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From: Marius Bakke <mbakke@fastmail.com>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH 0/1] Update pardre source hash.
Date: Thu, 08 Dec 2016 15:45:43 +0100	[thread overview]
Message-ID: <87wpfaxyw8.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> (raw)
In-Reply-To: <idjoa0m5wuy.fsf@bimsb-sys02.mdc-berlin.net>

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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 :-)

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  parent reply	other threads:[~2016-12-08 14:45 UTC|newest]

Thread overview: 7+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2016-12-08 13:12 [PATCH 0/1] Update pardre source hash Ben Woodcroft
2016-12-08 13:12 ` [PATCH] gnu: pardre: Update " Ben Woodcroft
2016-12-08 13:37 ` [PATCH 0/1] Update pardre " Marius Bakke
2016-12-08 14:17   ` Ricardo Wurmus
2016-12-08 14:19     ` Ricardo Wurmus
2016-12-08 14:45     ` Marius Bakke [this message]
2016-12-10  1:08       ` Ben Woodcroft

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