diff options
| -rw-r--r-- | README.org | 2 | ||||
| -rw-r--r-- | gn/packages/pangenome-rust.scm | 51 |
2 files changed, 45 insertions, 8 deletions
diff --git a/README.org b/README.org index 5d7cc33..2ab2229 100644 --- a/README.org +++ b/README.org @@ -73,7 +73,7 @@ root with All important packages are listed in manifest.scm.example. Test with -: guix build -L . -m manifest.scm.example +: guix build -L . -m manifest.scm.example --tune=native * An important note on AI diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index 3e9d8cc..00155bd 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -34,6 +34,27 @@ (crate-source "anyhow" "1.0.66" "1xj3ahmwjlbiqsajhkaa0q6hqwb4l3l5rkfxa7jk1498r3fn2qi1")) +;; Phase snippet to set RUSTFLAGS for CPU tuning. +;; Detects the tuning CPU from PATH (tuning-compiler-<cpu> directory) +;; and sets RUSTFLAGS=-C target-cpu=<cpu>. +(define %rust-tuning-phase + #~(add-before 'build 'set-rust-target-cpu + (lambda _ + (let loop ((dirs (string-split (or (getenv "PATH") "") #\:))) + (if (null? dirs) + #t + (let ((base (basename (dirname (car dirs))))) + (if (string-contains base "tuning-compiler-") + (let ((cpu (substring base + (+ (string-contains base "tuning-compiler-") + (string-length "tuning-compiler-"))))) + (setenv "RUSTFLAGS" + (string-append (or (getenv "RUSTFLAGS") "") + " -C target-cpu=" cpu)) + (format #t " RUSTFLAGS set for CPU tuning: ~a~%" (getenv "RUSTFLAGS"))) + (loop (cdr dirs))))))))) + + (define rust-autocfg-1.1.0 (crate-source "autocfg" "1.1.0" "1ylp3cb47ylzabimazvbz9ms6ap784zhb6syaz6c1jqpmcmq0s6l")) @@ -3287,7 +3308,9 @@ (base32 "1kv1abwwj1m5d7y61ymrrj309bg543vk5dlfq56h5d4qswmb7zyv")))) (build-system cargo-build-system) - (arguments (list #:install-source? #f)) + (arguments (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) ;; No upstream test data; tests require GFA/BAM input files. (inputs (cargo-inputs 'gfainject #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) @@ -3316,7 +3339,9 @@ names must match the path names in the GFA.") "0nzhgg7sqalrpl1mzlp0rvaj4dgcwghv1jngcsfqqk1mhx4hvj0n")))) (build-system cargo-build-system) (arguments - (list #:install-source? #f)) + (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (inputs (cargo-inputs 'onecode #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) (home-page "https://github.com/pangenome/onecode-rs") @@ -3352,7 +3377,9 @@ data. The C library (ONElib) is bundled and compiled at build time.") #:tests? #f #:cargo-build-flags ''("--release" "--package" "ragc-cli") ;; Workspace root has no [[bin]], must specify the CLI member - #:cargo-install-paths ''("ragc-cli"))) + #:cargo-install-paths ''("ragc-cli") + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (properties '((tunable? . #t))) (home-page "https://github.com/AndreaGuarracino/ragc") (synopsis "Genome compression tool implementing the AGC format in Rust") @@ -3386,6 +3413,7 @@ similar genome sequences and is compatible with the C++ AGC format.") #:tests? #f #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase (add-after 'unpack 'fix-sources ;; Cargo.toml uses a git source for onecode but Cargo.lock ;; resolved it to the registry version 0.1.0. @@ -3596,6 +3624,7 @@ sequences to accelerate the alignment process.") #:install-source? #f #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase ;; The ragc workspace root has no [package] so crate-src? returns #f ;; and configure skips it. Copy it manually. (add-before 'build 'copy-ragc-workspace @@ -3814,7 +3843,9 @@ and alignments for analysis. It can also compute graphs for the sequences.") (base32 "0r51kz2vwmj8kkxr1az45g68m0acn652mcddsscc78m78yxh85v1")))) (build-system cargo-build-system) - (arguments (list #:install-source? #f)) + (arguments (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (inputs (cargo-inputs 'gfautil #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) (home-page "https://github.com/pangenome/rs-gfa-utils") @@ -3839,7 +3870,9 @@ Graphical Fragment Assembly} files and related formats.") (base32 "0yn8i70ww3x544qm4fwr33vklsxf3fvivpfpv46prkfz9hsmd9ps")))) (build-system cargo-build-system) (arguments - `(#:install-source? #f)) + (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (inputs (cargo-inputs 'gfaffix #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) @@ -3865,7 +3898,9 @@ collapses them into a non-redundant graph structure.") (sha256 (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk")))) (build-system cargo-build-system) - (arguments (list #:install-source? #f)) + (arguments (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (inputs (cargo-inputs 'gafpack #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) (home-page "https://github.com/ekg/gafpack") @@ -3890,7 +3925,9 @@ maps useful in haplotype-based genotyping.") (sha256 (base32 "0sk2ab22z6qa00j1w8a8f5kbb7q2xb10fhd32zy4lh351v3mqmyg")))) (build-system cargo-build-system) - (arguments (list #:install-source? #f)) + (arguments (list #:install-source? #f + #:phases #~(modify-phases %standard-phases + #$%rust-tuning-phase))) (inputs (cargo-inputs 'vcfbub #:module '(gn packages pangenome-rust))) (properties '((tunable? . #t))) (home-page "https://github.com/pangenome/vcfbub") |