[Swift-commit] r4278 - SwiftApps/modFTdock
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Tue Apr 5 10:22:48 CDT 2011
Author: ketan
Date: 2011-04-05 10:22:48 -0500 (Tue, 05 Apr 2011)
New Revision: 4278
Added:
SwiftApps/modFTdock/cf
SwiftApps/modFTdock/ftdock.swift
SwiftApps/modFTdock/sites-beagle.xml
SwiftApps/modFTdock/tc
Modified:
SwiftApps/modFTdock/run.sh
Log:
Added: SwiftApps/modFTdock/cf
===================================================================
--- SwiftApps/modFTdock/cf (rev 0)
+++ SwiftApps/modFTdock/cf 2011-04-05 15:22:48 UTC (rev 4278)
@@ -0,0 +1,12 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=4
+lazy.errors=true
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+#clustering.enabled=false
+#clustering.queue.delay=10
+#clustering.min.time=86400
+foreach.max.threads=1600
+provenance.log=true
Added: SwiftApps/modFTdock/ftdock.swift
===================================================================
--- SwiftApps/modFTdock/ftdock.swift (rev 0)
+++ SwiftApps/modFTdock/ftdock.swift 2011-04-05 15:22:48 UTC (rev 4278)
@@ -0,0 +1,51 @@
+type file_pdb;
+type file_dat;
+
+app (file_dat dat_file)
+ do_one_dock(
+ string param_root,
+ string param_modulo,
+ file_pdb param_file_static,
+ file_pdb param_file_mobile )
+{
+ modftdock 32
+ "-modulo" @param_modulo
+ "-root" @param_root
+ "-static" @param_file_static
+ "-mobile" @param_file_mobile
+ "-calculate_grid" @arg("grid","2.5")
+ "-angle_step" "10"
+ "-keep" "10"
+ "-noelec";
+}
+
+string modulus = @arg("m","100");
+string str_roots[] = readData( @arg( "list" ) );
+
+foreach str_root in str_roots
+{
+ trace( str_root );
+
+ string str_file_static = @strcat( "input/", str_root, ".pdb" );
+ string str_file_mobile = "input/4TRA.pdb";
+
+ file_pdb file_static < single_file_mapper; file = str_file_static >;
+ file_pdb file_mobile < single_file_mapper; file = str_file_mobile >;
+ file_dat dat_files[] < simple_mapper;
+ padding = 3,
+ location = "output",
+ prefix = @strcat( str_root, "_" ),
+ suffix = ".dat" >;
+
+ // break docking jobs + do 'em in parallel
+ int n = @toint(@arg("n","1"));
+ foreach mod_index in [0:n-1]
+ {
+ string str_modulo = @strcat(mod_index, ":", modulus);
+ dat_files[ mod_index ] = do_one_dock( str_root,
+ str_modulo,
+ file_static,
+ file_mobile );
+ }
+}
+
Modified: SwiftApps/modFTdock/run.sh
===================================================================
--- SwiftApps/modFTdock/run.sh 2011-04-05 15:20:37 UTC (rev 4277)
+++ SwiftApps/modFTdock/run.sh 2011-04-05 15:22:48 UTC (rev 4278)
@@ -1,10 +1,10 @@
##
# Note: The configuration in this package is suitable for Beagle environment only
##
-#SWIFT_HEAP_MAX=6000M swift -config ./swift/cf -tc.file ./swift/tc -sites.file ./swift/beagle-sites.xml ./swift/ftdock.swift -n=100 -list=./swift/pdb.list.100 -grid=0.5 >std.out 2>std.err < /dev/null &
+#SWIFT_HEAP_MAX=6000M swift -config cf -tc.file tc -sites.file beagle-sites.xml ftdock.swift -n=100 -list=pdb.list.100 -grid=0.5 >std.out 2>std.err < /dev/null &
#short run for testing purpose
-swift -config ./swift/cf -tc.file ./swift/tc -sites.file ./swift/sites-beagle.xml ./swift/ftdock.swift -n=1 -list=pdb.list.1 -grid=10
+swift -config cf -tc.file tc -sites.file sites-beagle.xml ftdock.swift -n=1 -list=pdb.list.1 -grid=10
#nohup execution for long runs
-#SWIFT_HEAP_MAX=6000M nohup swift -config ./swift/cf -tc.file ./swift/tc -sites.file ./swift/sites-beagle.xml ./swift/ftdock.swift -n=100 -list=pdb.list.100 -grid=0.5 >std.out 2>std.err < /dev/null &
+#SWIFT_HEAP_MAX=6000M nohup swift -config cf -tc.file tc -sites.file sites-beagle.xml ftdock.swift -n=100 -list=pdb.list.100 -grid=0.5 >std.out 2>std.err < /dev/null &
Added: SwiftApps/modFTdock/sites-beagle.xml
===================================================================
--- SwiftApps/modFTdock/sites-beagle.xml (rev 0)
+++ SwiftApps/modFTdock/sites-beagle.xml 2011-04-05 15:22:48 UTC (rev 4278)
@@ -0,0 +1,40 @@
+<config>
+ <!-- handle should be same as the sitename on transformation catalog(tc) -->
+ <pool handle="pbs">
+ <!-- -->
+ <execution provider="coaster" jobmanager="local:pbs"/>
+ <!-- <profile namespace="globus" key="queue">small</profile> -->
+
+ <profile namespace="globus" key="project">CI-CCR000013</profile>
+
+ <profile namespace="globus" key="ppn">24:cray:pack</profile>
+
+ <profile namespace="globus" key="workersPerNode">24</profile>
+
+ <profile namespace="globus" key="maxTime">30000</profile>
+
+ <!--How many times larger than the job walltime should a block's walltime be if all jobs are 1s long -->
+ <profile namespace="globus" key="lowOverallocation">100</profile>
+
+ <!--How many times larger than the job walltime should a block's walltime be if all jobs are infinitely long -->
+ <profile namespace="globus" key="highOverallocation">100</profile>
+
+ <!-- pbs slot map from job requirement to pbs jobs which are called slots, upto this many pbs jobs-->
+ <profile namespace="globus" key="slots">10</profile>
+
+ <!-- smaller it is more likely it is fit into a slot -->
+ <profile namespace="globus" key="nodeGranularity">5</profile>
+
+ <!-- maximum number of nodes per slot -->
+ <profile namespace="globus" key="maxNodes">10</profile>
+
+ <!--(Throttle + .01)*100 => # of parallel jobs to run -->
+ <profile namespace="karajan" key="jobThrottle">20.00</profile>
+
+ <profile namespace="karajan" key="initialScore">10000</profile>
+
+ <filesystem provider="local"/>
+ <!--IMP: Put a complete path of your choice for the workdir -->
+ <workdirectory >/tmp/swift.workdir</workdirectory>
+ </pool>
+</config>
Added: SwiftApps/modFTdock/tc
===================================================================
--- SwiftApps/modFTdock/tc (rev 0)
+++ SwiftApps/modFTdock/tc 2011-04-05 15:22:48 UTC (rev 4278)
@@ -0,0 +1,2 @@
+#Put a *complete* path of modftdock.sh here
+pbs modftdock modFTdock/app/modftdock.sh null null GLOBUS::maxwalltime="01:00:00"
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