463 lines
15 KiB
Plaintext
463 lines
15 KiB
Plaintext
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bscpkgs: User guide
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ABSTRACT
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This repository contains a set of nix packages used in the Barcelona
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Supercomputing Center by the Programming Models group.
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The current setup uses the xeon07 machine to build packages, which are
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automatically uploaded to MareNostrum4, due to lack of permissions in
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the latter to perform the build safely.
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Some preliminary steps must be done manually to be able to build and
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install packages (derivations in nix jargon).
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1. Introduction
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To easily connect to xeon07 in one step, setup the SSH (for version
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7.3 and upwards) configuration file in ~/.ssh/config adding these
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lines:
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Host cobi
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HostName ssflogin.bsc.es
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User your-username-here
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Host xeon07
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ProxyJump cobi
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HostName xeon07
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User your-username-here
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You should be able to connect with:
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laptop$ ssh xeon07
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1.1 Network access
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In order to use nix you would need to be able to download the sources
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from Internet. Usually the download requires the ports 22, 80 and 443
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to be open for outgoing traffic.
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Check that you have network access in xeon07 provided by the
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environment variables "http_proxy" and "https_proxy". Try to fetch a
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webpage with curl, to ensure the proxy is working:
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xeon07$ curl x.com
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x
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1.2 SSH keys
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Package sources are usually downloaded directly from the git server,
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so you must be able to access all repositories without a password
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prompt.
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Most repositories at https://pm.bsc.es/gitlab are open to read for
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logged in users, but there are some exceptions (for example the nanos6
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repository) where you must have explicitly granted read access.
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If you don't have a ssh key at ~/.ssh/*.pub in xeon07 create a new one
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without password protection by running:
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xeon07$ ssh-keygen
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Generating public/private rsa key pair.
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Enter file in which to save the key (~/.ssh/id_rsa):
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Enter passphrase (empty for no passphrase):
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Enter same passphrase again:
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Your identification has been saved in ~/.ssh/id_rsa.
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Your public key has been saved in ~/.ssh/id_rsa.pub.
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...
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By default it will create the private key at ~/.ssh/id_rsa. Copy the
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contents of your public ssh key in ~/.ssh/id_rsa.pub and paste it in
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GitLab at:
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https://pm.bsc.es/gitlab/profile/keys
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Then, configure it for use in the ~/.ssh/config file, adding:
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Host bscpm03.bsc.es
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IdentityFile ~/.ssh/id_rsa
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Finally verify the SSH connection to the server works and you get a
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greeting from the GitLab server with your username:
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xeon07$ ssh git@bscpm03.bsc.es
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PTY allocation request failed on channel 0
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Welcome to GitLab, @rarias!
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Connection to bscpm03.bsc.es closed.
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Verify that you can access nanos6/nanos6 repository (otherwise you
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first need to ask to be granted read access), at:
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https://pm.bsc.es/gitlab/nanos6/nanos6
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Finally, you should be able to download the nanos6/nanos6 git
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repository without any password interaction by running:
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xeon07$ git clone git@bscpm03.bsc.es:nanos6/nanos6.git
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You will also need to access MareNostrum 4 from the xeon07 node, in
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order to submit experiments. Add the following lines as well to the
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~/.ssh/config file and set your user name:
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Host mn0 mn1 mn2
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User your-mn4-username
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IdentityFile ~/.ssh/id_rsa
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Then copy the key to MareNostrum 4 (it will ask you the first time for
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your password):
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xeon07$ ssh-copy-id -i ~/.ssh/id_rsa.pub mn1
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And ensure that you can connect without a password:
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xeon07$ ssh mn1
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...
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login1$
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1.3 The bscpkgs repo
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Once you have Internet and you have granted access to the PM GitLab
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repositories you can begin building software with nix. First ensure
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that the nix binaries are available from your shell in xeon07:
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xeon07$ nix --version
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nix (Nix) 2.3.6
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Now you are ready to build and install packages with nix. Clone the
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bscpkgs repository:
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xeon07$ git clone git@bscpm03.bsc.es:rarias/bscpkgs.git
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Nix looks in the current folder for a file named "default.nix" for
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packages, so go to the repo directory:
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xeon07$ cd bscpkgs
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Now you should be able to build nanos6:
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xeon07$ nix-build -A bsc.nanos6
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..
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/nix/store/3i0qkdywm9xjv2cm1ldx9smb552sf6r1-nanos6-2.4-6f10a32
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The installation is placed in the nix store (with the path stated in
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the last line of the build process), with the "result" symbolic link
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pointing to the same location:
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xeon07$ readlink result
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/nix/store/3i0qkdywm9xjv2cm1ldx9smb552sf6r1-nanos6-2.4-6f10a32
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1.4 Configuration of mn4 (MareNostrum 4)
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In order to execute the programs built at xeon07, you first need to
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enter nix environment. To do so, add to the end of the file ~/.bashrc
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in mn4 the following line:
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export PATH=/gpfs/projects/bsc15/nix/bin:$PATH
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Then logout and login again (our source the ~/.bashrc file) and you
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will now have the `nix-setup` command available. This command executes
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a new shell where the /nix store is available. To execute it:
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mn4$ nix-setup
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Now you will see a new shell, where you can access the nix store:
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nix|mn4$ ls /nix
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gcroots profiles store var
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The last build of nanos6 can be also found in mn4 at the same
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location:
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/nix/store/3i0qkdywm9xjv2cm1ldx9smb552sf6r1-nanos6-2.4-6f10a32
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Remember to enter the nix environment by running `nix-setup` when you
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need something from the nix store.
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You cannot perform any build operations from mn4: to do so use the
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xeon07 machine.
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2. Basic usage of nix
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Nix is a package manager which handles easily reproducibility and
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configuration of packages and dependencies. See more info here:
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https://nixos.org/nix/manual/
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We will only cover the basic usage of nix for the BSC packages.
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2.1 The user environment
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All nix packages are stored under the /nix directory. When you need to
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"install" some binary from nix, a symlink is added to a folder
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included in the $PATH variable. In particular, you should have
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something similar added to your $PATH:
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xeon07$ echo $PATH | sed 's/:/\n/g' | grep nix
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/home/Computational/rarias/.nix-profile/bin
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/nix/var/nix/profiles/default/bin
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The first one is your custom installation of packages that are stored
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in your home directory and the second one is the default installation
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which contains the nix tools (which are installed in the /nix
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directory as well).
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Use `nix search` to look for official packages in the "nixpkgs"
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channel (the default repository of packages):
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xeon07$ nix search cowsay
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warning: using cached results; pass '-u' to update the cache
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* cowsay (cowsay)
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A program which generates ASCII pictures of a cow with a message
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* neo-cowsay (neo-cowsay)
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Cowsay reborn, written in Go
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* ponysay (ponysay-3.0.3)
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Cowsay reimplemention for ponies
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* tewisay (tewisay-unstable-2017-04-14)
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Cowsay replacement with unicode and partial ansi escape support
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When you need a program that is not available in your environment,
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much like when you use "module load ..." you can use nix-env to modify
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what is currently loaded. For example:
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xeon07$ nix-env -iA nixpkgs.cowsay
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Notice that you should specify the prefix "nixpkgs." before. The
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command will download (if not found already in the nix store), compile
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(if necessary) and load the program `cowsay` from the nixpkgs
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repository in the environment. You should be able to run it as:
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xeon07$ cowsay "hello world"
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_____________
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< hello world >
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-------------
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\ ^__^
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\ (oo)\_______
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(__)\ )\/\
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||----w |
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|| ||
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You can now inspect the ~/.nix-profile/bin folder, and see that a new
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symlink was added to the actual installation of the binary:
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xeon07$ file ~/.nix-profile/bin/cowsay
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/home/Computational/rarias/.nix-profile/bin/cowsay: symbolic link to
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`/nix/store/673gczmhr5b449521srz2n7g1klykz6n-cowsay-3.03+dfsg2/bin/cowsay'
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You can list the current packages installed in your environment by
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running:
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xeon07$ nix-env -q
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cowsay-3.03+dfsg2
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nix-2.3.6
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Notice that this setup only affects your user environment. Also, it is
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permanent for any new session until you modify the environment again
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and is immediate, all sessions will have the new environment
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instantaneously.
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You can remove any package from the environment using:
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xeon07$ nix-env -e cowsay
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See the manual with `nix-env --help` if you want to know more details.
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2.2 Building packages
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Usually, all official packages are already compiled and distributed
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from a cache server so you don't need to rebuild them again. However,
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BSC packages are distributed only in source code form as we don't have
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any binary cache server yet.
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Nix will handle the build process without any user interaction (with a
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few exceptions which you shouldn't have to worry). If any other user
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has already built the package then the build process is not needed,
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and the package is used as is.
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In order to build a BSC package go to the `bscpkgs` directory, and
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run:
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xeon07$ nix-build -A bsc.dummy
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Notice the "bsc." prefix for BSC packages. The package will be built
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and installed in the /nix directory, then a symlink is placed in the
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result directory:
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xeon07$ find result/ -type f
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result/
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result/bin
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result/bin/dummy
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The way in which nix handles the packages and dependencies ensures
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that the environment of the build process of any package is exactly
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the same, so the generated output should be the same if the builds are
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deterministic.
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You can check the reproducibility of the build by adding the "--check"
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flag, which will rebuild the package and compare the checksum of every
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file with the ones previously built:
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xeon07$ nix-build -A bsc.dummy --check
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...
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xeon07$ echo $?
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0
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A return code of zero ensures the output is bit by bit identical to
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the one installed. There are some packages that include
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indeterministic information in the build process (such as the
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timestamp of the current time) which will produce an error. Those
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packages must be patched to ensure the output is deterministic.
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Notice that if you "cd" into the "result/" directory you will be at
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/nix directory (as you have follow the symlink) where you don't have
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write permission. Therefore if your program attempts to write to the
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current directory it will fail. It is recommended to instead run your
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program from the top directory:
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xeon07$ result/bin/dummy
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Hello world!
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Or you can install it in the environment:
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xeon07$ nix-env -i ./result
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And "cd" into any directory where you want to output some files and
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just run it by the name:
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xeon07$ cd /tmp
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xeon07$ dummy
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Hello world!
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Finally, you can remove it from the environment if you don't need it:
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xeon07$ nix-env -e dummy
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If you want to know more details use "nix-build --help" to see the
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manual.
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2.3 The build process
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Each package is built following a programmable configuration
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description in the nix language. Builds in nix are performed under
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very strict conditions. No access to any file in the file system is
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allowed, unless stated in the dependencies, which are in the /nix
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store only.
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There is no network access in the build process and other restrictions
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are enforced so that the build environment is reproducible. See more
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details here:
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https://nixos.wiki/wiki/Nix#Sandboxing
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The top level "default.nix" file of the bscpkgs serves as a index
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of all BSC packages. You can see the definition for each package, for
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example the nbody app:
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nbody = callPackage ./bsc/apps/nbody/default.nix {
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stdenv = pkgs.gcc9Stdenv;
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mpi = intel-mpi;
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icc = icc;
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tampi = tampi;
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nanos6 = nanos6-git;
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};
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The compilation details are specified in the
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"bsc/apps/nbody/default.nix" file. You can configure the package by
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changing the inputs, for example, what specific implementation of
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nanos6 or MPI you want to use. To change the MPI implementation to the
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official MPICH package use:
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nbody = callPackage ./bsc/apps/nbody/default.nix {
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stdenv = pkgs.gcc9Stdenv;
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mpi = pkgs.mpich; # Notice pkgs prefix for official packages
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icc = icc;
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tampi = tampi;
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nanos6 = nanos6-git;
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};
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Then you can rebuild the nbody package:
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xeon07$ nix-build -A bsc.nbody
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...
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And verify that the binary is indeed linked to MPICH now:
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xeon07$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
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libmpi.so.12 => /nix/store/dwkkcv78a5bs8smflpx9ppp3klhz3i98-mpich-3.3.2/lib/libmpi.so.12 (0x00007f6be0f07000)
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If you modify a package which another package requires as a
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dependency, nix will rebuild all required packages to propagate your
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changes on demand.
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However, if you come back to the original configuration, the package
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will still be in the /nix store (unless the garbage collector was
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manually run and removed your old build), so you don't need to rebuild
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it again.
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For example if nbody is configured back to use Intel MPI:
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nbody = callPackage ./bsc/apps/nbody/default.nix {
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stdenv = pkgs.gcc9Stdenv;
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mpi = intel-mpi;
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icc = icc;
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tampi = tampi;
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nanos6 = nanos6-git;
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};
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The build process now is not required:
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xeon07$ nix-build -A bsc.nbody
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/nix/store/rbq7wrjcmg6fzd6yhrlnkfvzcavdbdpc-nbody
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xeon07$ ldd result/bin/nbody_mpi.N2.2048.exe | grep mpi
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libmpifort.so.12 => /nix/store/jvsjvxj2a08340fpdrqbqix9z3mpp3bd-intel-mpi-2019.7.217/lib/libmpifort.so.12 (0x00007f3a00402000)
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libmpi.so.12 => /nix/store/jvsjvxj2a08340fpdrqbqix9z3mpp3bd-intel-mpi-2019.7.217/lib/libmpi.so.12 (0x00007f39fed34000)
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Take a look at the different package description files in the
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bscpkgs repository if you want to understand more details. Also
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the nix pills are a very good reference:
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https://nixos.org/nixos/nix-pills/
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2.4 Debugging the build process
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It may happen that the build process fails in an unexpected way. Most
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problems are related to missing dependencies and can be easily found
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by looking at the error messages.
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Other build problems are more subtle and require more debugging time.
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One way of inspecting a build problem is by adding the breakpointHook
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hook to the nativeBuildInputs array in a nix derivation (see
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https://nixos.org/nixpkgs/manual/#ssec-setup-hooks for more info),
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which will stop the build process and allow a shell to be attached to
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the sandbox.
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xeon07$ nix-build -A bsc.nbody
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...
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/nix/store/gvqm2yc9xx4vh3nglgckz8siya66jnkx-stdenv-linux/setup: line
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83: fake-missing-command: command not found
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build failed in buildPhase with exit code 127
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To attach install cntr and run the following command as root:
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cntr attach -t command \
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cntr-/nix/store/sk2nsj7xfr62cjk6m3725ydfyswqz7n1-nbody
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The command must run as root user, so you can use `sudo -i` to run it,
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(the -i option is required to load the shell profile which provides
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the nix path containing the cntr tool):
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xeon$ sudo -i cntr attach -t command \
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cntr-/nix/store/sk2nsj7xfr62cjk6m3725ydfyswqz7n1-nbody
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nixbld@localhost:/var/lib/cntr> ls
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bin build dev etc nix proc tmp var
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Then you can inspect the build environment to see why the build
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failed. Source the build/env-vars file to get the same environment
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variables (which include the $PATH) of the build process.
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/* vim: set ts=2 sw=2 tw=72 fo=watqc expandtab spell autoindent: */
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