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LTO flags in 4.1.0 Ubuntu 21.04 Makeconf

7 messages · Karl Dunkle Werner, Dirk Eddelbuettel

Original
Karl Dunkle Werner
# 
Hello,

I noticed the Makeconf file that comes with the Ubuntu version of R 4.1.0
has link-time optimization (LTO) flags enabled. For instance:
CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=.
-flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)

If I understand things correctly, these flags cause a bit of a problem
trying to install the arrow package, since that package does not want to
override the CXX11FLAGS, but also does not work with LTO. Setting "UseLTO:
false" in the package description doesn't seem to work.
Would it be possible to remove the flags -flto=auto and -ffat-lto-objects?

See https://issues.apache.org/jira/browse/ARROW-12853 for a discussion of
installation with these flags and
https://issues.apache.org/jira/browse/ARROW-9616 for a broader discussion
of LTO in Arrow.

My apologies if this is the wrong place to report this kind of issue.

The entire Makeconf file is attached to the first of those Arrow issues:
https://issues.apache.org/jira/secure/attachment/13025950/Makeconf_local
The file appears in the package
https://cloud.r-project.org/bin/linux/ubuntu/hirsute-cran40/r-base-core_4.1.0-1.2104.0_amd64.deb.
These flags are not set in the Debian Bullseye version (
https://cloud.r-project.org/bin/linux/debian/bullseye-cran40/r-base-core_4.1.0-1~bullseyecran.0_amd64.deb)
or the Ubuntu 20.10 version (
https://cloud.r-project.org/bin/linux/ubuntu/groovy-cran40/r-base-core_4.1.0-1.2010.0_amd64.deb
).
(For anyone who is unfamiliar, as I was, the Makeconf file is in
data/etc/R/, after extracting both the deb package and the data.tar.xz
directory.)


Thank you,
Karl
Dirk Eddelbuettel
# 
Hi Karl,
On 1 June 2021 at 22:22, Karl Dunkle Werner wrote:
| I noticed the Makeconf file that comes with the Ubuntu version of R 4.1.0
| has link-time optimization (LTO) flags enabled. For instance:
| CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=.
| -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat
| -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)

Upstream decision by R Core, see the NEWS entry:

  LINK-TIME OPTIMIZATION on a UNIX-ALIKE:

    * Configuring with flag --enable-lto=R now also uses LTO when
      installing the recommended packages.

    * R CMD INSTALL and R CMD SHLIB have a new flag --use-LTO to use
      LTO when compiling code, for use with R configured with
      --enable-lto=R.  For R configured with --enable-lto, they have
      the new flag --no-use-LTO.

      Packages can opt in or out of LTO compilation _via_ a UseLTO
      field in the DESCRIPTION file.  (As usual this can be overridden
      by the command-line flags.)

| If I understand things correctly, these flags cause a bit of a problem
| trying to install the arrow package, since that package does not want to
| override the CXX11FLAGS,

I doubt that, based on a wee bit of experience with C++, C++11, and all that
based coming up on 15 years with Rcpp, RInside and all that jazz.

| but also does not work with LTO. Setting "UseLTO:
| false" in the package description doesn't seem to work.

That is something you may need to discuss with either R Core upstream (for
the Makeconf), or maybe with the Arrow team for how they build the
package. And there could of course be a bug but I remind you that Arrow
itself is on CRAN.


| Would it be possible to remove the flags -flto=auto and -ffat-lto-objects?

Not likely for the package I ship. I tend to not second guess upstream, and
have followed R Core pretty much without changes to the program for 20 years.

If you think you need a locally modified version I may be able to help you
build one.

Hope this helps,  Dirk

PS As for my experiences with Arrow, well. I will try to remain brief:
 - while I have 25-ish years of experience building for Debian I _could
   never_ build Arrow even as shipped for R; I did file (GitHub) bug reports
   but they went nowhere (and I had no time for signing up for Jira, sorry)
 - this included failure on the "rather unusual" second installation as the
   Arrow build appears to not be entirely truthful by installing ... and then
   not working telling you to reinstall
 - that was generally on Ubuntu 'current at the time', but also on the Debian
   testing machine I use for Rcpp reverse depends (and where I build well
   over 2000 CRAN packages, yet Arrow remains "special")
 - as of Arrow 4.0.0 I can at least succeed at the second stage
but I would be interested to hear how others fared on Debian or Ubuntu systems.
Dirk Eddelbuettel
# 
Two more follow-ups if I may:

- the Debian and hence derived Ubuntu package of R 4.1.0 does *not* enable
  LTO yet, in other words I have not yet add --enable-lto to the configure
  call and we use to default of 'nope'
- my dev box is still 20.10; I only run 21.04 on one small machine where I
  have not tried to build arrow; but under 20.10 + R 4.1.0 + arrow 4.0.? the
  two step dance that they force on us works

Dirk
Karl Dunkle Werner
# 
Hello Dirk,

Thanks for the very helpful response!


Answering the points you made, not in order:
Got it, and thank you for the offer! I can edit my Makeconf (everything 
works when I remove the LTO-related flags). I was hoping to make 
installation smoother for other Arrow and Ubuntu users, but maybe that's 
something users or the Arrow developers will need to tackle.
In my experience, installing Arrow has gotten a lot better over time 
(including the reinstall requirement; see 
https://cran.r-project.org/web/packages/arrow/vignettes/install.html). 
It's still the most finicky of the packages I install, but substantially 
improved.




I think I'm confused by this comment (because I don't know much about 
the packaging process).
I'm confused because the R 4.1.0 Debian versions have flags like:
CXX11FLAGS = -g -O2 
-ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.1.0=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g $(LTO)

The R 4.1.0 Ubuntu 20.10 flags are:
CXX11FLAGS = -g -O2 
-fdebug-prefix-map=/build/r-base-2Aokdc/r-base-4.1.0=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g $(LTO)

While the R 4.1.0 Ubuntu 21.04 flags are:
CXX11FLAGS = -g -O2 
-ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto 
-ffat-lto-objects -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)

Should the Ubuntu 21.04 LTO flags be different than the others?
The GCC docs note that the -flto flag will enable LTO, but it can be 
disabled by passing -fno-lto in the link command 
(https://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html#index-flto). 
I'll see if the Arrow folks are able to set -fno-lto.



If it's at all helpful, here's a reproducible example using Rocker 
(thank you for making this easy to troubleshoot across R installations).

1. Download the Makeconf file with these LTO flags 
(https://issues.apache.org/jira/secure/attachment/13025950/Makeconf_local) 
or extract it from the Ubuntu 21.04 deb file 
(https://cloud.r-project.org/bin/linux/ubuntu/hirsute-cran40/r-base-core_4.1.0-1.2104.0_amd64.deb).
2. Start docker: docker run -e "LIBARROW_BINARY=false" -e 
"ARROW_R_DEV=true" -e "LIBARROW_MINIMAL=true" --rm -ti rocker/r-base:4.1.0
3. In a different terminal, find the docker container ID: docker ps
4. Copy Makeconf: docker cp Makeconf_local <container ID>:/etc/R/Makeconf
5. In the docker R:
 ??? tools::Rcmd("config CXX11FLAGS") to see the new flags
 ??? install.packages("arrow") now fails

My challenges are with the Makeconf flags packaged with Ubuntu 21.04's R 
4.1.0, but the example above also fails when the same Makeconf file is 
copied into the rocker/r-base:4.0.5 image.


Thanks,
Karl
On 6/1/21 3:50 PM, Dirk Eddelbuettel wrote:

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
Hi Karl,

        
On 1 June 2021 at 19:12, Karl Dunkle Werner wrote:

        
| Thanks for the very helpful response!

Thanks for weaving the threads back together.

| Got it, and thank you for the offer! I can edit my Makeconf (everything 
| works when I remove the LTO-related flags). I was hoping to make 
| installation smoother for other Arrow and Ubuntu users, but maybe that's 
| something users or the Arrow developers will need to tackle.

Yes indeed. One difficulty is that package authors can generally not override
what is in R's makeconf. As e.g. with my Rcpp maintainer hat on I have found
that frustrating. But such is life with R: not everything can be altered on
the fly.
 
| I think I'm confused by this comment (because I don't know much about 
| the packaging process).
| > - the Debian and hence derived Ubuntu package of R 4.1.0 does*not*  enable
| >    LTO yet, in other words I have not yet add --enable-lto to the configure
| >    call and we use to default of 'nope'
| I'm confused because the R 4.1.0 Debian versions have flags like:
| CXX11FLAGS = -g -O2 
| -ffile-prefix-map=/home/jranke/git/r-backports/bullseye/r-base-4.1.0=. 
| -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
| -D_FORTIFY_SOURCE=2 -g $(LTO)
| 
| The R 4.1.0 Ubuntu 20.10 flags are:
| CXX11FLAGS = -g -O2 
| -fdebug-prefix-map=/build/r-base-2Aokdc/r-base-4.1.0=. 
| -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
| -D_FORTIFY_SOURCE=2 -g $(LTO)
| 
| While the R 4.1.0 Ubuntu 21.04 flags are:
| CXX11FLAGS = -g -O2 
| -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto 
| -ffat-lto-objects -fstack-protector-strong -Wformat 
| -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)
| 
| Should the Ubuntu 21.04 LTO flags be different than the others?

<shrug emoji here>

Bbut these come from two (or three) distinct sources
- default compiler settings plus distro settings (really two players)
- package changes

and here you only one of the three constant (R 4.1.0). I think the -flto=auto
(amd -ffat-lto-objects) may come from gcc itself.  I can assure you (and you
can test that by looking at the git log at salsa.debian.org under my 'edd'
handle for the r-base package) that the debian/rules files configuring the
build _has not changed_ recently and does not set either.  In particularly no
with/without lto settings.  It's all 'without lto by default' from my end. So
back to ... distribution and compiler changes. And I have learned in the 20+
years here to trust my colleagues looking after gcc et al.

Also, and just to be plain, recall that $(LTO) is calling a variable which
may, or may not, bet set.  When I look at my most recent package build logs
I see the compilation (in the long log) commence with

make[4]: Entering directory '/build/r-base-4.1.0/src/main'
gcc -std=gnu99 -I../../src/extra  -I. -I../../src/include -I../../src/include   -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CommandLineArgs.c -o CommandLineArgs.o

No LTO or -flto here (or in the rest of the file). I may of course have
missed something.

| My challenges are with the Makeconf flags packaged with Ubuntu 21.04's R 
| 4.1.0, but the example above also fails when the same Makeconf file is 
| copied into the rocker/r-base:4.0.5 image.

I have not looked as deeply into this as you but I can assure that I myself
of the maintainer of 'r-base' have been deeply and profoundly frustrated by
the inability of this one package to build properly.  If you can improve that
without heavy surgery, side effects to other packages, or other shenanigans I
would be all ears.

Cheers, Dirk

  
    

      
      
    

  


  


      

    

    
2 days later

    

      
      

        


  

        

      Karl Dunkle Werner
    

    

      
      #
    

  


  

      
Hello Dirk,

I see, this is all very helpful. Thank you!


For anyone else who runs into this issue, you can do either of the 
following;
(a) Remove the flags "-flto=auto" and "-ffat-lto-objects" from the 
CXX11FLAGS in your /etc/R/Makeconf
(b) Set CXX11FLAGS in your Makevars (in $HOME/.R/Makevars) to something 
like the following:

CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g

(This is just the Makeconf CXX11FLAGS with LTO flags removed).
Note that these may turn off LTO for other packages you install, 
depending on how they manage build flags.


Thanks,
Karl

        
On 6/1/21 7:48 PM, Dirk Eddelbuettel wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
Hi Karl,

Thanks for circling back!

        
On 4 June 2021 at 17:00, Karl Dunkle Werner wrote:

        
| For anyone else who runs into this issue, you can do either of the 
| following;
| (a) Remove the flags "-flto=auto" and "-ffat-lto-objects" from the 
| CXX11FLAGS in your /etc/R/Makeconf
| (b) Set CXX11FLAGS in your Makevars (in $HOME/.R/Makevars) to something 
| like the following:
| 
| CXX11FLAGS = -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
| 
| (This is just the Makeconf CXX11FLAGS with LTO flags removed).
| Note that these may turn off LTO for other packages you install, 
| depending on how they manage build flags.

Thanks for the concise summary.

The other side of all this is that you reminded me that I should probably
enable lto as a default. I may need to reach out with some testing help.

Best, Dirk