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Re: [PATCH 0/1] Update pardre source hash.
|
From: |
Ricardo Wurmus |
|
Subject: |
Re: [PATCH 0/1] Update pardre source hash. |
|
Date: |
Thu, 8 Dec 2016 15:17:09 +0100 |
|
User-agent: |
mu4e 0.9.16; emacs 25.1.1 |
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;
}