One question on `clusterMeanDist()`… maybe it doesn’t matter, but when computing cluster means with `mean(temp.dist)`, that is taking the means of a symmetric matrix with a diagonal of zeros. Would it be better to take the means of the unique pairs of distances and do not include the zero self-distances? Or does the general trend hold anyway? I was thinking it might matter if the clusters are very imbalanced…

Hello,
as the help site for pbdMPI (?pbdMPI) says, you need some sort of MPI-Library installed. For me, Windows 10, the current version of MS-MPI solved the loading problem and the code runs fine. If your OS differs, then you need to search for a compatible library.

Cheers

Thanks for the comment Ananya. That’s a package question so I encourage you to reach out to the pmclust and pdbMPI developers if there’s an issue installing those packages.

Thanks for the tutorial, but I am also getting the same error as David. Can you help in fixing it?

I’d try installing pbdMPI separately. Watch the install closely for warnings and errors.

> library(pmclust)
Loading required package: pbdMPI
Error: package or namespace load failed for ‘pbdMPI’:
.onLoad failed in loadNamespace() for ‘pbdMPI’, details:
call: inDL(x, as.logical(local), as.logical(now), …)
error: unable to load shared object ‘C:/Users/covelld/Documents/R/win-library/4.0/pbdMPI/libs/x64/pbdMPI.dll’:
LoadLibrary failure: The specified module could not be found.

Error: package ‘pbdMPI’ could not be loaded
In addition: Warning message:
package ‘pmclust’ was built under R version 4.0.5
> install.packages(‘pbdMPI’,dependencies=T)
Installing package into ‘C:/Users/covelld/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL ‘https://cloud.r-project.org/bin/windows/contrib/4.0/pbdMPI_0.4-3.zip’
Content type ‘application/zip’ length 1043651 bytes (1019 KB)
downloaded 1019 KB

package ‘pbdMPI’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\covelld\AppData\Local\Temp\1\Rtmp8iQt9j\downloaded_packages
> library(pbdMPI)
Error: package or namespace load failed for ‘pbdMPI’:
.onLoad failed in loadNamespace() for ‘pbdMPI’, details:
call: inDL(x, as.logical(local), as.logical(now), …)
error: unable to load shared object ‘C:/Users/covelld/Documents/R/win-library/4.0/pbdMPI/libs/x64/pbdMPI.dll’:
LoadLibrary failure: The specified module could not be found.

Zk, given time constraints we’re not in a position to customize the tutorial, but if you figure it out I encourage you to post your solution! I’m not familiar with that term though. By topographical error do you mean the distance between observations and the final codebook vector?

🙂