Paste number 322501: pardre

Paste number 322501: pardre
Pasted by: rekado
When:6 years, 15 hours ago
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diff -ur ParDRe-rel1.1.5*
diff -ur ParDRe-rel1.1.5/.cproject ParDRe-rel1.1.5.new/.cproject
--- ParDRe-rel1.1.5/.cproject	2015-12-21 13:02:38.000000000 +0100
+++ ParDRe-rel1.1.5.new/.cproject	2016-07-05 14:10:22.000000000 +0200
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
 	<storageModule moduleId="org.eclipse.cdt.core.settings">
-		<cconfiguration id="0.1063792236">
-			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1063792236" moduleId="org.eclipse.cdt.core.settings" name="Default">
+		<cconfiguration id="0.1124212066">
+			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="0.1124212066" moduleId="org.eclipse.cdt.core.settings" name="Default">
 				<externalSettings/>
 				<extensions>
 					<extension id="org.eclipse.cdt.core.VCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
@@ -14,23 +14,23 @@
 				</extensions>
 			</storageModule>
 			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
-				<configuration buildProperties="" description="" id="0.1063792236" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg">
-					<folderInfo id="0.1063792236." name="/" resourcePath="">
-						<toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain">
-							<targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.1515125278.1242880487" name=""/>
-							<builder id="org.eclipse.cdt.build.core.settings.default.builder.570926900" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/>
-							<tool id="org.eclipse.cdt.build.core.settings.holder.libs.347518546" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/>
-							<tool id="org.eclipse.cdt.build.core.settings.holder.82023976" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder">
-								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1424918997" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
+				<configuration buildProperties="" description="" id="0.1124212066" name="Default" parent="org.eclipse.cdt.build.core.prefbase.cfg">
+					<folderInfo id="0.1124212066." name="/" resourcePath="">
+						<toolChain id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441" name="No ToolChain" resourceTypeBasedDiscovery="false" superClass="org.eclipse.cdt.build.core.prefbase.toolchain">
+							<targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441.64028961" name=""/>
+							<builder id="org.eclipse.cdt.build.core.settings.default.builder.665305288" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="org.eclipse.cdt.build.core.settings.default.builder"/>
+							<tool id="org.eclipse.cdt.build.core.settings.holder.libs.867303933" name="holder for library settings" superClass="org.eclipse.cdt.build.core.settings.holder.libs"/>
+							<tool id="org.eclipse.cdt.build.core.settings.holder.1856622227" name="CUDA C" superClass="org.eclipse.cdt.build.core.settings.holder">
+								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.909738042" languageId="com.nvidia.cuda.ide.editor.cudac" languageName="CUDA C" sourceContentType="com.nvidia.cuda.ide.cudac" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
 							</tool>
-							<tool id="org.eclipse.cdt.build.core.settings.holder.6574913" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder">
-								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1386917292" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
+							<tool id="org.eclipse.cdt.build.core.settings.holder.725125478" name="Assembly" superClass="org.eclipse.cdt.build.core.settings.holder">
+								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.724128993" languageId="org.eclipse.cdt.core.assembly" languageName="Assembly" sourceContentType="org.eclipse.cdt.core.asmSource" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
 							</tool>
-							<tool id="org.eclipse.cdt.build.core.settings.holder.262515108" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder">
-								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1691140733" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
+							<tool id="org.eclipse.cdt.build.core.settings.holder.1986690789" name="GNU C++" superClass="org.eclipse.cdt.build.core.settings.holder">
+								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.732922424" languageId="org.eclipse.cdt.core.g++" languageName="GNU C++" sourceContentType="org.eclipse.cdt.core.cxxSource,org.eclipse.cdt.core.cxxHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
 							</tool>
-							<tool id="org.eclipse.cdt.build.core.settings.holder.1213540964" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder">
-								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.452835573" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
+							<tool id="org.eclipse.cdt.build.core.settings.holder.549406725" name="GNU C" superClass="org.eclipse.cdt.build.core.settings.holder">
+								<inputType id="org.eclipse.cdt.build.core.settings.holder.inType.1364314318" languageId="org.eclipse.cdt.core.gcc" languageName="GNU C" sourceContentType="org.eclipse.cdt.core.cSource,org.eclipse.cdt.core.cHeader" superClass="org.eclipse.cdt.build.core.settings.holder.inType"/>
 							</tool>
 						</toolChain>
 					</folderInfo>
@@ -41,41 +41,44 @@
 		</cconfiguration>
 	</storageModule>
 	<storageModule moduleId="cdtBuildSystem" version="4.0.0">
-		<project id="ParDRe-V5.null.640329154" name="ParDRe-V5"/>
+		<project id="ParDRe-rel1.1.5.null.1822510023" name="ParDRe-rel1.1.5"/>
 	</storageModule>
 	<storageModule moduleId="scannerConfiguration">
 		<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
-		<scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547">
-			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/>
-		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="0.1927259477">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="0.823736429">
+		<scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939">
+			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/>
+		</scannerConfigBuildInfo>
+		<scannerConfigBuildInfo instanceId="0.1063792236">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="0.1602656032">
+		<scannerConfigBuildInfo instanceId="0.1124212066">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
+		<scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cpp.956304547">
+			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/>
+		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.cu.2021164641">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="0.1773641691">
+		<scannerConfigBuildInfo instanceId="0.823736429">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="com.nvidia.cuda.ide.configuration.debug.457684223;com.nvidia.cuda.ide.configuration.debug.457684223.;nvcc.compiler.base.1486896679;nvcc.compiler.input.c.198358939">
-			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="com.nvidia.cuda.ide.build.NVCCPerProjectProfile"/>
+		<scannerConfigBuildInfo instanceId="0.1773641691">
+			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="0.629582981">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="0.1063792236">
+		<scannerConfigBuildInfo instanceId="0.553699542">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
 		<scannerConfigBuildInfo instanceId="0.620900899">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
-		<scannerConfigBuildInfo instanceId="0.553699542">
+		<scannerConfigBuildInfo instanceId="0.1602656032">
 			<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
 		</scannerConfigBuildInfo>
 	</storageModule>
diff -ur ParDRe-rel1.1.5/PairedEnd.cpp ParDRe-rel1.1.5.new/PairedEnd.cpp
--- ParDRe-rel1.1.5/PairedEnd.cpp	2016-05-18 11:46:38.000000000 +0200
+++ ParDRe-rel1.1.5.new/PairedEnd.cpp	2016-07-06 12:15:02.000000000 +0200
@@ -210,6 +210,7 @@
     				}
     			}
     		}
+    		fflush(NULL);
     	}
     	MPI::COMM_WORLD.Barrier();
     }
diff -ur ParDRe-rel1.1.5/SingleEnd.cpp ParDRe-rel1.1.5.new/SingleEnd.cpp
--- ParDRe-rel1.1.5/SingleEnd.cpp	2016-05-18 11:47:07.000000000 +0200
+++ ParDRe-rel1.1.5.new/SingleEnd.cpp	2016-07-06 12:13:13.000000000 +0200
@@ -27,12 +27,12 @@
 	if(!myRank){
 		Utils::log("Process %d/%d: To print in %s\n", myRank, MPI::COMM_WORLD.Get_size(), outPath.c_str());
 	}
-	if(myRank){
+	/*if(myRank){
 		outPath.append("_id");
 		outPath.append(to_string(myRank));
 	}
 	_parserOut = new SeqFileParser(options, outPath.c_str(), true, false);
-	_parserOut->setFormat(_parser->getFormat());
+	_parserOut->setFormat(_parser->getFormat());*/
 	}
 }
 
@@ -186,6 +186,7 @@
     				}
     			}
     		}
+    		fflush(NULL);
     	}
     	MPI::COMM_WORLD.Barrier();
     }
diff -ur ParDRe-rel1.1.5/Utils.cpp ParDRe-rel1.1.5.new/Utils.cpp
--- ParDRe-rel1.1.5/Utils.cpp	2015-11-17 16:16:54.000000000 +0100
+++ ParDRe-rel1.1.5.new/Utils.cpp	2016-05-27 14:03:38.000000000 +0200
@@ -62,5 +62,12 @@
 }
 
 uint64_t Utils::popcount(uint64_t v){
-	return __builtin_popcount(v);
+     uint64_t b = (v & 0x5555555555555555LU) + (v >> 1 & 0x5555555555555555LU);
+     b = (b & 0x3333333333333333LU) + (b >> 2 & 0x3333333333333333LU);
+     b = b + (b >> 4) & 0x0F0F0F0F0F0F0F0FLU;
+     b = b + (b >> 8);
+     b = b + (b >> 16);
+     b = b + (b >> 32) & 0x0000007F;
+
+     return b;
 }

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