fixing the BLAS hot-switching mechanism #390

kforner · 2022-03-16T12:48:42Z

There is a regression with the BLAS switching mechanism, as described here: https://www.rocker-project.org/use/other_topics/,
in rocker-versioned2:

%docker run --rm rocker/verse:4.1.2 bash

R -q -e 'sessionInfo()' | grep so
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3

# nothing changed
R -q -e 'sessionInfo()' | grep so
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

# expected considering that
# ldd /usr/local/lib/R/lib/libR.so | grep blas
	libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007f20400b0000)

This seems to be related to the auto-detection of the openblas lib during the R configuration, so that the --with-blas="-lopenblas" is used (cf https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#OpenBLAS).

One simple way to fix that is to postpone the openblas installation AFTER the R compilation:

git diff scripts/install_R.sh
diff --git i/scripts/install_R.sh w/scripts/install_R.sh
index bad57c4..30f996b 100755
--- i/scripts/install_R.sh
+++ w/scripts/install_R.sh
@@ -24,11 +24,7 @@ export DEBIAN_FRONTEND=noninteractive
 R_HOME=${R_HOME:-/usr/local/lib/R}
 
 READLINE_VERSION=8
-OPENBLAS=libopenblas-dev
-if [ ${UBUNTU_VERSION} == "bionic" ]; then
-  READLINE_VERSION=7
-  OPENBLAS=libopenblas-dev
-fi
+
 
 apt-get update \
   && apt-get install -y --no-install-recommends \
@@ -46,7 +42,6 @@ apt-get update \
     libicu* \
     libpcre2* \
     libjpeg-turbo* \
-    ${OPENBLAS} \
     libpangocairo-* \
     libpng16* \
     libreadline${READLINE_VERSION} \
@@ -127,6 +122,14 @@ make
 make install
 make clean
 
+# Openblas installation: N.B: this must happen AFTER the R compilation otherwise the BLAS hot-swapping does not work
+OPENBLAS=libopenblas-dev
+if [ ${UBUNTU_VERSION} == "bionic" ]; then
+  READLINE_VERSION=7
+  OPENBLAS=libopenblas-dev
+fi
+apt-get install -y --no-install-recommends ${OPENBLAS}
+
 ## Add a default CRAN mirror
 echo "options(repos = c(CRAN = '${CRAN}'), download.file.method = 'libcurl')" >> ${R_HOME}/etc/Rprofile.site

then:

docker build -f dockerfiles/r-ver_4.1.2.Dockerfile  -t r-ver_4.1.2_fixed  .
docker run --rm -ti r-ver_4.1.2_fixed bash

R -q -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/local/lib/R/lib/libRlapack.so

update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3

R -q -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/local/lib/R/lib/libRlapack.so

# fixed because:
ldd /usr/local/lib/R/lib/libR.so | grep blas
	libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x00007febf46aa000)

So AFAIU, this restores the previous and expected behaviour (for BLAS only, not for Lapack, as pointed out by Dirk).

The text was updated successfully, but these errors were encountered:

eddelbuettel · 2022-03-16T12:56:21Z

Please explain why you only switch BLAS -- and not both BLAS and LAPACK as is common.

C.f. https://wiki.debian.org/DebianScience/LinearAlgebraLibraries

kforner · 2022-03-16T13:18:08Z

I was just following the instructions from the rocker website: https://www.rocker-project.org/use/other_topics/ and focusing on the BLAS lib.
But you're right, this fix does not work for Lapack.
It seems now to be hard-coded to /usr/local/lib/R/lib/libRlapack.so, the internal implementation, which is not what we want.
I'll have a closer look on managing lapack as well...

eddelbuettel · 2022-03-16T13:21:12Z

See what I stated in the other thread. If desired, using --with-blas and --with-lapack with the build-dependencies is all.

kforner · 2022-03-16T14:18:09Z

I think I got it: pre-installing a lapack lib will trigger the proper R configuration: LAPACK(generic).

The install script is modified:

to postpone the openblas lib install
to pre-install a lapack lib

▶ git diff scripts/install_R.sh
diff --git i/scripts/install_R.sh w/scripts/install_R.sh
index bad57c4..aae8549 100755
--- i/scripts/install_R.sh
+++ w/scripts/install_R.sh
@@ -24,11 +24,7 @@ export DEBIAN_FRONTEND=noninteractive
 R_HOME=${R_HOME:-/usr/local/lib/R}
 
 READLINE_VERSION=8
-OPENBLAS=libopenblas-dev
-if [ ${UBUNTU_VERSION} == "bionic" ]; then
-  READLINE_VERSION=7
-  OPENBLAS=libopenblas-dev
-fi
+
 
 apt-get update \
   && apt-get install -y --no-install-recommends \
@@ -46,7 +42,6 @@ apt-get update \
     libicu* \
     libpcre2* \
     libjpeg-turbo* \
-    ${OPENBLAS} \
     libpangocairo-* \
     libpng16* \
     libreadline${READLINE_VERSION} \
@@ -103,6 +98,10 @@ else                                                                 \
 fi &&                                                                \
     tar xzf R-${R_VERSION}.tar.gz &&
 
+
+# install a lapack so that R is configured using with "LAPACK(generic)"
+apt-get install -y --no-install-recommends liblapack-dev
+
 cd R-${R_VERSION}
 R_PAPERSIZE=letter \
 R_BATCHSAVE="--no-save --no-restore" \
@@ -127,6 +126,14 @@ make
 make install
 make clean
 
+# Openblas installation: N.B: this must happen AFTER the R compilation otherwise the BLAS hot-swapping does not work
+OPENBLAS=libopenblas-dev
+if [ ${UBUNTU_VERSION} == "bionic" ]; then
+  READLINE_VERSION=7
+  OPENBLAS=libopenblas-dev
+fi
+apt-get install -y --no-install-recommends ${OPENBLAS}
+update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
 ## Add a default CRAN mirror
 echo "options(repos = c(CRAN = '${CRAN}'), download.file.method = 'libcurl')" >> ${R_HOME}/etc/Rprofile.site

Then:

docker build -f dockerfiles/r-ver_4.1.2.Dockerfile  -t r-ver_4.1.2_fixed  .
docker run --rm -ti r-ver_4.1.2_fixed bash

# use openblas for both BLAS and lapack
R -q -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

# hot-switch BLAS
update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3
R -q -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

# hot-switch lapack
update-alternatives --set liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3
R -q -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

# ldd /usr/local/lib/R/lib/libR.so | grep blas
	libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x00007faa57ae0000)

for reference, the R configuration summary:

R is now configured for x86_64-pc-linux-gnu

  Source directory:            .
  Installation directory:      /usr/local

  C compiler:                  gcc  -g -O2
  Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2

  Default C++ compiler:        g++ -std=gnu++14  -g -O2
  C++11 compiler:              g++ -std=gnu++11  -g -O2
  C++14 compiler:              g++ -std=gnu++14  -g -O2
  C++17 compiler:              g++ -std=gnu++17  -g -O2
  C++20 compiler:              g++ -std=gnu++2a  -g -O2
  Fortran free-form compiler:  gfortran -fno-optimize-sibling-calls -g -O2
  Obj-C compiler:	        

  Interfaces supported:        X11, tcltk
  External libraries:          pcre2, readline, BLAS(generic), LAPACK(generic), curl
  Additional capabilities:     PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:             shared R library, R profiling, memory profiling

  Capabilities skipped:        
  Options not enabled:         shared BLAS

  Recommended packages:        yes

Is that the correct and intended behaviour ?

cboettig · 2022-03-16T14:26:40Z

nice @kforner ! was just having the same thought -- I think we should probably have included an external lapack lib. Glad you got to the bottom of this! The proposed changes seem reasonable to me.

Having the openblas install in a later layer probably makes sense too.

I guess we stick with pthread as the default openblas? I'm in favor of a threaded open default, but not convinced pthread is preferable to the openmp flavor (merely chose that as it is the ubuntu repos default for openblas).

kforner · 2022-03-16T15:09:44Z

Thanks @cboettig. There's probably a problem in my changes since READLINE gets fixed AFTER being used.
Would you want me to do a MR, or will you take care of it?

I have really no informed opinion on the flavor of openblas to use.

eitsupi · 2022-03-16T15:17:06Z

I'm currently doing a major rewrite of the script that installs R in #386.
Do you think we can fix it in this PR?

kforner · 2022-03-16T16:02:47Z

fine with me [but I'm not sure whom you're asking]

cboettig · 2022-03-16T16:21:28Z

@eitsupi yup, was thinking the same thing, do you want to roll @kforner 's proposed changes re blas into #386 ? That's probably the simplest.

benz0li · 2022-03-17T08:41:24Z

See what I stated in the other thread. If desired, using --with-blas and --with-lapack with the build-dependencies is all.

Here's what I've noticed with Debian 11, which also seems to be the case for Ubuntu 21.10 (and 22.04?).

A build using --with-blas and --with-lapack having libopenblas-dev installed returns

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: aarch64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS/LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
[...]

A build using --with-blas and --with-lapack having liblapack-dev installed and hot-switching to libopenblas-dev afterwards returns

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: aarch64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so

Does anyone know what the difference is between [openblas-pthread/]libopenblasp-r0.3.13.so and [openblas-pthread/]libblas.so.3?

Is [openblas-pthread/]libopenblasp-r0.3.13.so simply the superset of [openblas-pthread/]libblas.so.3 and [openblas-pthread/]liblapack.so.3?

Is there a difference in linking? Does it cause any trouble?

eitsupi · 2022-03-20T02:29:57Z

I believe I made the changes proposed in #390 (comment).
dbe9026

I have not yet built and tested it.

eitsupi · 2022-03-20T08:32:39Z

I was able to build rocker/r-ver:4.1.3 from dbe9026.
Does this look good?

amd64

$ R -s -e "sessionInfo()"
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.3

arm64

$ R -s -e "sessionInfo()"
R version 4.1.3 (2022-03-10)
Platform: aarch64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.3

kforner · 2022-03-21T08:46:09Z

Could you share the output of ldd /usr/local/lib/R/lib/libR.so | grep blas ?

And check that it correctly switches when you do:

update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3
update-alternatives --set liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3

kforner · 2022-03-21T09:18:48Z

@benz0li

Is [openblas-pthread/]libopenblasp-r0.3.13.so simply the superset of [openblas-pthread/]libblas.so.3 and [openblas-pthread/]liblapack.so.3?

according to this (message 5) it seems so

The problem is that libopenblasp-r0.3.5.so contains exactly the same
symbols as libblas.so and liblapack.so. This seems to be confusing
linkers, e.g. see Bug#914655 for python-scipy.

and that it should NOT be used, cf message 12

libopenblasp-r0.3.5.so should never be used as BLAS / LAPACK provider
as it's SONAME unmatches the depencency template and would incur
breakage to our dependency tree.

and even be deleted:

I'm sure libopenblasp-r0.3.5.so cannot be removed. Every OpenBLAS
flavor will ship 3 shared objects:

Is there a difference in linking?
yes. The SONAME seems to have an impact.

benz0li · 2022-03-21T09:28:28Z

@kforner Thank you for the feedback. /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so can't be deleted, though.

root@295f1f17b708:/# ldd /usr/local/lib/R/lib/libR.so | grep blas
	libblas.so.3 => /usr/lib/aarch64-linux-gnu/libblas.so.3 (0x0000ffff8af1b000)
	libopenblas.so.0 => /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (0x0000ffff894a3000)
root@295f1f17b708:/#
root@295f1f17b708:/# ls -al /usr/lib/aarch64-linux-gnu/openblas-pthread/
total 54476
drwxr-xr-x 4 root root     4096 Mar 21 09:15 .
drwxr-xr-x 1 root root    12288 Mar 21 09:15 ..
drwxr-xr-x 3 root root     4096 Mar 21 09:15 cmake
lrwxrwxrwx 1 root root       13 Apr 18  2021 libblas.a -> libopenblas.a
lrwxrwxrwx 1 root root       12 Apr 18  2021 libblas.so -> libblas.so.3
-rw-r--r-- 1 root root   399904 Apr 18  2021 libblas.so.3
lrwxrwxrwx 1 root root       13 Apr 18  2021 liblapack.a -> libopenblas.a
lrwxrwxrwx 1 root root       14 Apr 18  2021 liblapack.so -> liblapack.so.3
-rw-r--r-- 1 root root  5418760 Apr 18  2021 liblapack.so.3
lrwxrwxrwx 1 root root       22 Apr 18  2021 libopenblas.a -> libopenblasp-r0.3.13.a
-rw-r--r-- 1 root root 31903102 Apr 18  2021 libopenblasp-r0.3.13.a
-rw-r--r-- 1 root root 18031736 Apr 18  2021 libopenblasp-r0.3.13.so
lrwxrwxrwx 1 root root       23 Apr 18  2021 libopenblas.so -> libopenblasp-r0.3.13.so
lrwxrwxrwx 1 root root       23 Apr 18  2021 libopenblas.so.0 -> libopenblasp-r0.3.13.so
drwxr-xr-x 2 root root     4096 Mar 21 09:15 pkgconfig
root@295f1f17b708:/#

kforner · 2022-03-21T09:34:39Z

@benz0li With the above proposed changes, libR.so should no longer be linked to libopenblas.so.0, but instead to libblas.so and liblapack.so

eitsupi · 2022-03-21T09:42:27Z

Could you share the output of ldd /usr/local/lib/R/lib/libR.so | grep blas ?

And check that it correctly switches when you do:
update-alternatives --set libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3
update-alternatives --set liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3

Of course, those commands seem to work.

$ ldd /usr/local/lib/R/lib/libR.so | grep blas
        libblas.so.3 => /lib/aarch64-linux-gnu/libblas.so.3 (0x0000ffff8d14f000)

$ R -s -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3

$ update-alternatives --set libblas.so.3-aarch64-linux-gnu /usr/lib/aarch64-linux-gnu/blas/libblas.so
.3
update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in manual mode

$ R -s -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/aarch64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3

$ update-alternatives --set liblapack.so.3-aarch64-linux-gnu /usr/lib/aarch64-linux-gnu/lapack/liblap
ack.so.3
update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in manual mode

$ R -s -e 'sessionInfo()' | grep so
BLAS:   /usr/lib/aarch64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3.9.0

kforner · 2022-03-21T10:34:16Z

@eitsupi That looks good !

kforner · 2022-03-21T18:38:20Z

@eitsupi Any idea about when your dev will be available ?

eitsupi · 2022-03-22T10:30:17Z

Sorry for the delay in work.
It appears to be functionally fine, so I will complete the minor work and merge #386 today or tomorrow.

eitsupi · 2022-03-23T13:09:18Z

Note that rocker/r-ver:4.1.3 and rocker/rstudio:4.1.3, which reflect this fix, will be pushed to DockerHub today, but the other images will not be built due to the rocker/tidyverse build failure (#393).

eitsupi · 2022-04-11T09:39:35Z

@kforner We have no problem uninstalling liblapack-dev after installing R, right?
If we can uninstall it, we can reduce the size of the rocker/r-ver by 30 MB.

kforner · 2022-04-11T09:51:19Z

I think so, if it's not set to be used via the update-alternatives mechanism.

eitsupi · 2022-04-11T09:55:08Z

Even after uninstalling liblapack-dev on current rocker/r-ver:latest, update-alternatives seems to be running fine.

eitsupi · 2022-04-11T15:13:13Z

Sorry, as I wrote in #412, I was mistaken.
It does not seem to be possible to remove it.

kforner · 2022-04-14T09:40:12Z

I've noticed that the latest (as of today) rocker/verse:4.1.3 has these changes, but not the latest rocker/verse:4.1.2.
Is this expected ?

eitsupi · 2022-04-14T10:11:31Z

@kforner Please check the README

Latest R version images will be built on a rolling basis; when the definition files or Rocker scripts are updated, they are immediately built by GitHub Actions.

Non-latest R version images will be built when a new R version is released. At this time, a tag and a GitHub release will also be created.

All currently tagged images are listed on the wiki as to which commits they were built from.
https://github.com/rocker-org/rocker-versioned2/wiki

(However, due to a GitHub Actions error that has been occurring since yesterday #420, images built yesterday have not been reflected.)

kforner mentioned this issue Mar 16, 2022

reconsider openblas defaults for parallelization? #34

Closed

cboettig mentioned this issue Mar 18, 2022

Split install_R.sh into two scripts and some improvements in the R installation process #386

Merged

9 tasks

eitsupi added a commit to eitsupi/rocker-versioned2 that referenced this issue Mar 20, 2022

change BLAS installation order (rocker-org#390)

dbe9026

eitsupi closed this as completed in #386 Mar 23, 2022

eitsupi mentioned this issue Apr 11, 2022

Remove liblapack-dev after R installation to reduce image size #412

Closed

eitsupi mentioned this issue Apr 26, 2022

rocker/r-ver:4.0.0-ubuntu18.04 can't be built now #432

Closed

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fixing the BLAS hot-switching mechanism #390

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fixing the BLAS hot-switching mechanism #390

fixing the BLAS hot-switching mechanism #390

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