apt install intel-mkl in a non-interactive session
myoung3 opened this issue · 4 comments
myoung3 commented
Trying to use apt install intel-mkl is hanging at a prompt in a non-interactive (singularity) build session. Here's my def file. any idea how to get around this prompt?
Bootstrap: docker
From: rocker/geospatial:4.1.0
Stage: build
############################################
%post
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##intel mkl###
apt update
apt install -y gnupg2
apt install -y intel-mkl
singularity build --remote mkl.sif mkl.def
INFO: Access Token Verified!
INFO: Token stored in /root/.singularity/remote.yaml
INFO: Remote "default" now in use.
INFO: Starting build...
Getting image source signatures
Copying blob sha256:16ec32c2132b43494832a05f2b02f7a822479f8250c173d0ab27b3de78b2f058
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INFO: Running post scriptlet
+ apt update
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
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Reading package lists...
Building dependency tree...
Reading state information...
2 packages can be upgraded. Run 'apt list --upgradable' to see them.
+ apt install -y gnupg2
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
dirmngr gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libassuan0 libksba8 libnpth0 pinentry-curses
Suggested packages:
dbus-user-session libpam-systemd pinentry-gnome3 tor parcimonie xloadimage
scdaemon pinentry-doc
The following NEW packages will be installed:
dirmngr gnupg gnupg-l10n gnupg-utils gnupg2 gpg gpg-agent gpg-wks-client
gpg-wks-server gpgconf gpgsm libassuan0 libksba8 libnpth0 pinentry-curses
0 upgraded, 15 newly installed, 0 to remove and 2 not upgraded.
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Setting up libassuan0:amd64 (2.5.3-7ubuntu2) ...
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Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
+ apt install -y intel-mkl
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
gcc-7-base gcc-8-base libasan4 libcilkrts5 libgcc-7-dev libmkl-avx
libmkl-avx2 libmkl-avx512 libmkl-avx512-mic libmkl-computational-dev
libmkl-core libmkl-def libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64
libmkl-gnu-thread libmkl-intel-ilp64 libmkl-intel-lp64 libmkl-intel-thread
libmkl-interface-dev libmkl-locale libmkl-mc libmkl-mc3
libmkl-meta-computational libmkl-meta-interface libmkl-meta-threading
libmkl-pgi-thread libmkl-rt libmkl-sequential libmkl-tbb-thread
libmkl-threading-dev libmkl-vml-avx libmkl-vml-avx2 libmkl-vml-avx512
libmkl-vml-avx512-mic libmkl-vml-cmpt libmkl-vml-def libmkl-vml-mc
libmkl-vml-mc2 libmkl-vml-mc3 libmpx2 libomp-10-dev libomp-dev libomp5-10
libtbb-dev libtbb2 libubsan0
Suggested packages:
intel-mkl-doc libomp-10-doc libtbb-doc
The following NEW packages will be installed:
gcc-7-base gcc-8-base intel-mkl libasan4 libcilkrts5 libgcc-7-dev libmkl-avx
libmkl-avx2 libmkl-avx512 libmkl-avx512-mic libmkl-computational-dev
libmkl-core libmkl-def libmkl-dev libmkl-gf-ilp64 libmkl-gf-lp64
libmkl-gnu-thread libmkl-intel-ilp64 libmkl-intel-lp64 libmkl-intel-thread
libmkl-interface-dev libmkl-locale libmkl-mc libmkl-mc3
libmkl-meta-computational libmkl-meta-interface libmkl-meta-threading
libmkl-pgi-thread libmkl-rt libmkl-sequential libmkl-tbb-thread
libmkl-threading-dev libmkl-vml-avx libmkl-vml-avx2 libmkl-vml-avx512
libmkl-vml-avx512-mic libmkl-vml-cmpt libmkl-vml-def libmkl-vml-mc
libmkl-vml-mc2 libmkl-vml-mc3 libmpx2 libomp-10-dev libomp-dev libomp5-10
libtbb-dev libtbb2 libubsan0
0 upgraded, 48 newly installed, 0 to remove and 2 not upgraded.
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Get:47 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 libmkl-dev amd64 2020.0.166-1 [519 kB]
Get:48 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 intel-mkl amd64 2020.0.166-1 [11.7 kB]
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debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
Intel Math Kernel Library (Intel MKL)
-------------------------------------
Intel MKL's Single Dynamic Library (SDL) is installed on your machine. This
shared object can be used as an alternative to both libblas.so.3 and
liblapack.so.3, so that packages built against BLAS/LAPACK can directly use MKL
without rebuild.
However, MKL is non-free software, and in particular its source code is not
publicly available. By using MKL as the default BLAS/LAPACK implementation, you
might be violating the licensing terms of copyleft software that would become
dynamically linked against it. Please verify that the licensing terms of the
program(s) that you intend to use with MKL are compatible with the MKL
licensing terms. For the case of software under the GNU General Public License,
you may want to read this FAQ:
https://www.gnu.org/licenses/gpl-faq.html#GPLIncompatibleLibs
If you don't know what MKL is, or unwilling to set it as default, just choose
the preset value or simply type Enter.
Use libmkl_rt.so as the default alternative to BLAS/LAPACK? [yes/no]
eddelbuettel commented
No and also out of scope.
Can I ask you to not bother this repo with things that are not within scope? This is a one-off and simple helper script to aid in MKL installation on normal Linux machines that was written a few years ago. Shoehorning into other applications is not its scope, and (sorry to be bearer of bad news here) I never signed a contract to offer semi-random debugging help.
There is mega-corporation standing behind the product you are wrestling with. Maybe ask them?
myoung3 commented
Totally reasonable. Again, sorry for the issue spam. My reasoning was that this github repo is a nexus for people trying to link MKL on deb/ubuntu, and that documenting/asking issues here might attract a larger audience, and also be helpful to others if I figure these out myself and post my own solutions. I'll take these up with intel, although finding the right contact address in a mega corporation is certainly the biggest hurdle there.
eddelbuettel commented
I haven't followed it this all that closely but I MKL is now in Debian's non-free: https://packages.debian.org/sid/libmkl-intel
So if I were you'd start with the basics. A Debian based container. The r-base aka rocker/r-base comes to mind too as it already has R and all that. The build from up there, and remain cognizant of the fact that some Rocker stacks are Debian-based whereas others are Ubuntu-based.
eddelbuettel commented
Also at the very bottom of the top-level README for this repo has this Appendix:
2021 Update: The post and script were originally written in 2018, and while they have been updated, things do sometimes change. So these days for example Ubuntu has (meta-)package intel-mkl starting from release 20.04 ("focal") and never---so there you can just say sudo apt install intel-mkl.