Bootstrapping Guix on HPC without Root

Bootstrapping Guix on HPC without Root

[Wm Salt Hale]

Hello,

I have been attempting to install Guix on the University of
Washington's HPC using a modified bootstrapping script based on
https://github.com/pjotrp/nix-no-root

The script can currently be found here (to be forked and pushed to GH
when verified as working):

https://communitydata.cc/~salt/guix-bootstrap.sh


This produces a semi-working installation, it can spit out a version
and spend a good deal of time trying to complete `guix pull`

The first run was logged via `|& tee -a`

https://communitydata.cc/~salt/guix_first_run.log


As you can see, the build fails. Subsequent runs fail at the same
point. I've tried a variety of debugging steps including: side-load
libstdc++ directly from the Store with not effect, reduce number of
cores daemon is allowed, and imitate linux-2.6.

Any assistance or direction would be greatly appreciated!

--
Wm Salt Hale

Re: Bootstrapping Guix on HPC without Root

[Pjotr Prins]

Just read the script. I think this is actually the hard way of doing
it and 'guix pull' should not work if you are not on /gnu/store.

How about using proot (Ludo has some info here) and to bootstrap guix
instead with guix and configure the build system like 

   https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix

That way you get a reproducible build environment and then build guix
in a non-root path. I have not tried this yet, but I can try it this
weekend (I am on the road right now).

Pj.

On Wed, Jul 12, 2017 at 05:46:15PM -0700, Wm Salt Hale wrote:
> Hello,
> 
> I have been attempting to install Guix on the University of
> Washington's HPC using a modified bootstrapping script based on
> https://github.com/pjotrp/nix-no-root
> 
> The script can currently be found here (to be forked and pushed to GH
> when verified as working):
> 
> https://communitydata.cc/~salt/guix-bootstrap.sh
> 
> 
> This produces a semi-working installation, it can spit out a version
> and spend a good deal of time trying to complete `guix pull`
> 
> The first run was logged via `|& tee -a`
> 
> https://communitydata.cc/~salt/guix_first_run.log
> 
> 
> As you can see, the build fails. Subsequent runs fail at the same
> point. I've tried a variety of debugging steps including: side-load
> libstdc++ directly from the Store with not effect, reduce number of
> cores daemon is allowed, and imitate linux-2.6.
> 
> Any assistance or direction would be greatly appreciated!
> 
> --
> Wm Salt Hale

-- 

Re: Bootstrapping Guix on HPC without Root

[Ludovic Courtès]

Hello!

Wm Salt Hale <salt@altsalt.net> skribis:

> I have been attempting to install Guix on the University of
> Washington's HPC using a modified bootstrapping script based on
> https://github.com/pjotrp/nix-no-root
>
> The script can currently be found here (to be forked and pushed to GH
> when verified as working):
>
> https://communitydata.cc/~salt/guix-bootstrap.sh
>
>
> This produces a semi-working installation, it can spit out a version
> and spend a good deal of time trying to complete `guix pull`
>
> The first run was logged via `|& tee -a`
>
> https://communitydata.cc/~salt/guix_first_run.log

For the sake of those not following links ;-), the build error is:

--8<---------------cut here---------------start------------->8---
    build/genhooks.o build/errors.o ../build-x86_64-unknown-linux-gnu/libiberty/libiberty.a
g++   -g -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -Woverloaded-virtual -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common  -DHAVE_CONFIG_H -DGENERATOR_FILE -Wl,-rpath=/com/guix/guix/store/qrxkb00z8qmj0aql4gd8zcmf3ldvz583-glibc-2.25/lib -Wl,-dynamic-linker -Wl,/com/guix/guix/store/qrxkb00z8qmj0aql4gd8zcmf3ldvz583-glibc-2.25/lib/ld-linux-x86-64.so.2 -L/com/guix/guix/store/89f8avya4dzh8jrvzxw1q9pf27af702h-libstdc++-5.4.0/lib -L/com/guix/guix/store/yr6nya39hzwx960y8nbiqq91w5yk842x-zlib-1.2.11/lib -Wl,-rpath=/com/guix/guix/store/yr6nya39hzwx960y8nbiqq91w5yk842x-zlib-1.2.11/lib -o build/genchecksum \
    build/genchecksum.o ../build-x86_64-unknown-linux-gnu/libiberty/libiberty.a
x86_64-guix-linux-gnu-ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:2613: build/genhooks] Error 1
make[3]: *** Waiting for unfinished jobs....
x86_64-guix-linux-gnu-ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:2613: build/genchecksum] Error 1
--8<---------------cut here---------------end--------------->8---

The ‘guix-bootstrap.sh’ script above runs guix-daemon with
‘--disable-chroot’, which means build processes are not being isolated.
I’m fairly confident that this is the root cause of the problem; for
instance because GCC’s build processes end up picking a few things from
/usr/bin instead of /gnu/store.  (ISTR Roel Janssen experienced a
similar issue back then, maybe Roel can comment.)

Pjotr mentioned PRoot.  An intermediate solution would be to build and
“pack” the software you want to run on your laptop (any machine where
Guix is already installed), to send it to the HPC machine, and to run it
there with PRoot.  I gave instructions at:

  https://lists.gnu.org/archive/html/guix-devel/2017-05/msg00182.html

I know Pjotr has been experimenting with another nice option, I’ll let
him explain.  :-)

HTH!

Ludo’.