diff mbox

[0/1] Update pardre source hash.

Message ID idjoa0m5wuy.fsf@bimsb-sys02.mdc-berlin.net
State New
Headers show

Commit Message

Ricardo Wurmus Dec. 8, 2016, 2:17 p.m. UTC
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:

Comments

Ricardo Wurmus Dec. 8, 2016, 2:19 p.m. UTC | #1
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. UTC | #2
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="">
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> +							<targetPlatform id="org.eclipse.cdt.build.core.prefbase.toolchain.383755441.64028961" name=""/>
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> +							<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=""/>
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> -			<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">
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>  			<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. UTC | #3
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
diff mbox

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;
 }