fix bug in mgf parser with null charge, change gc, added gc hints to …

…buffer, release 5.8.1
sirius-ms · Jul 7, 2023 · c101b5f · c101b5f
1 parent 60fa58b
commit c101b5f
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Showing 4 changed files with 15 additions and 6 deletions.
diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/BackgroundRuns.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/BackgroundRuns.java
@@ -274,6 +274,7 @@ protected void cleanup() {
                 logInfo("Freeing up memory...");
                 computation = null;
                 System.gc(); //hint for the gc to collect som trash after computations
+                System.runFinalization();
                 logInfo("Memory freed!");
             } finally {
                 if (AUTOREMOVE.get())

diff --git a/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/workflow/SimpleInstanceBuffer.java b/sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/workflow/SimpleInstanceBuffer.java
@@ -95,6 +95,13 @@ public void start(final boolean invalidate) throws InterruptedException {
                     }
                 }
 
+                { //gc hint
+                    if (instanceComputed.get() % bufferSize == 0) {
+                        System.gc(); //hint for the gc to collect som trash after computations
+                        System.runFinalization();
+                    }
+                }
+
                 lock.lock();
                 try {
                     //wait for free slot in buffer if it is full
@@ -103,7 +110,6 @@ public void start(final boolean invalidate) throws InterruptedException {
                         checkForCancellation();
                     }
 
-
                     checkForCancellation();
 
                     final Instance instance = instances.next();

diff --git a/sirius_cli/src/main/resources/sirius_frontend.build.properties b/sirius_cli/src/main/resources/sirius_frontend.build.properties
@@ -1,7 +1,7 @@
 #here you can provide properties that may be needed during build- AND during runtime and should not be editable by the user at runtime
-de.unijena.bioinf.siriusFrontend.version=5.8.1-SNAPSHOT
-de.unijena.bioinf.sirius.version=4.13.0
-de.unijena.bioinf.fingerid.version=2.6.15
+de.unijena.bioinf.siriusFrontend.version=5.8.1
+de.unijena.bioinf.sirius.version=4.13.1
+de.unijena.bioinf.fingerid.version=2.6.16
 #
 de.unijena.bioinf.sirius.http.job.fingerprint.limit = 5000
 de.unijena.bioinf.sirius.http.job.canopus.limit = 5000

diff --git a/sirius_dist/sirius_gui_dist/build.gradle b/sirius_dist/sirius_gui_dist/build.gradle
@@ -78,8 +78,10 @@ def mainJar = getRootProject().getChildProjects().get('sirius_rest_service').tas
 application {
     mainClass = project.mainClassName
     applicationDefaultJvmArgs = ['-Xms1G',
-                                 '-XX:MaxRAMPercentage=85',
-                                 '-XX:+UseG1GC',
+                                 '-XX:MaxRAMPercentage=65',
+//                                 '-XX:+UseG1GC',
+//                                 '-XX:+UseShenandoahGC',
+                                 '-XX:+UseZGC',
                                  '-XX:+UseStringDeduplication',
                                  '-XX:+ExitOnOutOfMemoryError']
     executableDir = 'bin'