dist function in R is very slow

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dist function in R is very slow

R devel mailing list
Dear R developers,
I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computing such thing in R takes many hours (I am doing this on a Linux server with more than 100 GB of RAM, so this is not the problem). When I write the matrix to disk, read it ans compute the distances in C, write them to the disk and read them into R it takes 10 - 15 minutes (and I did not spend much time on optimising my C code).The question is why the R function is so slow? I understand that it calls C (or C++) to compute the distance. My suspicion is that the transposed matrix is passed to C and so each time a distance between two columns of a matrix is computed, and since C stores matrices by rows it is very inefficient and causes many cache misses (my first C implementation was like this and I had to stop the r
 un after an hour when it failed to complete).If my suspicion is correct, is it possible to re-write the dist function so that it works faster on large matrices?
Best regards,Moshe OlshanskyMonash University

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Re: dist function in R is very slow

Stefan Evert-3

> On 17 Jun 2017, at 08:47, Moshe Olshansky via R-devel <[hidden email]> wrote:
>
> I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computing such thing in R takes many hours (I am doing this on a Linux server with more than 100 GB of RAM, so this is not the problem). When I write the matrix to disk, read it ans compute the distances in C, write them to the disk and read them into R it takes 10 - 15 minutes (and I did not spend much time on optimising my C code).The question is why the R function is so slow? I understand that it calls C (or C++) to compute the distance. My suspicion is that the transposed matrix is passed to C and so each time a distance between two columns of a matrix is computed, and since C stores matrices by rows it is very inefficient and causes many cache misses (my first C implementation was like this and I had to stop the
  run after an hour when it failed to complete).

There are two many reasons for the relatively low speed of the built-in dist() function: (i) it operates on row vectors, which leads to many cache misses because matrices are stored by column in R (as you guessed); (ii) the function takes care to handle missing values correctly, which adds a relatively expensive test and conditional branch to each iteration of the inner loop.

A faster implementation, which omits the NA test and can compute distances between column vectors, is available as dist.matrix() in the "wordspace" package.  However, it cannot be used with matrices that might contain NAs (and doesn't warn about such arguments).

If you want the best possible speed, use cosine similarity (or equivalently, angular distance).  The underlying cross product is very efficient with a suitable BLAS implementation.

Best,
Stefan
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Re: dist function in R is very slow

R devel mailing list
In reply to this post by R devel mailing list
Hi Stefan,
Thank you very much for pointing me to the wordspace package. It does the job a bit faster than my C code but is 100 times more convenient.
By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast:
euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);  sqrt(outer(sq,sq,"+") - 2*mtm)}
It takes less than 50 seconds for my (dense) matrix of 5,054 rows and 12,803 columns, while dist.matrix with method="euclidean" takes almost 10 minutes (which is still orders of magnitude faster than dist).


      From: Stefan Evert <[hidden email]>
 To: Moshe Olshansky <[hidden email]>
Cc: R-devel Mailing List <[hidden email]>
 Sent: Sunday, 18 June 2017, 2:33
 Subject: Re: [Rd] dist function in R is very slow
 

> On 17 Jun 2017, at 08:47, Moshe Olshansky via R-devel <[hidden email]> wrote:
>
> I am visualising high dimensional genomic data and for this purpose I need to compute pairwise distances between many points in a high-dimensional space (say I have a matrix of 5,000 rows and 20,000 columns, so the result is a 5,000x5,000 matrix or it's upper diagonal).Computing such thing in R takes many hours (I am doing this on a Linux server with more than 100 GB of RAM, so this is not the problem). When I write the matrix to disk, read it ans compute the distances in C, write them to the disk and read them into R it takes 10 - 15 minutes (and I did not spend much time on optimising my C code).The question is why the R function is so slow? I understand that it calls C (or C++) to compute the distance. My suspicion is that the transposed matrix is passed to C and so each time a distance between two columns of a matrix is computed, and since C stores matrices by rows it is very inefficient and causes many cache misses (my first C implementation was like this and I had to stop the run after an hour when it failed to complete).

There are two many reasons for the relatively low speed of the built-in dist() function: (i) it operates on row vectors, which leads to many cache misses because matrices are stored by column in R (as you guessed); (ii) the function takes care to handle missing values correctly, which adds a relatively expensive test and conditional branch to each iteration of the inner loop.

A faster implementation, which omits the NA test and can compute distances between column vectors, is available as dist.matrix() in the "wordspace" package.  However, it cannot be used with matrices that might contain NAs (and doesn't warn about such arguments).

If you want the best possible speed, use cosine similarity (or equivalently, angular distance).  The underlying cross product is very efficient with a suitable BLAS implementation.

Best,
Stefan

   
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Re: dist function in R is very slow

Stefan Evert-3

> By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast:

Indeed.

> euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);  sqrt(outer(sq,sq,"+") - 2*mtm)}

There are two reasons why I didn't use this optimization in "wordspace":

1) It can be inaccurate for small distances between vectors of large Euclidean length because of loss of significance in the subtraction step.  This is not just a theoretical concern – I've seen data sets were this became a real problem.

2) It incurs substantial memory overhead for a large distance matrix. Your code allocates at least five matrices of this size: outer(…), mtm, 2 * mtm, outer(…) - 2*mtm, and the final result obtained by taking the square root.  [Actually, there is additional overhead for m*m (an even larger matrix) when computing the Euclidean norms, but this could be avoided with sq <- rowNorms(m, method="euclidean").]

I am usually more concerned about RAM than raw processing speed, so the package was designed to keep memory overhead as low as possible and allow users to work with realistic data sets on ordinary laptop computers.


> It takes less than 50 seconds for my (dense) matrix of 5,054 rows and 12,803 columns, while dist.matrix with method="euclidean" takes almost 10 minutes (which is still orders of magnitude faster than dist).

It's a little disappointing that dist.matrix() is still relatively slow despite all simplifications and better cache consistency (the function automatically transposes the input matrix and computes distances by columns rather than rows).  I'm a little surprised about your timing, though.  Testing with a random 5000 x 20000 matrix, my MacBook computers the full Euclidean distance matrix in about 5 minutes.  

If your machine (and version of R) supports OpenMP, you can improve performance by allowing multithreading with wordspace.openmp(threads=<n>).  In my test case, I get a 2.2x speed-up with 4 threads (2m 15s instead of 5m).


Best wishes,
Stefan
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Re: dist function in R is very slow

R devel mailing list
Hi Stefan,
You are right about the possible loss of accuracy computing the Euclidean distance the way I did. In some cases you probably even can get a negative value to compute a square root (so I am making all negative numbers 0). To do what I did one must know that it is all right in their case.I tried wordspace.openmp wuth 8 threads and it reduces the time to just over 2.5 minutes. This is more than enough for me.I am not sure whether you have any chance to beat the speed of (t)crossprod since they may be using a (complexity-wise) faster algorithm for matrix multiplication (may be with FFT - I am not sure).
Once again, thank you very much for your comments and help.



      From: Stefan Evert <[hidden email]>
 To: Moshe Olshansky <[hidden email]>
Cc: R-devel Mailing List <[hidden email]>
 Sent: Monday, 19 June 2017, 2:23
 Subject: Re: [Rd] dist function in R is very slow
   

> By the way, since the tcrossprod function in the Matrix package is so fast, the Euclidean distance can be computed very fast:

Indeed.

> euc_dist <- function(m) {mtm <- Matrix::tcrossprod(m); sq <- rowSums(m*m);  sqrt(outer(sq,sq,"+") - 2*mtm)}

There are two reasons why I didn't use this optimization in "wordspace":

1) It can be inaccurate for small distances between vectors of large Euclidean length because of loss of significance in the subtraction step.  This is not just a theoretical concern – I've seen data sets were this became a real problem.

2) It incurs substantial memory overhead for a large distance matrix. Your code allocates at least five matrices of this size: outer(…), mtm, 2 * mtm, outer(…) - 2*mtm, and the final result obtained by taking the square root.  [Actually, there is additional overhead for m*m (an even larger matrix) when computing the Euclidean norms, but this could be avoided with sq <- rowNorms(m, method="euclidean").]

I am usually more concerned about RAM than raw processing speed, so the package was designed to keep memory overhead as low as possible and allow users to work with realistic data sets on ordinary laptop computers.


> It takes less than 50 seconds for my (dense) matrix of 5,054 rows and 12,803 columns, while dist.matrix with method="euclidean" takes almost 10 minutes (which is still orders of magnitude faster than dist).

It's a little disappointing that dist.matrix() is still relatively slow despite all simplifications and better cache consistency (the function automatically transposes the input matrix and computes distances by columns rather than rows).  I'm a little surprised about your timing, though.  Testing with a random 5000 x 20000 matrix, my MacBook computers the full Euclidean distance matrix in about 5 minutes. 

If your machine (and version of R) supports OpenMP, you can improve performance by allowing multithreading with wordspace.openmp(threads=<n>).  In my test case, I get a 2.2x speed-up with 4 threads (2m 15s instead of 5m).


Best wishes,
Stefan

   
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