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BSC Nixpkgs: User guide
BSC Nixpkgs: User guide
1 Introduction
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Some preliminary steps must be done manually to be able to build and
install packages (derivations in nix jargon).
This guide is specific for the nix installation in the xeon07 node,
accessed by the ssfhead.bsc.es login node, but it may be used in other
machines as well.
To easily connect to xeon07 in one step, setup the SSH (for version
7.3 and upwards) configuration file in ~/.ssh/config adding these
lines:
Host cobi
HostName ssflogin.bsc.es
User your-username-here
Host xeon07
ProxyJump cobi
HostName xeon07
User your-username-here
You should be able to connect with:
$ ssh xeon07
1.1 Network access
In order to use nix you need to be able to download the sources from
Internet. Usually the download requires the ports 22, 80 and 443 to be
open for outgoing traffic.
In order to use nix would you need to be able to download the sources
from Internet. Usually the download requires the ports 22, 80 and 443
to be open for outgoing traffic.
Unfortunately, in some clusters (as is the case in xeon07) access to
Internet is disabled. However you can tunnel the connection by SSH to
your local machine, and then reach the Internet.
There are some guides on how to prepare the proxy server and the
tunnel in SSH such as:
In order to tell nix to use the proxy connection, you will need to
export the "https_proxy" and "http_proxy" variables. A proxy
connection is already configured in xeon07 and you can automatically
set those variables to the correct address by loading:
https://www.seniorlinuxadmin.co.uk/ssh-over-proxy.html
In order to instruct nix to use the proxy connection, you will need to
export the https_proxy and http_proxy variables. In the xeon07 node is
already configured and you can automatically set those variables to
the correct address by loading:
$ . /scratch/nix/internet
xeon07$ . /scratch/nix/internet
Consider adding the command to your ~/.bashrc file so you don't need
to do it every time you want to use nix.
Now you should be able to reach the outside world by running:
$ curl google.com
xeon07$ curl google.com
<HTML><HEAD><meta http-equiv="content-type" content="text/html;charset=utf-8">
<TITLE>301 Moved</TITLE></HEAD><BODY>
<H1>301 Moved</H1>
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prompt.
Most repositories at https://pm.bsc.es/gitlab are open to read for
logged users, but there are some exceptions for example the nanos6
repository where you must have explicitly granted read access.
logged in users, but there are some exceptions (for example the nanos6
repository) where you must have explicitly granted read access.
If you don't have a ssh key at ~/.ssh/*.pub create a new one without
password protection by running:
If you don't have a ssh key at ~/.ssh/*.pub in xeon07 create a new one
without password protection by running:
$ ssh-keygen
xeon07$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (~/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
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https://pm.bsc.es/gitlab/profile/keys
If you want to select another key rather than the default
~/.ssh/id_rsa then you must configure it for use in the ~/.ssh/config
file, adding:
Then, configure it for use in the ~/.ssh/config file, adding:
Host bscpm02.bsc.es
IdentityFile ~/.ssh/your-private-key
IdentityFile ~/.ssh/id_rsa
Finally verify the SSH connection to the server works and you get a
greeting from the GitLab server with your username:
$ ssh git@bscpm02.bsc.es
xeon07$ ssh git@bscpm02.bsc.es
PTY allocation request failed on channel 0
Welcome to GitLab, @rarias!
Connection to bscpm02.bsc.es closed.
@ -97,32 +111,32 @@
Finally, you should be able to download the rarias/nanos6 git
repository without any password interaction by running:
$ git clone git@bscpm02-bsc-es:rarias/nanos6.git
xeon07$ git clone git@bscpm02-bsc-es:rarias/nanos6.git
1.3 Prepare the bsc-nixpkgs repo
Once you have Internet and you have granted access to the PM GitLab
repositories you can begin down the rabbit hole of nix. First ensure
that the nix binaries are available in your machine:
that the nix binaries are available from your shell in xeon07:
$ nix --version
xeon07$ nix --version
nix (Nix) 2.3.6
Now you are set to install packages with nix. Clone the bsc-nixpkgs
repository:
$ git clone git@bscpm02-bsc-es:rarias/bsc-nixpkgs.git
xeon07$ git clone git@bscpm02-bsc-es:rarias/bsc-nixpkgs.git
Nix looks in the current folder for a file named "default.nix" for
packages, so go to the repo:
$ cd bsc-nixpkgs
xeon07$ cd bsc-nixpkgs
Now you should be able to build nanos6 from the git repository:
$ nix-build -A bsc.nanos6-git
xeon07$ nix-build -A bsc.nanos6-git
The output is placed in the "result" symlink.
The output is placed in the "result" symbolic link.
2. Basic usage of nix
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All nix packages are stored under the /nix directory. When you need to
"install" some binary from nix, a symlink is added to a folder
included in the $PATH variable. In particular, you should have the
included in the $PATH variable. In particular, you should have
something similar added to your $PATH:
$ echo $PATH | sed 's/:/\n/g' | grep nix
xeon07$ echo $PATH | sed 's/:/\n/g' | grep nix
/home/Computational/rarias/.nix-profile/bin
/nix/var/nix/profiles/default/bin
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which contains the nix tools (which are installed in the /nix
directory as well).
Use `nix search` to look for official packages in the "nixpkgs"
channel (the default repository of packages):
xeon07$ nix search cowsay
warning: using cached results; pass '-u' to update the cache
* cowsay (cowsay)
A program which generates ASCII pictures of a cow with a message
* neo-cowsay (neo-cowsay)
Cowsay reborn, written in Go
* ponysay (ponysay-3.0.3)
Cowsay reimplemention for ponies
* tewisay (tewisay-unstable-2017-04-14)
Cowsay replacement with unicode and partial ansi escape support
When you need a program that is not available in your environment,
much like when you use "module load ..." you can use nix-env to modify
what is currently loaded. For example:
$ nix-env -iA nixpkgs.cowsay
xeon07$ nix-env -iA nixpkgs.cowsay
The command will download (if not found already in the nix store),
compile (if necessary) and load the program `cowsay` from the nixpkgs
Notice that you should specify the prefix "nixpkgs." before. The
command will download (if not found already in the nix store), compile
(if necessary) and load the program `cowsay` from the nixpkgs
repository in the environment. You should be able to run it as:
$ cowsay "hello world"
xeon07$ cowsay "hello world"
_____________
< hello world >
-------------
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||----w |
|| ||
You can inspect now the ~/.nix-profile/bin folder, and see that a new
You can now inspect the ~/.nix-profile/bin folder, and see that a new
symlink was added to the actual installation of the binary:
$ file ~/.nix-profile/bin/cowsay
xeon07$ file ~/.nix-profile/bin/cowsay
/home/Computational/rarias/.nix-profile/bin/cowsay: symbolic link to
`/nix/store/673gczmhr5b449521srz2n7g1klykz6n-cowsay-3.03+dfsg2/bin/cowsay'
You can list the current packages installed in your environment by
running:
$ nix-env -q
xeon07$ nix-env -q
cowsay-3.03+dfsg2
nix-2.3.6
@ -191,7 +223,7 @@
You can remove any package from the environment using:
$ nix-env -e cowsay
xeon07$ nix-env -e cowsay
See the manual with `nix-env --help` if you want to know more details.
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any binary cache server yet.
Nix will handle the build process without any user interaction (with a
few exceptions stated later, which you shouldn't have to worry). If
any other user has already built the package then the build process is
not needed, and the package is used as is.
few exceptions which you shouldn't have to worry). If any other user
has already built the package then the build process is not needed,
and the package is used as is.
In order to build a BSC package go to the `bsc-nixpkgs` directory, and
run:
$ nix-build -A bsc.dummy
xeon07$ nix-build -A bsc.dummy
The package will be built and installed in the /nix directory, then a
symlink is placed in the result directory:
Notice the "bsc." prefix for BSC packages. The package will be built
and installed in the /nix directory, then a symlink is placed in the
result directory:
$ find result/ -type f
xeon07$ find result/ -type f
result/
result/bin
result/bin/dummy
The way in which nix handles the packages and dependencies ensures
that the output of a compilation of any package is exactly the same.
that the environment of the build process of any package is exactly
the same, so the generated output should be the same if the builds are
deterministic.
You can check the reproducibility of the build by adding the "--check"
flag, which will rebuild the package and compare the checksum of every
file with the ones installed:
file with the ones previously built:
$ nix-build -A bsc.dummy --check
xeon07$ nix-build -A bsc.dummy --check
...
$ echo $?
xeon07$ echo $?
0
A return code of zero ensures the output is bit by bit identical to
the one installed. There are some packages that try to include
non-reproducible information in the build process as the timestamp
which will produce an error. Those packages must be patched to ensure
the output is deterministic.
the one installed. There are some packages that include
indeterministic information in the build process (such as the
timestamp of the current time) which will produce an error. Those
packages must be patched to ensure the output is deterministic.
Notice that if you "cd" into the result/ directory you will be at /nix
directory (as you follow the symlink) where you don't have write
permission. Therefore if your program attempts to write to the current
directory it will fail. It is recommended to instead run your program
from the top directory:
Notice that if you "cd" into the "result/" directory you will be at
/nix directory (as you have follow the symlink) where you don't have
write permission. Therefore if your program attempts to write to the
current directory it will fail. It is recommended to instead run your
program from the top directory:
$ result/bin/dummy
xeon07$ result/bin/dummy
Hello world!
Or you can install it in the environment:
$ nix-env -i ./result
xeon07$ nix-env -i ./result
And "cd" into any directory where you want to output some files and
just run it by the name:
$ cd /tmp
$ dummy
xeon07$ cd /tmp
xeon07$ dummy
Hello world!
Finally, you can remove it from the environment if you don't need it:
$ nix-env -e dummy
xeon07$ nix-env -e dummy
If you want to know more details use "nix-build --help" to see the
manual.
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2.3 The build process
Each package is built following a programmable configuration
description in the nix language. Build in nix are performed under very
strict conditions. No access any file in the file system is allowed,
unless stated in the dependencies of the package which are then
available in the build environment.
description in the nix language. Builds in nix are performed under
very strict conditions. No access to any file in the file system is
allowed, unless stated in the dependencies, which are in the /nix
store only.
There is no network access in the build process and other restrictions
are enforced that the build is deterministic. See more details here:
are enforced so that the build environment is reproducible. See more
details here:
https://nixos.wiki/wiki/Nix#Sandboxing
In the "default.nix" file of the bsc-nixpkgs you can see the
definition for each package, for example the nbody app:
The top level "default.nix" file of the bsc-nixpkgs serves as a index
of all BSC packages. You can see the definition for each package, for
example the nbody app:
nbody = callPackage ./bsc/apps/nbody/default.nix {
stdenv = pkgs.gcc9Stdenv;
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Then you can rebuild the nbody package:
$ nix-build -A bsc.nbody
xeon07$ nix-build -A bsc.nbody
...
And verify that the binary is indeed linked to MPICH now:
$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
xeon07$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
libmpi.so.12 => /nix/store/dwkkcv78a5bs8smflpx9ppp3klhz3i98-mpich-3.3.2/lib/libmpi.so.12 (0x00007f6be0f07000)
If you modify a package which another package requires as a
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The build process now is not required:
$ nix-build -A bsc.nbody
xeon07$ nix-build -A bsc.nbody
/nix/store/rbq7wrjcmg6fzd6yhrlnkfvzcavdbdpc-nbody
$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
xeon07$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
libmpifort.so.12 => /nix/store/jvsjvxj2a08340fpdrqbqix9z3mpp3bd-intel-mpi-2019.7.217/lib/libmpifort.so.12 (0x00007f3a00402000)
libmpi.so.12 => /nix/store/jvsjvxj2a08340fpdrqbqix9z3mpp3bd-intel-mpi-2019.7.217/lib/libmpi.so.12 (0x00007f39fed34000)