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Re: [PATCH 0/1] Update pardre source hash.
|
From: |
Marius Bakke |
|
Subject: |
Re: [PATCH 0/1] Update pardre source hash. |
|
Date: |
Thu, 08 Dec 2016 15:45:43 +0100 |
|
User-agent: |
Notmuch/0.23.3 (https://notmuchmail.org) Emacs/25.1.1 (x86_64-unknown-linux-gnu) |
Ricardo Wurmus <address@hidden> writes:
> Marius Bakke <address@hidden> writes:
>
>> Ben Woodcroft <address@hidden> 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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