af126b8f0cf9ddc553a78869a3c820a4bd4fdc59
braney
  Mon Aug 17 13:36:13 2026 -0700
build: link the browser against zlib-ng instead of the system zlib, refs #38125

Adds zlib-ng as a second git submodule, alongside htslib, and points ZLIB at it.
It is built with --zlib-compat, so the header and the symbol names are the
ordinary zlib ones and no calling code has to change.

Measured over the eight Recommended Track Set pages, hgTracks uses 29 percent
less processor time and 26 percent less wall clock, and the image it produces is
pixel identical. Writing the PNG is about three times faster and reading a
bigBed data block about twice as fast, which is why the gain is larger than the
image work alone would give.

This also makes the platforms agree. x86_64 was linking a static /lib64/libz.a
only because that file happened to be present, the arm64 Docker build fell
through to a shared -lz, and Darwin was taking MacPorts zlib. All three now use
the submodule.

Verified on x86_64 Linux, aarch64 Linux and Apple silicon: zlib-ng builds, its
own test suite passes, the makefiles pick it up, and bigBedToBed output is byte
identical to before the change.

diff --git src/makefile src/makefile
index 5063b868a3a..de267ff054f 100644
--- src/makefile
+++ src/makefile
@@ -1,202 +1,210 @@
 include inc/localEnvironment.mk
 include inc/common.mk
 
 all: utils cgi blatSuite
 
 alpha: clean
 	${MAKE} utils-alpha cgi-alpha blatSuite
 
 beta: check-beta clean
 	${MAKE} cgi-beta
 
 # do a git update and clean
 update:
 	${GIT} pull
 	${MAKE} clean
 ##
 # topLibs
 ##
 TOP_LIBS = lib parasol/lib submodules/htslib
 ifneq ($(wildcard jkOwnLib/*),)
   TOP_LIBS += jkOwnLib
 endif
-topLibs: ${TOP_LIBS:%=%.topLibs}
+topLibs: zlibNg ${TOP_LIBS:%=%.topLibs}
 %.topLibs: topChecks
 	${MAKE} -C $*
 
+# zlib-ng is a submodule but it is not in TOP_LIBS, because its default target
+# builds the shared library and the test programs too and we only link libz.a.
+# Its Makefile is written by configure, which topChecks runs.  refs #38125
+.PHONY: zlibNg
+zlibNg: topChecks
+	${MAKE} -C submodules/zlib-ng libz.a
+
 .PHONY: topChecks
 topChecks:
 	@./checkUmask.sh
 	@./checkCompileFlags.sh
 	@MACHTYPE=${MACHTYPE} ./machTest.sh
 	@./submodules/submoduleSetup
 
 optLib:
 	cd optimalLeaf && ${MAKE}
 
 ##
 # hgLib
 ##
 ifneq ($(wildcard hg/makefile),)
    HGLIB_DIRS += hg/lib
    HGLIB_CHECK = hgLibChecks
 endif
 ifneq ($(wildcard hg/cgilib/makefile),)
    HGLIB_DIRS += hg/cgilib
 endif
 
 hgLib: ${HGLIB_CHECK} | ${HGLIB_DIRS:%=%.hgLib}
 %.hgLib:
 	${MAKE} -C $*
 hgLibChecks:
 	@./hg/sqlEnvTest.sh
 
 libs: topLibs hgLib optLib
 
 cgi: libs
 	cd hg && ${MAKE} cgi
 	cd utils/bedToBigBed && ${MAKE} cgi
 
 cgi-alpha: libs logUser
 	cd hg && ${MAKE} alpha
 	cd utils/bedToBigBed && ${MAKE} alpha
 
 cgi-beta: check-beta libs logUser
 	cd hg && ${MAKE} beta
 	cd utils/bedToBigBed && ${MAKE} beta
 
 # This log file can be useful when debugging problems on the alpha and beta builds.
 logUser:
 ifeq (${IS_HGWDEV},yes)
 	echo ${USER}, $(MAKECMDGOALS), `date` >> ${CGI_BIN}/buildLog.txt
 endif
 
 check-beta:
 	# this will fail if we are not in a beta checkout:
 	${GIT} branch | egrep '\* v[0-9]+_branch' > /dev/null	
 
 BLAT_SUITE_DIRS = blat gfClient gfServer webBlat hg/pslPretty hg/pslReps \
 	hg/pslSort utils/nibFrag utils/faToNib utils/faToTwoBit utils/twoBitToFa \
 	utils/twoBitInfo isPcr blatz
 
 blatSuite: ${BLAT_SUITE_DIRS:%=%.blatSuite}
 
 %.blatSuite: topLibs hgLib
 	 ${MAKE} -C $*
 
 # all of these application makefiles have been updated to include use
 #	of DESTDIR and BINDIR
 
 # common subdirs uses by multiple targets
 STD_DIRS = ameme index dnaDust protDust weblet aladdin primeMate fuse meta tagStorm \
 	tabFile parasol blat
 
 USER_APP_DIRS = utils parasol hg hg/utils \
 	hg/makeDb tabFile
 ALMOST_USER_APP_DIRS = blat gfClient gfServer isPcr ameme index/ixIxx utils/userApps
 
 .PHONY: userApps
 userApps: ${USER_APP_DIRS:%=%.userApps} ${ALMOST_USER_APP_DIRS:%=%.almostUserApps}
 
 %.userApps: topLibs hgLib destBin
 	${MAKE} -C $* userApps
 
 # these dont have userApps targets
 %.almostUserApps: topLibs hgLib destBin
 	${MAKE} -C $*
 
 destBin:
 	${MKDIR} ${DESTBINDIR}
 
 CLEAN_DIRS = ${STD_DIRS} lib hg jkOwnLib submodules/htslib utils webBat isPcr
 
 clean: ${CLEAN_DIRS:%=%.clean}
+	if [ -e submodules/zlib-ng/Makefile ] ; then ${MAKE} -C submodules/zlib-ng clean ; fi
 	find . -name \*.o -print | xargs --no-run-if-empty rm
 	rm -f tags TAGS
 	rm -f cscope.out cscope.files cscope.po.out
 
 %.clean:
 	if [ -e "$*/makefile" ] ; then ${MAKE} -C $* clean ; fi
 
 
 TEST_DIRS = blat gfServer hg lib utils
 test:: $(TEST_DIRS:%=%.test)
 %.test:
 	if test -d $* ; then ${MAKE} -C $* test; fi
 
 LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] */*/*/lib/*.[hc] jkOwnLib/*.c \
 	inc/*.h */inc/*.h */*/inc/*.h */*/*/inc/*.h */cgilib/*.[hc]
 
 # build tags for libraries
 .PHONY: tags
 tags:
 	ctags ${LIB_TAGS_IN}
 
 cscope.out:
 	find `pwd` -name '*.c' -o -name '*.h' > cscope.files
 	cscope -qRb `cat cscope.files`
 search: cscope.out
 	cscope -d
 
 # build emacs tags for libraries
 .PHONY: etags
 etags:
 	etags ${LIB_TAGS_IN}
 
 # build tags for all files
 .PHONY: tags-all
 tags-all:
 	find . -name '*.[ch]' | grep -v "/userApps/" | ctags -L -
 
 # build emacs tags for all files
 .PHONY: etags-all
 etags-all:
 	find . -name '*.[ch]' | etags -
 
 UTILS_DIRS = ${DIRS} utils
 .PHONY: utils
 utils: ${UTILS_DIRS:%=%.utils} ${STD_DIRS:%=%.utils}
 
 %.utils: libs destBin hgutils
 	@${MKDIR} ${SCRIPTS}
 	${MAKE} -C $*
 
 utils-alpha: ${UTILS_DIRS:%=%.utils-alpha}
 
 %.utils-alpha: libs destBin hgutils
 	if [ -e "$*/makefile" ] ; then ${MAKE} -C $* ; fi
 
 hgutils: libs destBin
 	cd hg && ${MAKE} utils
 
 ##  cellar archive for obsolete programs
 
 cellarDirs = cdnaAli getgene idbQuery reformat scanIntrons tracks wormAli \
 	xenoAli
 
 buildCellar: $(cellarDirs:%=%.cellar)
 
 %.cellar: libs destBin
 	cd $* && echo $* && $(MAKE)
 
 cleanCellar: $(cellarDirs:%=%.cellarClean)
 %.cellarClean:
 	cd $* && echo $* && $(MAKE) clean
 
 ## top level target for everything html related
 DOCS_LIST = hg/htdocs hg/js hg/htdocs/style
 doc: ${DOCS_LIST:%=%.docuser}
 %.docuser:
 	cd $* && $(MAKE)
 
 doc-alpha: ${DOCS_LIST:%=%.docalpha}
 %.docalpha:
 	cd $* && $(MAKE) alpha
 
 doc-beta: ${DOCS_LIST:%=%.docbeta}
 %.docbeta:
 	cd $* && $(MAKE) beta
 
 doc-install: ${DOCS_LIST:%=%.docinstall}
 %.docinstall:
 	cd $* && $(MAKE) install