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[Issue #1299] fix the static loading issue with jemalloc and avoid hardcoding of tile size #1300

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Merged
bianhq merged 7 commits into from
Mar 4, 2026
Merged

[Issue #1299] fix the static loading issue with jemalloc and avoid hardcoding of tile size #1300

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9e27997
fix: set rpath
gengdy1545 Mar 3, 2026
75dad69
fix: add prefix for jemalloc
gengdy1545 Mar 3, 2026
bff7347
fix: set jemalloc default off
gengdy1545 Mar 3, 2026
45a9c6a
fix: avoid hardcoding RETINA_CAPACITY
gengdy1545 Mar 3, 2026
92028a1
fix: gitHub ci is missing the PIXELS_HOME environment variable
gengdy1545 Mar 3, 2026
c52a0ee
fix: comment
gengdy1545 Mar 4, 2026
3c85103
fix: keep jemalloc on
gengdy1545 Mar 4, 2026
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11 changes: 10 additions & 1 deletion cpp/pixels-retina/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ if(ENABLE_JEMALLOC)
URL https://github.com/jemalloc/jemalloc/releases/download/5.3.0/jemalloc-5.3.0.tar.bz2
CONFIGURE_COMMAND <SOURCE_DIR>/configure
--prefix=${JEMALLOC_INSTALL_DIR}
--with-jemalloc-prefix=je_
--enable-prof
--enable-stats
--enable-shared
Expand All @@ -51,7 +52,6 @@ if(ENABLE_JEMALLOC)
add_dependencies(jemalloc_lib jemalloc_ext)

add_definitions(-DENABLE_JEMALLOC)
add_definitions(-DJEMALLOC_MANGLE)
endif()

# Disable gtest installation
Expand Down Expand Up @@ -93,10 +93,19 @@ add_library(pixels-retina SHARED ${SOURCES})
set_target_properties(pixels-retina PROPERTIES
OUTPUT_NAME "pixels-retina"
LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib"
# Set the rpath to the current directory, so that the jemalloc library can be found at runtime
INSTALL_RPATH "$ORIGIN"
BUILD_RPATH "$ORIGIN"
)

target_link_libraries(pixels-retina PRIVATE ${JNI_LIBRARIES})

# Disable rpath
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
set_target_properties(pixels-retina PROPERTIES
INSTALL_RPATH_USE_LINK_PATH FALSE
)

if(ENABLE_JEMALLOC)
target_link_libraries(pixels-retina PRIVATE jemalloc_lib pthread dl)
if(UNIX)
Expand Down
4 changes: 2 additions & 2 deletions cpp/pixels-retina/lib/RGVisibilityJni.cpp
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Expand Up @@ -155,13 +155,13 @@ JNIEXPORT jlong JNICALL Java_io_pixelsdb_pixels_retina_RGVisibility_getNativeMem

// 1. Try to refresh jemalloc epoch to ensure stats are current.
// Return -2 if this fails, as defined in Java's handleMemoryMetric.
if (mallctl("epoch", NULL, NULL, &epoch, sizeof(uint64_t)) != 0) {
if (je_mallctl("epoch", NULL, NULL, &epoch, sizeof(uint64_t)) != 0) {
return -2;
}

// 2. Try to read the actual allocated bytes.
// Return -3 if this fails, which often implies a config/prefix mismatch.
if (mallctl("stats.allocated", &allocated, &sz, NULL, 0) != 0) {
if (je_mallctl("stats.allocated", &allocated, &sz, NULL, 0) != 0) {
return -3;
}

Expand Down
2 changes: 2 additions & 0 deletions pixels-common/src/main/resources/pixels.properties
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Expand Up @@ -269,6 +269,8 @@ memspl = [1,8,16,32,64]

# set to true to enable pixels-retina
retina.enable=false
# number of rows in each tile visibility, must be a multiple of 64
retina.tile.visibility.capacity=10240
# number of rows recorded in memTable, must be a multiple of 64
retina.buffer.memTable.size=10240
# the scheme of the storage for retina buffer object storage, e.g., s3, minio
Expand Down
8 changes: 5 additions & 3 deletions pixels-retina/pom.xml
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Expand Up @@ -15,7 +15,6 @@
<maven.compiler.target>1.8</maven.compiler.target>
<maven.compiler.source>1.8</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<pixels.retina.capacity>10240</pixels.retina.capacity>
</properties>

<dependencies>
Expand Down Expand Up @@ -163,11 +162,14 @@
<goal>run</goal>
</goals>
<configuration>
<target>
<target xmlns:if="ant:if">
<!-- Load only if pixels.properties exists, and only when the configuration file contains the retina tile visibility capacity setting. -->
<available file="${env.PIXELS_HOME}/etc/pixels.properties" property="pixels.properties.exists"/>
<loadproperties srcFile="${env.PIXELS_HOME}/etc/pixels.properties" if:set="pixels.properties.exists"/>
<exec executable="cmake" failonerror="true" outputproperty="cmake.output" errorproperty="cmake.error">
<arg line="-B ${project.basedir}/../cpp/pixels-retina/build"/>
<arg line="-S ${project.basedir}/../cpp/pixels-retina"/>
<arg line="-DRETINA_CAPACITY=${pixels.retina.capacity}"/>
<arg line="-DRETINA_CAPACITY=${retina.tile.visibility.capacity}" if:set="retina.tile.visibility.capacity"/>
</exec>
<exec executable="make" dir="${project.basedir}/../cpp/pixels-retina/build" failonerror="true" outputproperty="make.output" errorproperty="make.error">
<arg value="install"/>
Expand Down