guix: fixed static build and merged into main guix.scm

doc/performance-tuning.md

@@ -142,6 +142,10 @@ nts()::{lambda()#3}> > >::_M_run()
 
 According to the profiler `MurmurHash3_x64_128` gets hit often. I tried the optimization in this [patch](https://github.com/aappleby/smhasher/pull/87/files), but it did not appear to make any difference on Ryzen. Probably too narrow an impact.
 
+Above gprof results are puzzling. In the next step I am going to use perf instead on top of clang.
+
+=> https://www.brendangregg.com/perf.html
+
 # Conclusion
 
 With a bit of tweaking a 10-20% speed gain is easily possible on my Ryzen. Native compilation, openmp, lto and the static build appears to have the largest impact. PGO is, somewhat surprisingly, detrimental. Running outside a container is faster than running inside a container.

guix-static.scm

@@ -1,124 +1,3 @@
-;; To use this file to build a static version of wfmash using git HEAD:
+;; To use this file to build a static version of wfmash using git HEAD.
 ;;
-;;   guix build -f guix.scm
-;;
-;; To get a development container using a recent guix (see `guix pull`)
-;;
-;;   guix shell -C -D -f guix.scm
-;;
-;; and inside the container
-;;
-;;   mkdir build
-;;   cd build
-;;   cmake -DBUILD_STATIC=1 ..
-;;   make
-;;
-;; For the tests you may need /usr/bin/env. Inside the container:
-;;
-;;   mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
-;;
-;; by Pjotr Prins (c) 2023-2024
-
-(use-modules
- ((guix licenses) #:prefix license:)
-  (guix build-system cmake)
-  (guix download)
-  (guix gexp)
-  (guix git-download)
-  (guix packages)
-  (guix utils)
-  (gnu packages algebra)
-  (gnu packages base)
-  (gnu packages bioinformatics)
-  (gnu packages build-tools)
-  (gnu packages compression)
-  (gnu packages gcc)
-  (gnu packages jemalloc)
-  (gnu packages llvm)
-  (gnu packages maths)
-  (gnu packages multiprecision)
-  (gnu packages pkg-config)
-  (gnu packages python)
-  (gnu packages version-control)
-  (srfi srfi-1)
-  (ice-9 popen)
-  (ice-9 rdelim))
-
-;; Guix does not come with a static version of libdeflate
-(define-public libdeflate-static
-  (package
-    (inherit libdeflate)
-    (name "libdeflate-static")
-    (version "1.19")
-    (arguments
-     (list #:configure-flags
-           #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=YES"
-                   "-DLIBDEFLATE_BUILD_TESTS=YES")))))
-
-;; A minimal static version of htslib that does not depend on curl and openssl. This
-;; reduces the number of higher order dependencies in static linking.
-(define-public htslib-static
-  (package
-    (inherit htslib)
-    (name "htslib-static")
-    (version "1.19")
-    (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "https://github.com/samtools/htslib/releases/download/"
-                  version "/htslib-" version ".tar.bz2"))
-            (sha256
-             (base32
-              "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7"))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments htslib)
-       ((#:configure-flags flags ''())
-        ''())))
-    (inputs
-     (list bzip2 xz))))
-
-(define %source-dir (dirname (current-filename)))
-
-(define %git-commit
-    (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
-
-(define-public wfmash-git
-  (package
-    (name "wfmash-static-git")
-    (version (git-version "0.21" "HEAD" %git-commit))
-    (source (local-file %source-dir #:recursive? #t))
-    (build-system cmake-build-system)
-    (arguments
-     `(;; #:tests? #f
-       #:configure-flags
-       ,#~(list
-           "-DBUILD_STATIC=ON"
-           "-DBUILD_OPTIMIZED=ON"
-           "-DCMAKE_BUILD_TYPE=Release"
-           "-DCMAKE_INSTALL_RPATH="))) ; force cmake static build and do not rewrite RPATH
-    (inputs
-     `(
-       ("bzip2-static" ,bzip2 "static")    ; libz2 part of htslib for static builds
-       ("coreutils" ,coreutils) ; for echo and env in tests
-       ("gcc" ,gcc-12)
-       ("git" ,git)
-       ("gmp" ,gmp)
-       ("gsl-static" ,gsl "static")
-       ("gsl" ,gsl)
-       ("htslib-static" ,htslib-static)
-       ("jemalloc" ,jemalloc)
-       ("libdeflate-static" ,libdeflate-static)
-       ("make" ,gnu-make)
-       ("pkg-config" ,pkg-config)
-       ("xz-static" ,xz "static")     ; for static builds
-       ("zlib-static" ,zlib "static")))
-     (synopsis "wfmash")
-     (description
-      "wfmash is an aligner for pangenomes that combines efficient homology
-mapping with base-level alignment. It uses MashMap to find approximate
-mappings between sequences, then applies WFA (Wave Front Alignment) to
-obtain base-level alignments.")
-     (home-page "https://github.com/waveygang/wfmash")
-     (license license:expat)))
-
-wfmash-git
+;; See ./guix.scm in the git repo.

guix.scm

@@ -1,6 +1,5 @@
 ;; To use this file to build a version of wfmash using git HEAD:
 ;;
-;;  rm -rf build/*
 ;;  guix build -f guix.scm
 ;;
 ;; To get a development container using a recent guix (see `guix pull`)
@@ -11,15 +10,21 @@
 ;;
 ;;   mkdir build
 ;;   cd build
+;;   rm -rf ../build/*
 ;;   cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_OPTIMIZED=1 ..
 ;;   make -j 12 VERBOSE=1
 ;;   ctest . --verbose
 ;;
+;; alternative builds are
+;;
+;;   cmake -DBUILD_STATIC=1 ..
+;;
 ;; by Pjotr Prins & Andrea Guarracino (c) 2023-2024
 
 (use-modules
  ((guix licenses) #:prefix license:)
  (guix build-system cmake)
+ (guix download)
  (guix gexp)
  (guix git-download)
  (guix packages)
@@ -66,6 +71,7 @@
        ("gmp" ,gmp)
        ("gsl" ,gsl)
        ("htslib" ,htslib)
+       ("jemalloc" ,jemalloc)
        ("libdeflate" ,libdeflate)
        ("make" ,gnu-make)
        ("pkg-config" ,pkg-config)
@@ -104,6 +110,70 @@ obtain base-level alignments.")
                  )))
     ))
 
+;; ==== The following is for static binary builds using gcc - used mostly for deployment ===
+
+;; Guix does not come with a static version of libdeflate
+(define-public libdeflate-static
+  (package
+    (inherit libdeflate)
+    (name "libdeflate-static")
+    (version "1.19")
+    (arguments
+     (list #:configure-flags
+           #~(list "-DLIBDEFLATE_BUILD_STATIC_LIB=YES"
+                   "-DLIBDEFLATE_BUILD_TESTS=YES")))))
+
+;; A minimal static version of htslib that does not depend on curl and openssl. This
+;; reduces the number of higher order dependencies in static linking.
+(define-public htslib-static
+  (package
+    (inherit htslib)
+    (name "htslib-static")
+    (version "1.19")
+    (source (origin
+            (method url-fetch)
+            (uri (string-append
+                  "https://github.com/samtools/htslib/releases/download/"
+                  version "/htslib-" version ".tar.bz2"))
+            (sha256
+             (base32
+              "0dh79lwpspwwfbkmllrrhbk8nkvlfc5b5ib4d0xg5ld79w6c8lc7"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments htslib)
+       ((#:configure-flags flags ''())
+        ''())))
+    (inputs
+     (list bzip2 xz))))
+
+(define %source-dir (dirname (current-filename)))
+
+(define %git-commit
+    (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
+
+(define-public wfmash-static-gcc-git
+  (package
+    (inherit wfmash-base-git)
+    (name "wfmash-static-gcc-git")
+    (version (git-version "0.21" "HEAD" %git-commit))
+    (arguments
+     `(;; #:tests? #f
+       #:configure-flags
+       ,#~(list
+           "-DBUILD_STATIC=ON"
+           "-DBUILD_OPTIMIZED=ON"
+           "-DCMAKE_BUILD_TYPE=Release"
+           "-DCMAKE_INSTALL_RPATH="))) ; force cmake static build and do not rewrite RPATH
+    (inputs
+     (modify-inputs (package-inputs wfmash-gcc-git)
+                    (prepend
+                     `(,bzip2 "static")
+                     `(,zlib "static")
+                     `(,gsl "static")
+                     `(,xz "static")
+                     libdeflate-static
+                     htslib-static
+                     )))))
 
-wfmash-gcc-git
+wfmash-static-gcc-git ;; default deployment build
+;; wfmash-gcc-git
 ;; wfmash-clang-git