkback for Rank 3 done
Process died with signal 4: 'Illegal instruction'
View application merged backtrace tree with: STATview atpMergedBT.dot
You may need to: module load stat

srun: error: nid00009: tasks 0-3: Killed
srun: Terminating job step 3044170.0
srun: Force Terminated job step 3044170.0
[snip]

ATP creates a merged stack backtrace files in DOT fomat in atpMergedBT.dot (with function-level aggregation) and atpMergedBT_line.dot (with line-level aggregation). The latter shows source line numbers. To view the collected backtrace result, you need to load the stat module on Cori or cray-stat on Perlmutter, and run stat-view:

module load stat                # 'module load cray-stat' on Perlmutter
stat-view atpMergedBT.dot

ATP merged BT

ATP can be a useful tool in debugging a hung application, too. You can force ATP to generate backtraces for a hung application by killing the application. To do that, you should have done necessary preparatory work such as setting the ATP_ENABLED environment variable, etc. in the batch script for the job in question.

$ sacct -j 3169879                # find job step id for the application - it's 3169879.0
       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
3169879           runit        knl      mpccc        544    RUNNING      0:0
3169879.ext+     extern                 mpccc        544    RUNNING      0:0
3169879.0    jacobi_mp+                 mpccc          4    RUNNING      0:0
3169879.1    cti_dlaun+                 mpccc          2    RUNNING      0:0


$ scancel -s ABRT 3169879.0       # Kill the application

$ cat slurm-3169879.out
Application 3169879 is crashing. ATP analysis proceeding...

ATP Stack walkback for Rank 0 starting:
  _start@start.S:122
  __libc_start_main@libc-start.c:285
  main@0x40a59d
  MAIN__@jacobi_mpi.f90:174
ATP Stack walkback for Rank 0 done
Process died with signal 6: 'Aborted'
View application merged backtrace tree with: STATview atpMergedBT.dot
You may need to: module load stat
[snip]

$ stat-view atpMergedBT_line.dot

ATP merged BT for hung application

The above example is to use SIGABRT in killing the application. There are other signals accepted by ATP. For info, please read the atp man page.

If you cannot run your application interactively because your job requests a large number of nodes or it takes a long time to reach a problematic area, the above interactive approach is not practical. In that case, you can submit a non-interactive batch job where a signal is sent just before the job is supposed to end, and a signal handler cancels the application. The following example job script is to send the SIGUSR1 signal (a user-defined signal) 300 seconds before the job ends (#SBATCH --signal=B:USR1@300) -- this is when the application is presumed hung. The job runs a trap command which then sets the canceL_srun function to be invoked upon catching the signal. The function then cancels the application, triggering ATP to generate debug info. Note that, in this example, the srun process is canceled with the Slurm job step ID, ${SLURM_JOB_ID}.0, for the first srun ("0") of the job. If you have multiple srun's in a job script and you want to target a certain job step, the proper step ID should be used.

#!/bin/bash
#SBATCH -N 2
#SBATCH -C knl
#SBATCH -t 30
#SBATCH -q regular
#SBATCH --signal=B:USR1@300

 module load cray-cti
 export ATP_ENABLED=1
 export FOR_IGNORE_EXCEPTIONS=true   # Fortran code built with the Intel compiler

 cancel_srun() {
   echo SLURM_JOB_ID = $SLURM_JOB_ID
   scancel -s ABRT ${SLURM_JOB_ID}.0
 }

 srun -n 8 --cpu-bind=cores ./jacobi_mpi &

 trap cancel_srun SIGUSR1

 wait