How to run HPL/HPCG/IO500 in WSL

[TOC]

0. PC Info

Name	Info
Edition	Windows 11 Pro Insider Preview 64-bit 22H2 (10.0, Build 1000.23451.1000.0) (23451.ni_prerelease.230428-1438)
Processor	12th Gen Intel(R) Core(TM) i7-12700H (14 Cores 20 CPUs), ~2.3GHz
Memory	16384MB RAM + 18925MB Page File

1. HPL (High-Performance Linpack)

0. Info

Name	Version
OS	Ubuntu 22.04.2 LTS (GNU/Linux 5.15.90.1-microsoft-standard-WSL2 x86_64)
GCC	gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu1~22.04.1)
OpenMPI	4.1.5
OpenBLAS	0.3.23

1. Install WSL

In Windows 11, you can get WSL from Microsoft Store.

Run Ubuntu from the start menu and set a username and password. When finished you will see output like following:

Installing, this may take a few minutes...
Please create a default UNIX user account. The username does not need to match your Windows username.
For more information visit: https://aka.ms/wslusers
Enter new UNIX username: hangyi
New password:
Retype new password:
passwd: password updated successfully
The operation completed successfully.
Installation successful!
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

Welcome to Ubuntu 22.04.2 LTS (GNU/Linux 5.15.90.1-microsoft-standard-WSL2 x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage


This message is shown once a day. To disable it please create the
/home/hangyi/.hushlogin file.
hangyi@DESKTOP-VHIQPUO:~$

You can use the following commands to view system information.

uname -a && lsb_release -a

Output like this, I use Ubuntu 22.04.2 LTS:

Linux DESKTOP-VHIQPUO 5.15.90.1-microsoft-standard-WSL2 #1 SMP Fri Jan 27 02:56:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.2 LTS
Release:        22.04
Codename:       jammy

If you exit, you can run wsl -d Ubuntu --cd ~ to return Ubuntu.

2. Install OpenMPI and OpenBLAS

If you are not confident about your network situation, it is recommended to configure a mirror source.
```
sudo sed -i 's@//.*.ubuntu.com@//mirrors.ustc.edu.cn@g' /etc/apt/sources.list
```
Running the above command will change your source address to the USTC mirror source. You may need to enter the password you set during the WSL installation.

Install the compile tools.

sudo apt update && sudo apt install -y build-essential gfortran

Installing using the package manager should be the easy way out, but the version may be older.
```
sudo apt install -y libopenmpi-dev libopenblas-dev
```

Test if the installation was successful:

gcc --version && gfortran --version && mpirun --version && find /usr -name libmpi.so && find /usr -name libopenblas.a

If the outputs like the following, it's OK:

gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mpirun (Open MPI) 4.1.2

Report bugs to http://www.open-mpi.org/community/help/
/usr/lib/x86_64-linux-gnu/libmpi.so
/usr/lib/x86_64-linux-gnu/libopenblas.a

3. Compile HPL

Get HPL from https://www.netlib.org/benchmark/hpl.

wget https://www.netlib.org/benchmark/hpl/hpl-2.3.tar.gz

Unpack file.
```
tar -xzvf hpl-2.3.tar.gz && cd hpl-2.3
```
Copy a sample configuration from the Setups folder.
```
cp setup/Make.Linux_PII_CBLAS ./
```
Edit the Make.Linux_PII_CBLAS file. You can use editors like vi/vim/gedit/nano, I'll use nano as an example.
```
nano Make.Linux_PII_CBLAS
```
And change the following lines:
```
TOPdir       = $(HOME)/hpl-2.3

MPdir        = /usr/lib/x86_64-linux-gnu/openmpi
MPlib        = $(MPdir)/lib/libmpi.so

LAdir        = /usr/lib/x86_64-linux-gnu/openblas-pthread
LAlib        = $(LAdir)/libopenblas.a $(LAdir)/libbblas.a

CC           = /usr/bin/mpicc
LINKER       = /usr/bin/gfortran
```
For nano, Ctrl + o and Enter to save, Ctrl + x to exit.

If you have other MPI or BLAS libraries installed, you also need to modify MPdir MPlib and LAdir LAlib to the corresponding installation path and library files.
Compile HPL, -j8 is the number of threads you want to open, a larger number will speed up compilation.
```
make arch=Linux_PII_CBLAS -j8
```
Waiting for the end of compilation, if everything is fine with your configuration, you can find HPL.dat and xhpl under bin/Linux_PII_CBLAS.

If you don't find xhpl in bin, but can find in testing, you may have entered the wrong path. If you can't find even in tesing directory, there may be a configuration problem, please check the Make.Linux_PII_CBLAS file.

To run the sample HPL test, we use mpirun to run it in multiple threads, the number after -np is the number of processes to run.

cd bin/Linux_PII_CBLAS
touch HPL.out
mpirun -np 8 xhpl

You will get a lot of output, just a small snippet here.

================================================================================
HPLinpack 2.3  --  High-Performance Linpack benchmark  --   December 2, 2018
Written by A. Petitet and R. Clint Whaley,  Innovative Computing Laboratory, UTK
Modified by Piotr Luszczek, Innovative Computing Laboratory, UTK
Modified by Julien Langou, University of Colorado Denver
================================================================================

An explanation of the input/output parameters follows:
T/V    : Wall time / encoded variant.
N      : The order of the coefficient matrix A.
NB     : The partitioning blocking factor.
P      : The number of process rows.
Q      : The number of process columns.
Time   : Time in seconds to solve the linear system.
Gflops : Rate of execution for solving the linear system.

The following parameter values will be used:

N      :      29       30       34       35
NB     :       1        2        3        4
PMAP   : Row-major process mapping
P      :       2        1        4
Q      :       2        4        1
PFACT  :    Left    Crout    Right
NBMIN  :       2        4
NDIV   :       2
RFACT  :    Left    Crout    Right
BCAST  :   1ring
DEPTH  :       0
SWAP   : Mix (threshold = 64)
L1     : transposed form
U      : transposed form
EQUIL  : yes
ALIGN  : 8 double precision words

--------------------------------------------------------------------------------

- The matrix A is randomly generated for each test.
- The following scaled residual check will be computed:
      ||Ax-b||_oo / ( eps * ( || x ||_oo * || A ||_oo + || b ||_oo ) * N )
- The relative machine precision (eps) is taken to be               1.110223e-16
- Computational tests pass if scaled residuals are less than                16.0

================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR00L2L2          29     1     2     2               0.00             1.9114e-02
HPL_pdgesv() start time

HPL_pdgesv() end time

--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=   1.88218349e-02 ...... PASSED

...
...
...

================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR00R2R4          35     4     4     1               0.00             5.9052e-01
HPL_pdgesv() start time

HPL_pdgesv() end time

--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=   1.99396688e-02 ...... PASSED
================================================================================

Finished    864 tests with the following results:
            864 tests completed and passed residual checks,
              0 tests completed and failed residual checks,
              0 tests skipped because of illegal input values.
--------------------------------------------------------------------------------

End of Tests.
================================================================================

We need to focus on the Gflops value, my maximum value in the sample configuration is 1.3211e+00.

4. Performance Tuning.

0. It is a constant process of experimentation and requires patience.

1. Adjust the HPL.dat file

You can refer https://www.netlib.org/benchmark/hpl/tuning.html to adjust the HPL.dat file, or generate one directly from https://www.advancedclustering.com/act_kb/tune-hpl-dat-file.

Input	Num
Nodes	1
Cores per Node	1
Memory per Node (MB)	512
Block Size (NB)	192

Output:

HPLinpack benchmark input file
Innovative Computing Laboratory, University of Tennessee
HPL.out      output file name (if any) 
6            device out (6=stdout,7=stderr,file)
1            # of problems sizes (N)
7296         Ns
1            # of NBs
192          NBs
0            PMAP process mapping (0=Row-,1=Column-major)
1            # of process grids (P x Q)
1            Ps
1            Qs
16.0         threshold
1            # of panel fact
2            PFACTs (0=left, 1=Crout, 2=Right)
1            # of recursive stopping criterium
4            NBMINs (>= 1)
1            # of panels in recursion
2            NDIVs
1            # of recursive panel fact.
1            RFACTs (0=left, 1=Crout, 2=Right)
1            # of broadcast
1            BCASTs (0=1rg,1=1rM,2=2rg,3=2rM,4=Lng,5=LnM)
1            # of lookahead depth
1            DEPTHs (>=0)
2            SWAP (0=bin-exch,1=long,2=mix)
64           swapping threshold
0            L1 in (0=transposed,1=no-transposed) form
0            U  in (0=transposed,1=no-transposed) form
1            Equilibration (0=no,1=yes)
8            memory alignment in double (> 0)
##### This line (no. 32) is ignored (it serves as a separator). ######
0                               Number of additional problem sizes for PTRANS
1200 10000 30000                values of N
0                               number of additional blocking sizes for PTRANS
40 9 8 13 13 20 16 32 64        values of NB

Modify HPL.dat to the above value and run xhpl again.

mpirun -np 4 xhpl

Output (partial):

================================================================================
HPLinpack 2.3  --  High-Performance Linpack benchmark  --   December 2, 2018
Written by A. Petitet and R. Clint Whaley,  Innovative Computing Laboratory, UTK
Modified by Piotr Luszczek, Innovative Computing Laboratory, UTK
Modified by Julien Langou, University of Colorado Denver
================================================================================

An explanation of the input/output parameters follows:
T/V    : Wall time / encoded variant.
N      : The order of the coefficient matrix A.
NB     : The partitioning blocking factor.
P      : The number of process rows.
Q      : The number of process columns.
Time   : Time in seconds to solve the linear system.
Gflops : Rate of execution for solving the linear system.

The following parameter values will be used:

N      :    7296
NB     :     192
PMAP   : Row-major process mapping
P      :       1
Q      :       1
PFACT  :   Right
NBMIN  :       4
NDIV   :       2
RFACT  :   Crout
BCAST  :  1ringM
DEPTH  :       1
SWAP   : Mix (threshold = 64)
L1     : transposed form
U      : transposed form
EQUIL  : yes
ALIGN  : 8 double precision words

--------------------------------------------------------------------------------

- The matrix A is randomly generated for each test.
- The following scaled residual check will be computed:
      ||Ax-b||_oo / ( eps * ( || x ||_oo * || A ||_oo + || b ||_oo ) * N )
- The relative machine precision (eps) is taken to be               1.110223e-16
- Computational tests pass if scaled residuals are less than                16.0

================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR11C2R4        7296   192     1     1               1.82             1.4243e+02
HPL_pdgesv() start time Fri May 19 23:52:43 2023

HPL_pdgesv() end time   Fri May 19 23:52:45 2023

--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=   3.98844764e-03 ...... PASSED
================================================================================

Finished      1 tests with the following results:
              1 tests completed and passed residual checks,
              0 tests completed and failed residual checks,
              0 tests skipped because of illegal input values.
--------------------------------------------------------------------------------

End of Tests.
================================================================================

You can see that the score has improved by 10781%.

Then I modify these:

file         device out (6=stdout,7=stderr,file)
2            # of problems sizes (N)
16384 20352  Ns
0 1 2        PFACTs (0=left, 1=Crout, 2=Right)
2 8          NBMINs (>= 1)
0 1 2        RFACTs (0=left, 1=Crout, 2=Right)
3 2          BCASTs (0=1rg,1=1rM,2=2rg,3=2rM,4=Lng,5=LnM)

Now run it again and get the output:

================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR13L2L2       16384   192     1     1              10.85             2.7028e+02
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=   2.48156500e-03 ...... PASSED
================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR13L2L2       20352   192     1     1              20.03             2.8064e+02
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=   1.90299920e-03 ...... PASSED
================================================================================

You can see that the score has improved by 22253% than the first. The result of 2.8064e+02 Gflops can enter the Top500 in 2003.06.

2. Change versions

You can install other versions by compiling from source, the version installed from source will be newer.

# For OpenMPI
cd ~ && wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
tar -xzvf openmpi-4.1.5.tar.gz && cd openmpi-4.1.5
./configure --prefix=/usr/local/openmpi
sudo make all install -j8
echo "export PATH=/usr/local/openmpi/bin:\$PATH" >> ~/.bashrc
echo "export LD_LIBRARY_PATH=/usr/local/openmpi/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc
source ~/.bashrc

# For OpenBLAS
cd ~ && wget https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz # If there is a network problem, please switch to https://ghproxy.com/https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz
tar -xzvf OpenBLAS-0.3.23.tar.gz && cd OpenBLAS-0.3.23
make FC=gfortran -j8
sudo make PREFIX=/usr/local/openblas install

# For MPL

cd ~ && wget https://www.netlib.org/benchmark/hpl/hpl-2.0.tar.gz
tar -xzvf hpl-2.0.tar.gz && cd hpl-2.0

You need to change the MPdir and LAdir to the corresponding installation paths, like this:

TOPdir       = $(HOME)/hpl-2.0

MPdir        = /usr/local/openmpi
MPlib        = $(MPdir)/lib/libmpi.so

LAdir        = /usr/local/openblas
LAlib        = $(LAdir)/lib/libopenblas.a

CC           = /usr/local/openmpi/bin/mpicc
LINKER       = /usr/local/openmpi/bin/mpif77

Then recompile MPL and test again.

cp ~/hpl-2.3/bin/Linux_PII_CBLAS/HPL-Tuning.dat ~/hpl-2.0/bin/Linux_PII_CBLAS/HPL.dat
cd ~/hpl-2.0/bin/Linux_PII_CBLAS
mpirun -np 8 xhpl

Output:

================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR13L2L2       16384   192     1     1              15.90              1.844e+02
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=        0.0022339 ...... PASSED
================================================================================
T/V                N    NB     P     Q               Time                 Gflops
--------------------------------------------------------------------------------
WR13L2L2       20352   192     1     1              35.05              1.604e+02
--------------------------------------------------------------------------------
||Ax-b||_oo/(eps*(||A||_oo*||x||_oo+||b||_oo)*N)=        0.0019320 ...... PASSED
================================================================================

~~It seems the results are even worse:>~~

5. In Windows

If you are on windows, you can simply install Intel® oneAPI Base Toolkit to get benchmarks and Intel® oneAPI HPC Toolkit to get mpiexec.

After installation, Run the terminal in administrator mode and go to the directory <oneAPI Install path>\mkl\2023.1.0\benchmarks\mp_linpack.

Then run runme_intel64_dynamic.bat Or run xhpl_intel64_dynamic.exe directly.

This is a SAMPLE run script. Change it to reflect the correct
number of CPUs/threads, number of nodes, MPI processes per node, etc..
This run started on:
05/20/2023 Sat
01:02
Capturing output into: xhpl_intel64_dynamic_outputs.txt

Done:
05/20/2023 Sat
01:02

And you will get a HPL report xhpl_intel64_dynamic_outputs.txt in the current directory.

Then you can refer to the performance tuning guide above to improve your score.

3. HPCG Test

Get source from https://github.com/hpcg-benchmark/hpcg.

git clone https://github.com/hpcg-benchmark/hpcg.git && cd hpcg

Copy example config.
```
cp setup/Make.Linux_MPI ./
```

Modify Configuration, using nano Make.Linux_MPI.

TOPdir       = $(HOME)/hpcg

MPdir        = /usr/lib/x86_64-linux-gnu/openmpi
MPinc        = -I$(MPdir)/include
MPlib        = $(MPdir)/lib/libmpi.so

HPCG_OPTS     = -DHPCG_NO_OPENMP -DHPCG_DETAILED_TIMING

Build from source. If the build fails, delete the folder and download the source code again.
```
make arch=Linux_MPI -j4
```
Now you can find the xhpcg and hpcg.dat files in the bin directory

Test HPCG.

cd bin
mpirun -np 4 xhpcg --nx=16 --rt=1800
# The test will last for 30 minutes (1800 seconds)

Output in file hpcg<identifier>.txt and HPCG-Benchmark_3.1_<identifier>.txt:

$ cat HPCG-Benchmark_3.1_<identifier>.txt | grep GFLOP
GFLOP/s Summary=
GFLOP/s Summary::Raw DDOT=1.46162
GFLOP/s Summary::Raw WAXPBY=18.9513
GFLOP/s Summary::Raw SpMV=10.583
GFLOP/s Summary::Raw MG=8.18653
GFLOP/s Summary::Raw Total=7.88411
GFLOP/s Summary::Total with convergence overhead=7.88411
GFLOP/s Summary::Total with convergence and optimization phase overhead=7.55894
Final Summary::HPCG result is VALID with a GFLOP/s rating of=7.55894

Result is 7.55894 GFLOP/s

Performance Tuning

See https://github.com/hpcg-benchmark/hpcg/blob/master/TUNING and modify the HPCG.dat
```
HPCG benchmark input file
Sandia National Laboratories; University of Tennessee, Knoxville
120 120 120
120
```
And run again.

4. IO500 Test

Clone the io500 source.

git clone https://github.com/IO500/io500.git && cd io500

To Retrieve the required packages and compile the library version, run:

sudo apt install pkg-config # to solve autoconf errors
./prepare.sh

When it’s OK,output:

OK: All required software packages are now prepared
ior  md-workbench  mdtest  pfind

In order to create a new INI file with all the options, you can execute:
```
./io500 --list > config-all.ini
```

(Optional) Modify config-all.ini (My disk space is not enough, you may need not modify).

[ior-easy]
blockSize = 100m

[mdtest-easy]
n = 100

[ior-hard]
segmentCount = 100

[find-hard]
pfind-queue-length = 100

Then you can running the io500 test:

mpiexec -np 8 ./io500 config-all.ini

Output:

IO500 version io500-isc23 (standard)
ERROR INVALID (src/phase_dbg.c:15) stonewall-time < 300s
ERROR INVALID (src/phase_ior.c:24) Write phase needed 1.370603s instead of stonewall 5s. Stonewall was hit at 0.2s
ERROR INVALID (src/main.c:437) Runtime of phase (1.379476) is below stonewall time. This shouldn't happen!
ERROR INVALID (src/main.c:443) Runtime is smaller than expected minimum runtime
[RESULT]       ior-easy-write        0.570005 GiB/s : time 1.379 seconds [INVALID]
ERROR INVALID (src/main.c:437) Runtime of phase (1.056533) is below stonewall time. This shouldn't happen!
ERROR INVALID (src/main.c:443) Runtime is smaller than expected minimum runtime
[RESULT]    mdtest-easy-write       15.711578 kIOPS : time 1.057 seconds [INVALID]
[      ]            timestamp        0.000000 kIOPS : time 0.000 seconds
ERROR INVALID (src/phase_ior.c:24) Write phase needed 0.484803s instead of stonewall 5s. Stonewall was hit at 0.0s
ERROR INVALID (src/main.c:437) Runtime of phase (0.485622) is below stonewall time. This shouldn't happen!
ERROR INVALID (src/main.c:443) Runtime is smaller than expected minimum runtime
[RESULT]       ior-hard-write        0.072243 GiB/s : time 0.486 seconds [INVALID]
ERROR INVALID (src/main.c:443) Runtime is smaller than expected minimum runtime
[RESULT]    mdtest-hard-write       56.509355 kIOPS : time 8.147 seconds [INVALID]
[RESULT]                 find     2339.353769 kIOPS : time 0.173 seconds
[RESULT]        ior-easy-read       14.772937 GiB/s : time 0.057 seconds
[RESULT]     mdtest-easy-stat     2115.664061 kIOPS : time 1.002 seconds
[RESULT]        ior-hard-read       18.307577 GiB/s : time 0.002 seconds
[RESULT]     mdtest-hard-stat     7693.419492 kIOPS : time 1.059 seconds
[RESULT]   mdtest-easy-delete      481.067125 kIOPS : time 1.003 seconds
[RESULT]     mdtest-hard-read     1630.211454 kIOPS : time 1.252 seconds
[RESULT]   mdtest-hard-delete      145.488834 kIOPS : time 3.870 seconds
[SCORE ] Bandwidth 1.826809 GiB/s : IOPS 499.212193 kiops : TOTAL 30.198765 [INVALID]

The result files are stored in the directory: ./results/<date>-<time>

Why is [INVALID], because the running time is not enough for 300 seconds :).

Performance Tuning.

Modify the config-all.ini

[ior-easy]
blockSize = 9920000m

[mdtest-easy]
n = 1000000

[ior-hard]
segmentCount = 10000000

[find-hard]
pfind-queue-length = 10000

And run it again.

5. Reference

https://chat.openai.com

https://www.deepl.com/translator

https://www.open-mpi.org

https://www.netlib.org/benchmark/hpl

https://www.hpcg-benchmark.org

https://github.com/hpcg-benchmark/hpcg

https://github.com/IO500/io500

-1. Advices

Don't keep things until the last day :) !!!

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How to run HPL/HPCG/IO500 in WSL

0. PC Info

1. HPL (High-Performance Linpack)

0. Info

1. Install WSL

2. Install OpenMPI and OpenBLAS

3. Compile HPL

4. Performance Tuning.

0. It is a constant process of experimentation and requires patience.

1. Adjust the HPL.dat file

2. Change versions

5. In Windows

3. HPCG Test

4. IO500 Test

5. Reference

-1. Advices

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images		images
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How to run HPL/HPCG/IO500 in WSL

0. PC Info

1. HPL (High-Performance Linpack)

0. Info

1. Install WSL

2. Install OpenMPI and OpenBLAS

3. Compile HPL

4. Performance Tuning.

0. It is a constant process of experimentation and requires patience.

1. Adjust the HPL.dat file

2. Change versions

5. In Windows

3. HPCG Test

4. IO500 Test

5. Reference

-1. Advices

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