[Swift-commit] r6601 - in SwiftApps/strains: . orthros
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Tue Jul 2 17:27:03 CDT 2013
Author: davidk
Date: 2013-07-02 17:27:03 -0500 (Tue, 02 Jul 2013)
New Revision: 6601
Added:
SwiftApps/strains/orthros/
SwiftApps/strains/orthros/Output/
SwiftApps/strains/orthros/Results/
SwiftApps/strains/orthros/badspots.txt
SwiftApps/strains/orthros/cf
SwiftApps/strains/orthros/clean.sh
SwiftApps/strains/orthros/logs/
SwiftApps/strains/orthros/paramstest.txt
SwiftApps/strains/orthros/run.sh
SwiftApps/strains/orthros/sites.xml
SwiftApps/strains/orthros/spots.txt
SwiftApps/strains/orthros/spots.txt.orig
SwiftApps/strains/orthros/strains.sh
SwiftApps/strains/orthros/strains.swift
SwiftApps/strains/orthros/tc.data
Log:
Orthros configs
Added: SwiftApps/strains/orthros/badspots.txt
===================================================================
--- SwiftApps/strains/orthros/badspots.txt (rev 0)
+++ SwiftApps/strains/orthros/badspots.txt 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,7 @@
+1873
+10840
+14640
+14936
+2765
+10954
+12143
Added: SwiftApps/strains/orthros/cf
===================================================================
--- SwiftApps/strains/orthros/cf (rev 0)
+++ SwiftApps/strains/orthros/cf 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,9 @@
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+status.mode=provider
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=true
+sitedir.keep=true
+file.gc.enabled=false
Added: SwiftApps/strains/orthros/clean.sh
===================================================================
--- SwiftApps/strains/orthros/clean.sh (rev 0)
+++ SwiftApps/strains/orthros/clean.sh 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,3 @@
+#!/bin/bash -x
+
+rm -rf Results/* logs/* *.log *.rlog *.d *.kml *.swiftx SpotsToIndex*.csv FitBest_*.csv OrientPosIndexer_*.csv NrDiffIndexerFit_*.csv
Property changes on: SwiftApps/strains/orthros/clean.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/strains/orthros/paramstest.txt
===================================================================
--- SwiftApps/strains/orthros/paramstest.txt (rev 0)
+++ SwiftApps/strains/orthros/paramstest.txt 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,33 @@
+LatticeConstant 3.550000;
+CellStruct 2.000000;
+Wavelength 0.141000;
+Distance 315696.000000;
+Rsample 500.000000;
+Hbeam 500.000000;
+StepsizePos 5.000000;
+StepsizeOrient 0.200000;
+MarginRadius 10.000000;
+OmeBinSize 0.100000;
+EtaBinSize 0.100000;
+ExcludePoleAngle 6;
+RingNumbers 1.000000;
+RingNumbers 2.000000;
+RingNumbers 3.000000;
+RingNumbers 4.000000;
+RingRadii 21757.300153;
+RingRadii 25137.927663;
+RingRadii 35634.653342;
+RingRadii 41860.082190;
+UseFriedelPairs 1.000000;
+Wedge 0.000000;
+OmegaRange -180.00 0.00
+OmegaRange 0.00 180.00
+BoxSize -100000.00 100000.00 -100000.00 100000.00
+BoxSize -100000.00 100000.00 -100000.00 100000.00
+MarginEta 150.000000;
+MarginOme 1.000000;
+MarginRadial 150.000000;
+MinMatchesToAcceptFrac 0.900000;
+SpotsFileName InputAll.csv
+IDsFileName SpotsToIndex.csv
+OutputFolder Output
Added: SwiftApps/strains/orthros/run.sh
===================================================================
--- SwiftApps/strains/orthros/run.sh (rev 0)
+++ SwiftApps/strains/orthros/run.sh 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+swift -sites.file sites.xml -tc.file tc.data -config cf strains.swift
Property changes on: SwiftApps/strains/orthros/run.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/strains/orthros/sites.xml
===================================================================
--- SwiftApps/strains/orthros/sites.xml (rev 0)
+++ SwiftApps/strains/orthros/sites.xml 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,16 @@
+<config>
+ <pool handle="orthros">
+ <execution provider="coaster" jobmanager="local:local"/>
+ <profile namespace="globus" key="jobsPerNode">16</profile>
+ <profile namespace="globus" key="maxWalltime">00:20:00</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="slots">20</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="queue">sec1all.q</profile> -->
+ <profile namespace="globus" key="pe">sec1_all</profile> -->
+ <filesystem provider="local"/>
+ <workdirectory>/clhome/WILDE/strains/swiftwork</workdirectory>
+ </pool>
+</config>
Added: SwiftApps/strains/orthros/spots.txt
===================================================================
--- SwiftApps/strains/orthros/spots.txt (rev 0)
+++ SwiftApps/strains/orthros/spots.txt 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1 @@
+67
Added: SwiftApps/strains/orthros/spots.txt.orig
===================================================================
--- SwiftApps/strains/orthros/spots.txt.orig (rev 0)
+++ SwiftApps/strains/orthros/spots.txt.orig 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,140 @@
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Added: SwiftApps/strains/orthros/strains.sh
===================================================================
--- SwiftApps/strains/orthros/strains.sh (rev 0)
+++ SwiftApps/strains/orthros/strains.sh 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+cat SpotsToIndex.*.csv > SpotsToIndex.csv
+/clhome/WILDE/strains/bin/run_FitPosOrStrains.sh /clhome/WILDE/strains/bin/v717
Property changes on: SwiftApps/strains/orthros/strains.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/strains/orthros/strains.swift
===================================================================
--- SwiftApps/strains/orthros/strains.swift (rev 0)
+++ SwiftApps/strains/orthros/strains.swift 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1,27 @@
+type file;
+
+app (file o, file e, file fb, file nrd, file ori) strains (file pos, file extra, file param, file spotsti)
+{
+ strains stdout=@o stderr=@e;
+}
+
+file extrainfo <"InputAllExtraInfoFittingAll.csv">;
+file params <"paramstest.txt">;
+
+int spots[] = readData("spots.txt");
+
+foreach i in spots {
+ file SpotsToIndex <single_file_mapper; file=@strcat("SpotsToIndex.", i, ".csv")>;
+ SpotsToIndex=writeData(i);
+
+ string spotlong = @strcut(@strcat("0000000", i), "([0-9]........$)");
+ file bestpos <single_file_mapper; file=@strcat("Output/BestPos_", spotlong, ".csv")>;
+ file fitbest <single_file_mapper; file=@strcat("Results/FitBest_", spotlong, ".csv")>;
+ file nrdiff <single_file_mapper; file=@strcat("Results/NrDiffIndexerFit_", spotlong, ".csv")>;
+ file orient <single_file_mapper; file=@strcat("Results/OrientPosIndexer_", spotlong, ".csv")>;
+
+ file olog <single_file_mapper; file=@strcat("logs/o.", i, ".log")>;
+ file elog <single_file_mapper; file=@strcat("logs/e.", i, ".log")>;
+ (olog, elog, fitbest, nrdiff, orient) = strains(bestpos, extrainfo, params, SpotsToIndex);
+}
+
Added: SwiftApps/strains/orthros/tc.data
===================================================================
--- SwiftApps/strains/orthros/tc.data (rev 0)
+++ SwiftApps/strains/orthros/tc.data 2013-07-02 22:27:03 UTC (rev 6601)
@@ -0,0 +1 @@
+orthros strains /clhome/WILDE/strains/orthros/strains.sh
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