Difference between revisions of "Profiling GEOS-Chem with the TAU performance system"

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== Installing TAU ==
 
== Installing TAU ==
  
'''''NOTE: These instructions are still in flux.'''''
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The best way to build TAU is with Spack.  Please see these instructions at [https://github.com/geoschem/geos-chem/issues/637 '''Github issue geoschem/geos-chem #637'''].
  
The best way to install TAU is to use Spack.
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== Compiling and running GEOS-Chem with TAU ==
  
(1) '''Download Spack''' as described at [https://github.com/geoschem/geos-chem/issues/637 |'''Github issue geoschem/geos-chem #637''']].
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You can use the <tt>tau_exec</tt> command to profile GEOS-Chem in order to reveal computational bottlenecks. Below is a job script that you can use.
  
(2) '''Define environment variables''' for Spack as described [[Use_Spack_to_install_netCDF_on_your_system#Set_up_the_environment_for_Spack|'''HERE''']].
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NOTE: The <tt>gcc.env</tt> file is the [https://github.com/geoschem/geos-chem/issues/637#issuecomment-788968697 script that loads your Spack modules].
  
(3) '''Check if Spack can find your compiler''' as described [[Use_Spack_to_install_netCDF_on_your_system#Make sure that Spack can find your compiler|'''HERE''']].
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#!/bin/bash
 
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(4) '''Install TAU''' with the following Spack command:
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spack install tau@2.28.1 openmp=True
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You can also force installation with a <span style="color:blue">specific compiler version</span> by typing:
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spack install tau@2.28.1 <span style="color:blue">%gcc@8.2.0</span> openmp=True
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(5) '''Define environment variables for TAU''' as shown below. 
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# TAU home location
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export TAU_HOME=$(spack location -i tau)
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  # Put the location of tau_f90.sh in the search path
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  #SBATCH -c 24
  export PATH=$PATH:$TAU_HOME/bin
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  #SBATCH -n 1
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#SBATCH -p YOUR-QUEUE-NAME
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#SBATCH --mem=15000
 
   
 
   
  # Define options for TAU
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  ### geoschem.profile.run
  export TAU_OPTIONS="-optRevert -optVerbose -optPreProcess -optContinueBeforeOMP -optPdtGnuFortranParser"
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  ### Job script to run GEOS-Chem with TAU profiling
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source ~/.bashrc  # Load bash settings
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source ~/gcc.env  # Environment file that loads TAU module from Spack
 
   
 
   
  # Define location of TAU makefile
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  # Set the # of OpenMP threads to the # of cores we requested
  export TAU_MAKEFILE=$TAU_HOME/x86_64/lib/Makefile.tau-papi-pthread-pdt-openmp
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  export OMP_NUM_THREADS=24
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# Run GEOS-Chem Classic and have TAU profile it
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srun -c $OMP_NUM_THREADS tau_exec -T serial,openmp -ebs -ebs_resolution=function ./gcclassic > log 2>&1
  
You can place these into one of your system environment files so that they are executed on startup.
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If you use SLURM, you can submit this with
 
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== Compiling and running GEOS-Chem with TAU ==
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To profile GEOS-Chem with TAU, you must first compile with the <tt>TAU_PROF=y</tt> Makefile option, e.g.:
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  # Remove files from a previous compilation with TAU (if necessary)
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  make tauclean
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  # Compile with TAU profiling
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  make TAU_PROF=y ...etc. other makefile options ...
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It is important that you compile on a single processor (i.e. don't pass <tt>-j4</tt> or <tt>-j8</tt>) to allow TAU to properly instrument the code.
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sbatch geoschem.profile.run
  
The <tt>TAU_PROF=y</tt> option will set <tt>COMPILE_CMD :=tau_f90.sh</tt> instead of <tt>COMPILE_CMD :=$(FC)</tt> where <tt>FC</tt> is <tt>gfortran</tt> or <tt>ifort</tt>.
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Otherwise you can just run it interactively:
  
Once you have compiled GEOS-Chem with <tt>TAU_PROF=y</tt>, you can run GEOS-Chem as you normally would. GEOS-Chem will create <tt>profile.*</tt> files containing the profiling information.
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./geoschem.profile.run
  
 
== Using ParaProf to create plots from the profiling data ==
 
== Using ParaProf to create plots from the profiling data ==

Latest revision as of 23:21, 2 March 2021

Previous | Next | Guide to GEOS-Chem performance

  1. Parallelizing GEOS-Chem
  2. GEOS-Chem 7-day timing tests
  3. GEOS-Chem scalability
  4. GEOS-Chem 1-month benchmark timing results
  5. Profiling GEOS-Chem with the TAU performance system
  6. Speeding up GEOS-Chem


NOTE: This page is still under development. The Spack installation guide is still being validated.

Overview

The TAU Performance System is a profiling tool for performance analysis of parallel programs in Fortran, C, C++, Java, and Python. TAU uses a visualization tool, ParaProf, to create graphical displays of the performance analysis results.

Installing TAU

The best way to build TAU is with Spack. Please see these instructions at Github issue geoschem/geos-chem #637.

Compiling and running GEOS-Chem with TAU

You can use the tau_exec command to profile GEOS-Chem in order to reveal computational bottlenecks. Below is a job script that you can use.

NOTE: The gcc.env file is the script that loads your Spack modules.

#!/bin/bash

#SBATCH -c 24
#SBATCH -n 1
#SBATCH -p YOUR-QUEUE-NAME
#SBATCH --mem=15000

### geoschem.profile.run
### Job script to run GEOS-Chem with TAU profiling
 
source ~/.bashrc  # Load bash settings
source ~/gcc.env  # Environment file that loads TAU module from Spack

# Set the # of OpenMP threads to the # of cores we requested
export OMP_NUM_THREADS=24

# Run GEOS-Chem Classic and have TAU profile it
srun -c $OMP_NUM_THREADS tau_exec -T serial,openmp -ebs -ebs_resolution=function ./gcclassic > log 2>&1

If you use SLURM, you can submit this with

sbatch geoschem.profile.run

Otherwise you can just run it interactively:

./geoschem.profile.run

Using ParaProf to create plots from the profiling data

In your run directory, there should be one or more profile.* files. The number of profile.* files will depend on the number of CPUs that you use for your GEOS-Chem simulation. To pack all of the profiling data into a single file, type:

paraprof --pack GEOS-Chem_Profile_Results.ppk

Then run paraprof on the packed format (.ppk) file using:

paraprof GEOS-Chem_Profile_Results.ppk

This will open two windows, the ParaProf Manager window and the Main Data window. For more information on how to interpret the profiling data, see the ParaProf User's Manual.

If you click on the the bar labeled "thread0" in the ParaProf manager window, you can generate a plot that looks like this:

V11-01-thread0.png

The value displayed, the units, and the sort order can be changed from the Options menu. The time that each subroutine spent on the master thread is displayed as a histogram. By examining the histogram you can see which routines are taking the longest to execute. For example, the above plot shows that the COMPUTE_F routine (highlighted with the red box) is spending 444 seconds on the master thread, which is longer than the Rosenbrock solver takes to run. This is a computational bottleneck, which was ultimately caused by an unparallelized DO loop.

To save the plot, select "Save as Bitmap Image" from the File menu. In the Save Image File window, you may select the output type (JPEG File or PNG file) and specify the file name and location.

--Melissa Sulprizio (talk) 22:48, 8 February 2017 (UTC)
--Bob Yantosca (talk) 16:55, 10 February 2017 (UTC)



Previous | Next | Guide to GEOS-Chem performance