[Swift-commit] r6592 - SwiftApps/strains/midway

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2013-07-02 11:58:36 -0500 (Tue, 02 Jul 2013)
New Revision: 6592

Added:
   SwiftApps/strains/midway/Output/
   SwiftApps/strains/midway/badspots.txt
   SwiftApps/strains/midway/cf
   SwiftApps/strains/midway/logs/
   SwiftApps/strains/midway/run.sh
   SwiftApps/strains/midway/spots.txt
Removed:
   SwiftApps/strains/midway/FitPosOrStrains
Modified:
   SwiftApps/strains/midway/clean.sh
   SwiftApps/strains/midway/sites.xml
   SwiftApps/strains/midway/strains.swift
Log:
Updated swift config file
Remove 'bad' spots, for now


Deleted: SwiftApps/strains/midway/FitPosOrStrains
===================================================================
(Binary files differ)

Added: SwiftApps/strains/midway/badspots.txt
===================================================================
--- SwiftApps/strains/midway/badspots.txt	                        (rev 0)
+++ SwiftApps/strains/midway/badspots.txt	2013-07-02 16:58:36 UTC (rev 6592)
@@ -0,0 +1,7 @@
+1873
+10840
+14640
+14936
+2765
+10954
+12143

Added: SwiftApps/strains/midway/cf
===================================================================
--- SwiftApps/strains/midway/cf	                        (rev 0)
+++ SwiftApps/strains/midway/cf	2013-07-02 16:58:36 UTC (rev 6592)
@@ -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

Modified: SwiftApps/strains/midway/clean.sh
===================================================================
--- SwiftApps/strains/midway/clean.sh	2013-07-01 16:33:46 UTC (rev 6591)
+++ SwiftApps/strains/midway/clean.sh	2013-07-02 16:58:36 UTC (rev 6592)
@@ -1,3 +1,3 @@
 #!/bin/bash -x
 
-rm -rf *.log *.rlog *.d *.kml *.swiftx SpotsToIndex*.csv FitBest_*.csv OrientPosIndexer_*.csv NrDiffIndexerFit_*.csv
+rm -rf Results/* logs/* *.log *.rlog *.d *.kml *.swiftx SpotsToIndex*.csv FitBest_*.csv OrientPosIndexer_*.csv NrDiffIndexerFit_*.csv

Added: SwiftApps/strains/midway/run.sh
===================================================================
--- SwiftApps/strains/midway/run.sh	                        (rev 0)
+++ SwiftApps/strains/midway/run.sh	2013-07-02 16:58:36 UTC (rev 6592)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+swift -sites.file sites.xml -tc.file tc.data -config cf strains.swift


Property changes on: SwiftApps/strains/midway/run.sh
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftApps/strains/midway/sites.xml
===================================================================
--- SwiftApps/strains/midway/sites.xml	2013-07-01 16:33:46 UTC (rev 6591)
+++ SwiftApps/strains/midway/sites.xml	2013-07-02 16:58:36 UTC (rev 6592)
@@ -1,11 +1,15 @@
 <config>
   <pool handle="midway-westmere">
     <execution provider="coaster" jobmanager="local:slurm"/>
-    <profile namespace="globus" key="jobsPerNode">12</profile>
-    <profile namespace="globus" key="maxWalltime">00:10:00</profile>
+    <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="queue">bigmem</profile>
+    <profile namespace="globus" key="queue">sandyb</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="slots">1</profile>
+    <profile namespace="globus" key="nodeGranularity">9</profile>
+    <profile namespace="globus" key="maxNodes">9</profile>
     <profile namespace="karajan" key="initialScore">10000</profile>
     <filesystem provider="local"/>
     <workdirectory>/scratch/midway/{env.USER}</workdirectory>

Added: SwiftApps/strains/midway/spots.txt
===================================================================
--- SwiftApps/strains/midway/spots.txt	                        (rev 0)
+++ SwiftApps/strains/midway/spots.txt	2013-07-02 16:58:36 UTC (rev 6592)
@@ -0,0 +1,140 @@
+67
+166
+269
+366
+467
+577
+683
+768
+882
+985
+1082
+1168
+1280
+1374
+1476
+1572
+1672
+1772
+1975
+2066
+2160
+2260
+2373
+2472
+2563
+2665
+2861
+2960
+3056
+3153
+3361
+3452
+3560
+3660
+3763
+3870
+3954
+4070
+4155
+4263
+4368
+4464
+4557
+4657
+4761
+4858
+4958
+5062
+5159
+5258
+5358
+5459
+5552
+5661
+5759
+5855
+5957
+6153
+6258
+6454
+6551
+6650
+6759
+6859
+6954
+7059
+7151
+7250
+7350
+7452
+7550
+7651
+7750
+7856
+7960
+8056
+8145
+8242
+8351
+8446
+8544
+8649
+8751
+8851
+8948
+9049
+9142
+9240
+9342
+9445
+9559
+9660
+9760
+9850
+9948
+10043
+10143
+10253
+10353
+10451
+10549
+10651
+10748
+11044
+11146
+11246
+11346
+11443
+11543
+11648
+11749
+11849
+11942
+12048
+12245
+12344
+12444
+12540
+12645
+12746
+12846
+12951
+13047
+13143
+13250
+13349
+13445
+13538
+13632
+13753
+13842
+13944
+14048
+14150
+14252
+14349
+14452
+14540
+14747
+14834

Modified: SwiftApps/strains/midway/strains.swift
===================================================================
--- SwiftApps/strains/midway/strains.swift	2013-07-01 16:33:46 UTC (rev 6591)
+++ SwiftApps/strains/midway/strains.swift	2013-07-02 16:58:36 UTC (rev 6592)
@@ -20,8 +20,8 @@
    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("o.", i, ".log")>;
-   file elog <single_file_mapper; file=@strcat("e.", i, ".log")>;
+   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);
 }