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diff --git a/topics/rust/guix-rust-bootstrap.gmi b/topics/rust/guix-rust-bootstrap.gmi new file mode 100644 index 0000000..cd3c322 --- /dev/null +++ b/topics/rust/guix-rust-bootstrap.gmi @@ -0,0 +1,173 @@ +# Guix Rust Bootstrap + +To develop code against rust you often need a recent edition of rust. With Guix this is possible because you don't depend on the underlying linux distribution to provide recent versions of glibc and other libraries. Here we have a recipe that should work anywhere on Linux. + +I succeeded in running the latest Rust on Octopus and building packages with guix. + +To make it work the following steps are required: + +* Update guix with guix-pull if your guix is older than 3 months +* Unset GUIX_PROFILE on some systems +* Set your updated guix profile vars +* Create a container that has all dependencies for rust itself +* Run rustup +* Run cargo with LD_LIBRARY_PATH set to $GUIX_ENVIRONMENT/lib + +# Get Guix updated + +Important is to have a recent version of Guix. This is achieved with 'guix pull' and making sure it works. + + +```sh +mkdir -p ~/opt +guix pull -p ~/opt/guix-pull --url=https://codeberg.org/guix/guix +``` + +it takes a few minutes. Next set the environment + +```sh +unset GUIX_PROFILE +. ~/opt/guix-pull/etc/profile +``` + +This will point the path to a recent guix. You can make sure with + +``` +guix describe + guix 772c456 + repository URL: https://codeberg.org/guix/guix + branch: master + commit: 772c456717e755829397a6ff6dba4c1e135426d8 +``` + +which can be validated against the Guix tree. Running + + +```sh +guix package -A rust +rust 1.85.1 rust-src,tools,out,cargo gnu/packages/rust.scm:1454:4 +``` + +shows the current *stable* version in Guix. Now, of course, we want something more to get rust latest. + +# Update Rust and Cargo to latest (stable) + +The trick is to set up a container with Rust in your git working directory: + +``` +mkdir -p ~/.cargo ~/.rustup # to prevent rebuilds +guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl +curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh +. ~/.cargo/env +rustup default stable +``` + +Now rustc shows it is recent: + +``` +rustc --version +rustc 1.90.0 (1159e78c4 2025-09-14) +``` + +Next run 'cargo build' with: + +``` +env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib cargo build + Compiling libagc-sys v0.1.0 (/home/wrk/iwrk/opensource/code/pangenome/libagc-sys) + Finished 'dev' profile [unoptimized + debuginfo] target(s) in 0.06s +$ ./target/debug/libagc-sys +./target/debug/libagc-sys: error while loading shared libraries: libgcc_s.so.1: cannot open shared object file: No such file or directory +$ env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./target/debug/libagc-sys +Hello, world! +``` + +and your source should build and run. Note the libgcc_s.so.1 error. + +## What if you get a libgcc or librt error? + +The problem is that cargo picks up the wrong libgcc: + +``` +$ ls /gnu/store/*/lib/libgcc_s.so.1 +/gnu/store/m2vhzr0dy352cn59sgcklcaykprrr4j6-gcc-14.3.0-lib/lib/libgcc_s.so.1 +/gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/lib/libgcc_s.so.1 +/gnu/store/v3bq3shn333kh7m6gj3r58l0v7mkn4in-profile/lib/libgcc_s.so.1 +/gnu/store/xm7i1gvi0i9pyndlkv627r08rsw1ny96-gcc-15.2.0-lib/lib/libgcc_s.so.1 +``` + +This is because Guix itself builds on an older libgcc and librt. You need to tell it explicitly what library to load that built your cargo: + +``` +ldd ~/.cargo/bin/cargo + linux-vdso.so.1 (0x00007ffd409b2000) + libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fd2cf433000) + librt.so.1 => /lib/librt.so.1 (0x00007fd2cf42e000) +``` + +in the container: + +``` +ls -l /lib/libgcc_s.so.1 +lrwxrwxrwx 1 65534 overflow 82 Jan 1 1970 /lib/libgcc_s.so.1 -> /gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/lib/libgcc_s.so.1 +``` + +which happens to be the one in $GUIX_ENVIRONMENT/lib! So setting the library path solves it. + +The reason that we don't get the automatically resolving libraries that you normally have in guix is that we have updated rust by *hand* using rustup. Guix has no control over this process. + +# spoa-rs on octopus01 + +I just did above to build spoa-rs. Only had to add cmake to the shell packages. + +# sweepga on octopus01 + +I just built sweepga. Only had the add clang to the shell: + +```sh +guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl zlib cmake clang +. ~/.cargo/env +env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib cargo build +env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./target/debug/sweepga +[sweepga::start::0.000*1.00] 2025-10-11 15:27:28 | ./target/debug/sweepga +[sweepga::detect::0.000*1.00] Using .1aln workflow (FastGA native format) +[sweepga] ERROR: No valid input provided +``` + +To run on the cluster you likely don't want to use the container. Make a note of GUIX_ENVIRONMENT: + +``` +echo $GUIX_ENVIRONMENT/ +/gnu/store/6khi7iv7l75595hwlfc1nwmdcv72m24s-profile/ +``` + +It has your libs! So, outsite the container you can run + +``` +export GUIX_ENVIRONMENT=/gnu/store/6khi7iv7l75595hwlfc1nwmdcv72m24s-profile +env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib /home/wrk/tmp/sweepga/target/debug/sweepga +``` + +# Updating the container + +Now your build may fail because you miss a crucial library or tool. This is a feature of guix containers as it makes dependencies explicit. + +Just add them to the guix shell command. Let's say we add zlib + +``` +guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl zlib +``` + +# Troubleshooting + +## Collisions + +Guix may complain about collisions. These are mostly naming issues: + +``` +warning: collision encountered: + /gnu/store/nym6kiinrg2mb8z4lwnvfx5my8df9vrs-glibc-for-fhs-2.41/bin/ldd + /gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/bin/ldd +warning: choosing /gnu/store/nym6kiinrg2mb8z4lwnvfx5my8df9vrs-glibc-for-fhs-2.41/bin/ldd +``` + +it will like one into your environment. You can still use both tools by using the full path and normally ignore the warning. |