thr3ads.net - R help - [R] fixed set.seed + kmeans output disagree on distinct platforms [Sep 2024]

If this information is useful, please help other people find it:
Share via:

Iago Giné Vázquez

2024-Sep-04 05:23 UTC

[R] fixed set.seed + kmeans output disagree on distinct platforms

Hi all,

I build a dataset processing in the same way the same data in Windows than in
Linux.

The output of Windows processing is:
https://gitlab.com/iagogv/repdata/-/raw/main/exdata.csv?ref_type=heads
The output of Linux processing is:
https://gitlab.com/iagogv/repdata/-/raw/main/exdata2.csv?ref_type=heads

exdata=as.matrix(read.csv("https://gitlab.com/iagogv/repdata/-/raw/main/exdata.csv?ref_type=heads",
header=FALSE))
exdata2=as.matrix(read.csv("https://gitlab.com/iagogv/repdata/-/raw/main/exdata2.csv?ref_type=heads",
header=FALSE))

They are not identical (`identical(exdata,exdata2)` is FALSE), but they are
essentially equal (`all.equal(exdata,exdata2)` is TRUE). If I run

set.seed(20232260)
exkmns <- kmeans(exdata, centers = 7, iter.max = 2000, nstart = 750)

I get

exkmns$centers
          V1         V2          V3          V4          V5           V6
1 -0.4910731 -0.2662055  0.57928758  0.14267293 -0.03013791  0.106472717
2  0.5301237  0.2815620 -0.23898532  1.00979412 -0.26123328  0.068099931
3  0.2255298 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.107538855
4 -0.2616257  0.5680582  0.55387437 -0.09562789 -0.01706577 -0.028248679
5 -0.4820078 -0.1667370 -0.46533618 -0.05271446  0.05477352  0.005236259
6  0.6455994 -0.1396674  0.05988547 -0.15557399  0.62766365  0.031051986
7  0.1072127  0.5538876 -0.33117098 -0.43209203 -0.18646403 -0.081273130

both in Windows  (1) and in Linux (2, 3) up to rows order. If I run in Linux in
my computer (2)

set.seed(20232260)
exkmns2 <- kmeans(exdata2, centers = 7, iter.max = 2000, nstart = 750)

then, I get

exkmns2$centers
           V1         V2          V3          V4          V5          V6
1  0.64559941 -0.1396674  0.05988547 -0.15557399  0.62766365  0.03105199
2 -0.26162573  0.5680582  0.55387437 -0.09562789 -0.01706577 -0.02824868
3  0.53012369  0.2815620 -0.23898532  1.00979412 -0.26123328  0.06809993
4  0.03409765  0.3492520 -0.36910409 -0.40721418 -0.21482793  0.03073180
5 -0.58527394 -0.1790337 -0.46778956  0.03573883  0.15473589 -0.07980379
6 -0.49107314 -0.2662055  0.57928758  0.14267293 -0.03013791  0.10647272
7  0.22552984 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.10753886

therefore, all rows essentially equal except for rows 5 and 7 of first dataset
(5 and 4 of second dataset).  With a bit more detail:

  *
Row 0.2255298 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.107538855
belongs to exdata (and exdata2) and is center of both outputs
  *
Row 0.1072127  0.5538876 -0.33117098 -0.43209203 -0.18646403 -0.081273130
belongs to the dataset and it is only center of exdata output
  *
Row -0.4820078 -0.1667370 -0.46533618 -0.05271446  0.05477352  0.005236259 does
not belong to the dataset and it is only center of exdata output
  *
Row -0.58527394 -0.1790337 -0.46778956  0.03573883  0.15473589 -0.07980379
belongs to the dataset and it is only center for exdata2 on Linux in my computer
  *
Row 0.03409765  0.3492520 -0.36910409 -0.40721418 -0.21482793  0.03073180 does
not belong to the dataset and it is only center for exdata2 on Linux in my
computer
  *
All other 4 rows (1,2,4 and 6 of first output) do not belong to the dataset and
are common centers.

Even, further, if I run

set.seed(20232260)
exkmns <- kmeans(exdata, centers = 7, iter.max = 2000, nstart = 750)

in  posit.cloud (3), I get the same result than above. However, if I run (both
in posit.cloud or in Windows)

set.seed(20232260)
exkmns2 <- kmeans(exdata2, centers = 7, iter.max = 2000, nstart = 750)

then I get


exkmns2$centers
          V1         V2          V3         V4          V5          V6
1  0.6426035 -0.1449498  0.05843435 -0.1527968  0.62943077  0.02984948
2 -0.4092382 -0.3740695  0.69597037  0.1956896 -0.05026200 -0.01453132
3  0.1072127  0.5538876 -0.33117098 -0.4320920 -0.18646403 -0.08127313
4  0.2255298 -0.5165964 -0.02498471 -0.2043827 -0.41224195 -0.10753886
5  0.5301237  0.2815620 -0.23898532  1.0097941 -0.26123328  0.06809993
6 -0.5223387 -0.1484517 -0.38982567 -0.0341488  0.06446446  0.03622056
7 -0.2701703  0.5263218  0.52942311 -0.1112202 -0.03460591  0.03577287

So only its rows 4 and 5 are common centers to both of previous outputs and row
3 is common width exdata centers.

Does all this have any sense?

Thanks!

Iago

(1)
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default

(2)
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so; 
LAPACK version 3.11.0

(3)
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

 Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so; 
LAPACK version 3.9.0




	[[alternative HTML version deleted]]

Bert Gunter

2024-Sep-04 06:32 UTC

head link

[R] fixed set.seed + kmeans output disagree on distinct platforms

I have no clue, but I did note that you are using different versions of
BLAS/LAPACK on the different platforms. Could that be (part) of the issue?

Cheers,
Bert

On Tue, Sep 3, 2024 at 10:24?PM Iago Gin? V?zquez <iago.gine at sjd.es>
wrote:
> Hi all,
>
> I build a dataset processing in the same way the same data in Windows than
> in Linux.
>
> The output of Windows processing is:
> https://gitlab.com/iagogv/repdata/-/raw/main/exdata.csv?ref_type=heads
> The output of Linux processing is:
> https://gitlab.com/iagogv/repdata/-/raw/main/exdata2.csv?ref_type=heads
>
> exdata=as.matrix(read.csv("
>
https://gitlab.com/iagogv/repdata/-/raw/main/exdata.csv?ref_type=heads",
> header=FALSE))
> exdata2=as.matrix(read.csv("
>
https://gitlab.com/iagogv/repdata/-/raw/main/exdata2.csv?ref_type=heads",
> header=FALSE))
>
> They are not identical (`identical(exdata,exdata2)` is FALSE), but they
> are essentially equal (`all.equal(exdata,exdata2)` is TRUE). If I run
>
> set.seed(20232260)
> exkmns <- kmeans(exdata, centers = 7, iter.max = 2000, nstart = 750)
>
> I get
>
> exkmns$centers
>           V1         V2          V3          V4          V5           V6
> 1 -0.4910731 -0.2662055  0.57928758  0.14267293 -0.03013791  0.106472717
> 2  0.5301237  0.2815620 -0.23898532  1.00979412 -0.26123328  0.068099931
> 3  0.2255298 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.107538855
> 4 -0.2616257  0.5680582  0.55387437 -0.09562789 -0.01706577 -0.028248679
> 5 -0.4820078 -0.1667370 -0.46533618 -0.05271446  0.05477352  0.005236259
> 6  0.6455994 -0.1396674  0.05988547 -0.15557399  0.62766365  0.031051986
> 7  0.1072127  0.5538876 -0.33117098 -0.43209203 -0.18646403 -0.081273130
>
> both in Windows  (1) and in Linux (2, 3) up to rows order. If I run in
> Linux in my computer (2)
>
> set.seed(20232260)
> exkmns2 <- kmeans(exdata2, centers = 7, iter.max = 2000, nstart = 750)
>
> then, I get
>
> exkmns2$centers
>            V1         V2          V3          V4          V5          V6
> 1  0.64559941 -0.1396674  0.05988547 -0.15557399  0.62766365  0.03105199
> 2 -0.26162573  0.5680582  0.55387437 -0.09562789 -0.01706577 -0.02824868
> 3  0.53012369  0.2815620 -0.23898532  1.00979412 -0.26123328  0.06809993
> 4  0.03409765  0.3492520 -0.36910409 -0.40721418 -0.21482793  0.03073180
> 5 -0.58527394 -0.1790337 -0.46778956  0.03573883  0.15473589 -0.07980379
> 6 -0.49107314 -0.2662055  0.57928758  0.14267293 -0.03013791  0.10647272
> 7  0.22552984 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.10753886
>
> therefore, all rows essentially equal except for rows 5 and 7 of first
> dataset (5 and 4 of second dataset).  With a bit more detail:
>
>   *
> Row 0.2255298 -0.5165964 -0.02498471 -0.20438275 -0.41224195 -0.107538855
> belongs to exdata (and exdata2) and is center of both outputs
>   *
> Row 0.1072127  0.5538876 -0.33117098 -0.43209203 -0.18646403 -0.081273130
> belongs to the dataset and it is only center of exdata output
>   *
> Row -0.4820078 -0.1667370 -0.46533618 -0.05271446  0.05477352  0.005236259
> does not belong to the dataset and it is only center of exdata output
>   *
> Row -0.58527394 -0.1790337 -0.46778956  0.03573883  0.15473589 -0.07980379
> belongs to the dataset and it is only center for exdata2 on Linux in my
> computer
>   *
> Row 0.03409765  0.3492520 -0.36910409 -0.40721418 -0.21482793  0.03073180
> does not belong to the dataset and it is only center for exdata2 on Linux
> in my computer
>   *
> All other 4 rows (1,2,4 and 6 of first output) do not belong to the
> dataset and are common centers.
>
> Even, further, if I run
>
> set.seed(20232260)
> exkmns <- kmeans(exdata, centers = 7, iter.max = 2000, nstart = 750)
>
> in  posit.cloud (3), I get the same result than above. However, if I run
> (both in posit.cloud or in Windows)
>
> set.seed(20232260)
> exkmns2 <- kmeans(exdata2, centers = 7, iter.max = 2000, nstart = 750)
>
> then I get
>
>
> exkmns2$centers
>           V1         V2          V3         V4          V5          V6
> 1  0.6426035 -0.1449498  0.05843435 -0.1527968  0.62943077  0.02984948
> 2 -0.4092382 -0.3740695  0.69597037  0.1956896 -0.05026200 -0.01453132
> 3  0.1072127  0.5538876 -0.33117098 -0.4320920 -0.18646403 -0.08127313
> 4  0.2255298 -0.5165964 -0.02498471 -0.2043827 -0.41224195 -0.10753886
> 5  0.5301237  0.2815620 -0.23898532  1.0097941 -0.26123328  0.06809993
> 6 -0.5223387 -0.1484517 -0.38982567 -0.0341488  0.06446446  0.03622056
> 7 -0.2701703  0.5263218  0.52942311 -0.1112202 -0.03460591  0.03577287
>
> So only its rows 4 and 5 are common centers to both of previous outputs
> and row 3 is common width exdata centers.
>
> Does all this have any sense?
>
> Thanks!
>
> Iago
>
> (1)
> R version 4.4.1 (2024-06-14 ucrt)
> Platform: x86_64-w64-mingw32/x64
> Running under: Windows 10 x64 (build 19045)
>
> Matrix products: default
>
> (2)
> R version 4.4.1 (2024-06-14)
> Platform: x86_64-pc-linux-gnu
> Running under: Debian GNU/Linux 12 (bookworm)
>
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so;
> LAPACK version 3.11.0
>
> (3)
> R version 4.4.1 (2024-06-14)
> Platform: x86_64-pc-linux-gnu
> Running under: Ubuntu 20.04.6 LTS
>
>  Matrix products: default
> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/
> libopenblasp-r0.3.8.so;  LAPACK version 3.9.0
>
>
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> https://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

R help - Sep 2024 - fixed set.seed + kmeans output disagree on distinct platforms

[R] fixed set.seed + kmeans output disagree on distinct platforms

[R] fixed set.seed + kmeans output disagree on distinct platforms