Patchwork [0/1] Update pardre source hash.

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Submitter Ricardo Wurmus
Date Dec. 8, 2016, 2:17 p.m.
Message ID <idjoa0m5wuy.fsf@bimsb-sys02.mdc-berlin.net>
Download mbox | patch
Permalink /patch/18288/
State New
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Comments

Ricardo Wurmus - Dec. 8, 2016, 2:17 p.m.
Marius Bakke <mbakke@fastmail.com> writes:

> Ben Woodcroft <donttrustben@gmail.com> writes:
>
>> Hi,
>>
>> It seems that the pardre source has been updated in place.  I'm not sure what
>> the procedure is for verifying that nothing untoward has taken place, since I
>> cannot download and old version from the hydra content addressed mirror -
>> it does not seem to exist there either.
>
> "diffoscope" has native support for tarballs and can quickly point out
> any differences. Perhaps Ricardo has a copy at the MDC?

I do!  I still have a copy of
/gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz

The diff looks very familiar.  Could it be that this has happened
before?  Or maybe I noticed the changed hash before and forgot to submit
an update...?

Anyway, here’s the full diff:
Ricardo Wurmus - Dec. 8, 2016, 2:19 p.m.
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> Marius Bakke <mbakke@fastmail.com> writes:
>
>> Ben Woodcroft <donttrustben@gmail.com> writes:
>>
>>> Hi,
>>>
>>> It seems that the pardre source has been updated in place.  I'm not sure what
>>> the procedure is for verifying that nothing untoward has taken place, since I
>>> cannot download and old version from the hydra content addressed mirror -
>>> it does not seem to exist there either.
>>
>> "diffoscope" has native support for tarballs and can quickly point out
>> any differences. Perhaps Ricardo has a copy at the MDC?
>
> I do!  I still have a copy of
> /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz
>
> The diff looks very familiar.  Could it be that this has happened
> before?  Or maybe I noticed the changed hash before and forgot to submit
> an update...?

In fact, Leo informed me about this in July, but it seems that both of
us forgot to follow up on this.

Thanks, Ben, for catching it!

~~ Ricardo
Marius Bakke - Dec. 8, 2016, 2:45 p.m.
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> Marius Bakke <mbakke@fastmail.com> writes:
>
>> Ben Woodcroft <donttrustben@gmail.com> writes:
>>
>>> Hi,
>>>
>>> It seems that the pardre source has been updated in place.  I'm not sure what
>>> the procedure is for verifying that nothing untoward has taken place, since I
>>> cannot download and old version from the hydra content addressed mirror -
>>> it does not seem to exist there either.
>>
>> "diffoscope" has native support for tarballs and can quickly point out
>> any differences. Perhaps Ricardo has a copy at the MDC?
>
> I do!  I still have a copy of
> /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz
>
> The diff looks very familiar.  Could it be that this has happened
> before?  Or maybe I noticed the changed hash before and forgot to submit
> an update...?
>
> Anyway, here’s the full diff:
>
>
> 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;
>  }

Looks like a portability fix, although I can't really tell what that
bitshifting is about. Assuming it's the same as the GCC builtin :-)
Ben Woodcroft - Dec. 10, 2016, 1:08 a.m.
On 09/12/16 00:45, Marius Bakke wrote:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> Marius Bakke <mbakke@fastmail.com> writes:
>>
>>> Ben Woodcroft <donttrustben@gmail.com> writes:
>>>
>>>> Hi,
>>>>
>>>> It seems that the pardre source has been updated in place.  I'm not sure what
>>>> the procedure is for verifying that nothing untoward has taken place, since I
>>>> cannot download and old version from the hydra content addressed mirror -
>>>> it does not seem to exist there either.
>>> "diffoscope" has native support for tarballs and can quickly point out
>>> any differences. Perhaps Ricardo has a copy at the MDC?
>> I do!  I still have a copy of
>> /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz
>>
>> The diff looks very familiar.  Could it be that this has happened
>> before?  Or maybe I noticed the changed hash before and forgot to submit
>> an update...?}
>>
>> [..]
> Looks like a portability fix, although I can't really tell what that
> bitshifting is about. Assuming it's the same as the GCC builtin :-)

Seems harmless enough, thanks you two.

I pushed an update to the hash to master, updating the version to 
"1.1.5-1" to reflect the fact that a change has been made, 
'7922ab8fe87154f3ccaa7daf9304632f974fbe5d'.

Is it possible to exclude sources from the GC on hydra or more 
importantly the new build system, for this reason?

ben

Patch

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;
 }