Thanks. I answer below.
And now I realize I must have read this not paying enough attention: "You can
specify a particular BLAS library via a value for the configuration option
--with-blas. If this is given with no =, its value is taken from the
environment variable BLAS_LIBS, set for example in config.site. If neither the
option nor the environment variable supply a value, a search is made for a
suitable59 BLAS."
(https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#BLAS ), and
footnote 59 says: "The search order is currently OpenBLAS, BLIS, ATLAS,
platform-specific choices (see below) and finally a generic libblas." It is in
the configure script of R: line 46396 searches for OpenBLAS, on 46453 it looks
for BLIS, later (46510) for ATLAS, etc.
Indeed, that is what I see looking more carefully at the output. If I have
OpenBLAS, then it locates it immediately:
configure: searching for an external BLAS
configure: searching for BLAS in default libraries
checking for dgemm_... no
configure: searching for OpenBLAS
checking for sgemm_ in -lopenblas... yes
checking whether double complex BLAS can be used... yes
If I don't, but I have ATLAS, it does this (OpenBLAS, then BLIS, then ATLAS)
configure: searching for an external BLAS
configure: searching for BLAS in default libraries
checking for dgemm_... no
configure: searching for OpenBLAS
checking for sgemm_ in -lopenblas... no
configure: searching for BLIS
checking for sgemm_ in -lblis... no
configure: searching for ATLAS
checking for ATL_xerbla in -latlas... yes
So I think what I am seeing is expected. But this would suggest your build
machine did not have OpenBLAS, but it seems it did (from your ldd output); or
else, maybe your machine had a config.site or BLAS_LIBS?
On Sat, 30-December-2023, at 19:16:42, Dirk Eddelbuettel <e...@debian.org>
wrote:
> If you match the exact build-deps I use and the exact options from
> debian/rules you should end up with the exact same output. As that is whay
> you desire but do not get we need to drill down into where it deviates. FWIW
> last time I build the Debian the (relevant) part (of the large) configure log
> was below. What do you get for BLAS/LAPACK?
>
>
> R is now configured for x86_64-pc-linux-gnu
>
> Source directory: .
> Installation directory: /usr
>
> C compiler: gcc -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> Fortran fixed-form compiler: gfortran -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -fcf-protection
>
> Default C++ compiler: g++ -std=gnu++17 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> C++11 compiler: g++ -std=gnu++11 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> C++14 compiler: g++ -std=gnu++14 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> C++17 compiler: g++ -std=gnu++17 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> C++20 compiler: g++ -std=gnu++20 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> C++23 compiler: g++ -std=gnu++23 -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -Wdate-time -D_FORTIFY_SOURCE=2
> Fortran free-form compiler: gfortran -g -O2
> -ffile-prefix-map=/build/r-base-4.3.2=. -fstack-protector-strong
> -fstack-clash-protection -fcf-protection
> 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: no
>
>
My configure log (from my "for real" builds)
==============================================
R is now configured for x86_64-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
Fortran fixed-form compiler: gfortran -g -O2 -march=native
-fstack-protector-strong -fstack-clash-protection -fcf-protection
Default C++ compiler: g++ -std=gnu++17 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
C++11 compiler: g++ -std=gnu++11 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
C++14 compiler: g++ -std=gnu++14 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
C++17 compiler: g++ -std=gnu++17 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
C++20 compiler: g++ -std=gnu++20 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
C++23 compiler: g++ -std=gnu++23 -O2 -g -march=native
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
Fortran free-form compiler: gfortran -g -O2 -march=native
-fstack-protector-strong -fstack-clash-protection -fcf-protection
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries: pcre2, readline, BLAS(OpenBLAS), LAPACK(in
blas), curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared R library, R profiling
Capabilities skipped:
Options not enabled: shared BLAS, memory profiling
Recommended packages: yes
Key differences:
================
- I am not using "-ffile-prefix-map" (but I can't imagine that being the cause
of the issue)
- I am configuring without memory profiling (but enabling memory profiling did
not change things)
- I am using "march=native" (but this is not the cause, since removing it gives
me the same issues)
- And the OpenBLAS, of course.
> Despite the display of 'shared BLAS' not enabled, I still have
>
> root@fb498fe53700:/# ldd /usr/lib/R/modules/lapack.so
> linux-vdso.so.1 (0x00007ffcb09c7000)
> libR.so => /lib/libR.so (0x00007ff7dd7f1000)
> liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3
> (0x00007ff7dd0f6000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007ff7dd017000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007ff7dce36000)
> libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3
> (0x00007ff7dcdd3000)
> libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8
> (0x00007ff7dcd7b000)
> libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0
> (0x00007ff7dccdf000)
> liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5
> (0x00007ff7dccb0000)
> libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0
> (0x00007ff7dcc9d000)
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007ff7dcc7e000)
> libtirpc.so.3 => /lib/x86_64-linux-gnu/libtirpc.so.3
> (0x00007ff7dcc50000)
> libicuuc.so.72 => /lib/x86_64-linux-gnu/libicuuc.so.72
> (0x00007ff7dca52000)
> libicui18n.so.72 => /lib/x86_64-linux-gnu/libicui18n.so.72
> (0x00007ff7dc726000)
> libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1
> (0x00007ff7dc6de000)
> /lib64/ld-linux-x86-64.so.2 (0x00007ff7ddc74000)
> libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0
> (0x00007ff7da3f0000)
> libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5
> (0x00007ff7da126000)
> libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6
> (0x00007ff7da0f3000)
> libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2
> (0x00007ff7da0a1000)
> libicudata.so.72 => /lib/x86_64-linux-gnu/libicudata.so.72
> (0x00007ff7d82cf000)
> libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007ff7d80b5000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007ff7d8095000)
> libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0
> (0x00007ff7d804e000)
> libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3
> (0x00007ff7d7f74000)
> libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3
> (0x00007ff7d7f47000)
> libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2
> (0x00007ff7d7f41000)
> libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0
> (0x00007ff7d7f33000)
> libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1
> (0x00007ff7d7f2c000)
> libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2
> (0x00007ff7d7f1b000)
> root@fb498fe53700:/# ls -l /lib/x86_64-linux-gnu/liblapack.so.3
> lrwxrwxrwx 1 root root 49 Nov 27 2022 /lib/x86_64-linux-gnu/liblapack.so.3
> -> /etc/alternatives/liblapack.so.3-x86_64-linux-gnu
> root@fb498fe53700:/# ls -l /lib/x86_64-linux-gnu/libblas.so.3
> lrwxrwxrwx 1 root root 47 Nov 27 2022 /lib/x86_64-linux-gnu/libblas.so.3 ->
> /etc/alternatives/libblas.so.3-x86_64-linux-gnu
> root@fb498fe53700:/#
~/tmp/R4/R-4.3.2-85742/modules $ ldd lapack.so
linux-vdso.so.1 (0x00007ffd96786000)
libR.so => /usr/lib/libR.so (0x00007f9d9d174000)
libopenblas.so.0 => /usr/lib/x86_64-linux-gnu/libopenblas.so.0
(0x00007f9d9ace0000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9d9ac01000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9d9aa1f000)
libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3
(0x00007f9d9a9a8000)
libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8
(0x00007f9d9a951000)
libpcre2-8.so.0 => /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0
(0x00007f9d9a8b9000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f9d9a891000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0
(0x00007f9d9a87e000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f9d9a861000)
libtirpc.so.3 => /lib/x86_64-linux-gnu/libtirpc.so.3
(0x00007f9d9a832000)
libicuuc.so.72 => /usr/lib/x86_64-linux-gnu/libicuuc.so.72
(0x00007f9d9a62b000)
libicui18n.so.72 => /usr/lib/x86_64-linux-gnu/libicui18n.so.72
(0x00007f9d9a2ef000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
(0x00007f9d9a29e000)
/lib64/ld-linux-x86-64.so.2 (0x00007f9d9d60d000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5
(0x00007f9d99fcb000)
libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6
(0x00007f9d99f9a000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f9d99f93000)
libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2
(0x00007f9d99f40000)
libicudata.so.72 => /usr/lib/x86_64-linux-gnu/libicudata.so.72
(0x00007f9d9816e000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f9d97f18000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f9d97ef4000)
libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3
(0x00007f9d97e17000)
libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3
(0x00007f9d97de7000)
libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2
(0x00007f9d97de1000)
libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0
(0x00007f9d97dd2000)
libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1
(0x00007f9d97dcb000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2
(0x00007f9d97db8000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f9d97db3000)
Interesting, you also have libopenblas.so.0 (in a different position).
>
> the /etc/alternatives mechanism you are after. (That was from rocker/r-base,
> a quick way for me to get to clean and current Debian build.)
ls -l /usr/lib/x86_64-linux-gnu/liblapack.so.3
lrwxrwxrwx 1 root root 49 Mar 28 2022 /usr/lib/x86_64-linux-gnu/liblapack.so.3
-> /etc/alternatives/liblapack.so.3-x86_64-linux-gnu
And that is the one from OpenBLAS
ls -l /etc/alternatives/liblapack.so.3-x86_64-linux-gnu
lrwxrwxrwx 1 root root 56 Dec 30 20:44
/etc/alternatives/liblapack.so.3-x86_64-linux-gnu ->
/usr/lib/x86_64-linux-gnu/openblas-openmp/liblapack.so.3
For libblas:
ls -l /usr/lib/x86_64-linux-gnu/libblas.so.3
lrwxrwxrwx 1 root root 47 Mar 28 2022 /usr/lib/x86_64-linux-gnu/libblas.so.3
-> /etc/alternatives/libblas.so.3-x86_64-linux-gnu
ls -l /etc/alternatives/libblas.so.3-x86_64-linux-gnu
lrwxrwxrwx 1 root root 54 Dec 30 20:44
/etc/alternatives/libblas.so.3-x86_64-linux-gnu ->
/usr/lib/x86_64-linux-gnu/openblas-openmp/libblas.so.3
To further try to understand, I've uninstalled openblas, but left atlas:
Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 35 auto
mode
1 /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3 35 manual
mode
2 /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 manual
mode
And then, configure shows its looking for this.
configure: searching for an external BLAS
configure: searching for BLAS in default libraries
checking for dgemm_... no
configure: searching for OpenBLAS
checking for sgemm_ in -lopenblas... no
configure: searching for BLIS
checking for sgemm_ in -lblis... no
configure: searching for ATLAS
checking for ATL_xerbla in -latlas... yes
And
External libraries: pcre2, readline, BLAS(ATLAS), LAPACK(generic), curl
ldd now shows
~/tmp/Rpt/R-patched/modules $ ldd lapack.so
linux-vdso.so.1 (0x00007ffd83045000)
libR.so => /usr/lib/libR.so (0x00007f89196e9000)
liblapack.so.3 => /usr/lib/x86_64-linux-gnu/liblapack.so.3
(0x00007f8918fb5000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8918ed6000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8918cf4000)
libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3
(0x00007f8918cb2000)
libreadline.so.8 => /lib/x86_64-linux-gnu/libreadline.so.8
(0x00007f8918c59000)
libpcre2-8.so.0 => /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0
(0x00007f8918bc1000)
liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f8918b99000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0
(0x00007f8918b86000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f8918b69000)
libtirpc.so.3 => /lib/x86_64-linux-gnu/libtirpc.so.3
(0x00007f8918b3a000)
libicuuc.so.72 => /usr/lib/x86_64-linux-gnu/libicuuc.so.72
(0x00007f8918933000)
libicui18n.so.72 => /usr/lib/x86_64-linux-gnu/libicui18n.so.72
(0x00007f89185f7000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
(0x00007f89185a6000)
/lib64/ld-linux-x86-64.so.2 (0x00007f8919b82000)
libatlas.so.3 => /usr/lib/x86_64-linux-gnu/libatlas.so.3
(0x00007f8918226000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5
(0x00007f8917f53000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f8917f2d000)
libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6
(0x00007f8917efc000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f8917ef7000)
libgssapi_krb5.so.2 => /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2
(0x00007f8917ea4000)
libicudata.so.72 => /usr/lib/x86_64-linux-gnu/libicudata.so.72
(0x00007f89160d2000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f8915e7a000)
libkrb5.so.3 => /usr/lib/x86_64-linux-gnu/libkrb5.so.3
(0x00007f8915d9f000)
libk5crypto.so.3 => /usr/lib/x86_64-linux-gnu/libk5crypto.so.3
(0x00007f8915d6f000)
libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2
(0x00007f8915d69000)
libkrb5support.so.0 => /usr/lib/x86_64-linux-gnu/libkrb5support.so.0
(0x00007f8915d5a000)
libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1
(0x00007f8915d51000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2
(0x00007f8915d40000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f8915d3b000)
Now we see libatlas.
R.
>
> Dirk
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-31
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdia...@gmail.com
r.d...@uam.es
ramon.d...@iib.uam.es
https://ligarto.org/rdiaz
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