10.00
10000
1
3600
- 00:05:00
+ 00:10:00
100
100
- 1000
+ 1
1
1
"group_friends.{env.USER}"
From davidk at ci.uchicago.edu Tue Oct 22 11:39:56 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 11:39:56 -0500 (CDT)
Subject: [Swift-commit] r7205 - in SwiftTutorials/swift-cloud-tutorial: app
doc part02
Message-ID: <20131022163956.569FA9CCA7@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 11:39:56 -0500 (Tue, 22 Oct 2013)
New Revision: 7205
Modified:
SwiftTutorials/swift-cloud-tutorial/app/simulate.py
SwiftTutorials/swift-cloud-tutorial/doc/README
SwiftTutorials/swift-cloud-tutorial/part02/apps
Log:
Python example
Modified: SwiftTutorials/swift-cloud-tutorial/app/simulate.py
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/app/simulate.py 2013-10-22 15:59:07 UTC (rev 7204)
+++ SwiftTutorials/swift-cloud-tutorial/app/simulate.py 2013-10-22 16:39:56 UTC (rev 7205)
@@ -5,6 +5,7 @@
import time
import math
import random
+import getpass
def parse():
from optparse import OptionParser
@@ -48,7 +49,7 @@
print >> sys.stderr, "Called as: ", str(sys.argv)
print >> sys.stderr, "Start time: ", datetime.datetime.now()
print >> sys.stderr, "Running on node: ", socket.gethostname()
- print >> sys.stderr, "Running as user: ",os.getlogin()
+ print >> sys.stderr, "Running as user: ", getpass.getuser()
print >> sys.stderr, "\nEnvironment:\n\n"
print >> sys.stderr, os.environ
Modified: SwiftTutorials/swift-cloud-tutorial/doc/README
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 15:59:07 UTC (rev 7204)
+++ SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 16:39:56 UTC (rev 7205)
@@ -345,6 +345,16 @@
example of naming the output files of an ensemble run. In this case, the output files will be named
`output/sim_N.out`.
+In part 2, we also update the apps file. Instead of using shell script (simulate.sh), we use
+the equivalent python version (simulate.py). The new apps file now looks like this:
+
+-----
+localhost simulate simulate.py
+-----
+
+Swift does not need to know anything about the language an application is written in. The application
+can be written in Perl, Python, Java, Fortran, or any other language.
+
To run the script and view the output:
-----
$ cd ../part02
Modified: SwiftTutorials/swift-cloud-tutorial/part02/apps
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part02/apps 2013-10-22 15:59:07 UTC (rev 7204)
+++ SwiftTutorials/swift-cloud-tutorial/part02/apps 2013-10-22 16:39:56 UTC (rev 7205)
@@ -1 +1 @@
-localhost simulate simulate.sh
+localhost simulate simulate.py
From davidk at ci.uchicago.edu Tue Oct 22 13:50:33 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 13:50:33 -0500 (CDT)
Subject: [Swift-commit] r7206 - SwiftTutorials/swift-cloud-tutorial/doc
Message-ID: <20131022185033.06A5D9CCA7@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 13:50:32 -0500 (Tue, 22 Oct 2013)
New Revision: 7206
Modified:
SwiftTutorials/swift-cloud-tutorial/doc/README
SwiftTutorials/swift-cloud-tutorial/doc/build_docs.sh
Log:
New section for tips on specific resources
Modified: SwiftTutorials/swift-cloud-tutorial/doc/README
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 16:39:56 UTC (rev 7205)
+++ SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 18:50:32 UTC (rev 7206)
@@ -767,3 +767,17 @@
modify the script to generate a unique seed value for each simulation,
which is a common practice in ensemble computations.
+Tips for Specific Resources
+---------------------------
+
+Open Science Data Cloud
+~~~~~~~~~~~~~~~~~~~~~~~
+1. When you start instances on OSDC, use the standard Ubuntu image.
+2. Ensure that your SSH key is added to the instance for password login.
+3. Swift should run on the OSDC headnode.
+4. You can use the following command within coaster-service.conf to automatically
+populate WORKER_HOSTS with the IP addresses of all active instances you have running.
+
+-----
+export WORKER_HOSTS=$( nova list | grep ACTIVE | sed -e 's/^.*private=//' -e 's/ .*//' |sed ':a;N;$!ba;s/\n/ /g' )
+-----
Modified: SwiftTutorials/swift-cloud-tutorial/doc/build_docs.sh
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/doc/build_docs.sh 2013-10-22 16:39:56 UTC (rev 7205)
+++ SwiftTutorials/swift-cloud-tutorial/doc/build_docs.sh 2013-10-22 18:50:32 UTC (rev 7206)
@@ -1,4 +1,4 @@
#!/bin/bash -e
-asciidoc -a icons -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o swift-cray-tutorial.html README
+asciidoc -a icons -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o tutorial.html README
From davidk at ci.uchicago.edu Tue Oct 22 13:53:17 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 13:53:17 -0500 (CDT)
Subject: [Swift-commit] r7207 - www/docs
Message-ID: <20131022185317.AFCB69CCA7@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 13:53:17 -0500 (Tue, 22 Oct 2013)
New Revision: 7207
Modified:
www/docs/index.php
Log:
Remove link to OSDC specific tutorial, replace with more general cloud tutorial
Modified: www/docs/index.php
===================================================================
--- www/docs/index.php 2013-10-22 18:50:32 UTC (rev 7206)
+++ www/docs/index.php 2013-10-22 18:53:17 UTC (rev 7207)
@@ -40,10 +40,9 @@
An older tutorial can be found here. It is worth a read.
From davidk at ci.uchicago.edu Tue Oct 22 14:03:27 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 14:03:27 -0500 (CDT)
Subject: [Swift-commit] r7208 - branches/release-0.94/etc/sites
Message-ID: <20131022190327.CD0CE9CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 14:03:27 -0500 (Tue, 22 Oct 2013)
New Revision: 7208
Added:
branches/release-0.94/etc/sites/cloud
Log:
Cloud site template (persistent-coasters)
Added: branches/release-0.94/etc/sites/cloud
===================================================================
--- branches/release-0.94/etc/sites/cloud (rev 0)
+++ branches/release-0.94/etc/sites/cloud 2013-10-22 19:03:27 UTC (rev 7208)
@@ -0,0 +1,13 @@
+
+
+
+ passive
+ _JOBSPERNODE_
+ _JOBTHROTTLE_
+ 10000
+
+ _WORK_
+
+
From davidk at ci.uchicago.edu Tue Oct 22 14:06:22 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 14:06:22 -0500 (CDT)
Subject: [Swift-commit] r7209 - trunk/etc/sites
Message-ID: <20131022190622.60A729CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 14:06:22 -0500 (Tue, 22 Oct 2013)
New Revision: 7209
Added:
trunk/etc/sites/cloud
Log:
Cloud site template
Added: trunk/etc/sites/cloud
===================================================================
--- trunk/etc/sites/cloud (rev 0)
+++ trunk/etc/sites/cloud 2013-10-22 19:06:22 UTC (rev 7209)
@@ -0,0 +1,13 @@
+
+
+
+ passive
+ _JOBSPERNODE_
+ _JOBTHROTTLE_
+ 10000
+
+ _WORK_
+
+
From davidk at ci.uchicago.edu Tue Oct 22 14:26:48 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 14:26:48 -0500 (CDT)
Subject: [Swift-commit] r7210 - tags/swift-0.94.2-RC2/etc/sites
Message-ID: <20131022192648.0B24B9CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 14:26:47 -0500 (Tue, 22 Oct 2013)
New Revision: 7210
Added:
tags/swift-0.94.2-RC2/etc/sites/cloud
Log:
Cloud site template
Added: tags/swift-0.94.2-RC2/etc/sites/cloud
===================================================================
--- tags/swift-0.94.2-RC2/etc/sites/cloud (rev 0)
+++ tags/swift-0.94.2-RC2/etc/sites/cloud 2013-10-22 19:26:47 UTC (rev 7210)
@@ -0,0 +1,13 @@
+
+
+
+ passive
+ _JOBSPERNODE_
+ _JOBTHROTTLE_
+ 10000
+
+ _WORK_
+
+
From davidk at ci.uchicago.edu Tue Oct 22 14:45:17 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 14:45:17 -0500 (CDT)
Subject: [Swift-commit] r7211 - in SwiftTutorials/swift-cloud-tutorial:
part04 part05 part06 scs
Message-ID: <20131022194517.62A199CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 14:45:17 -0500 (Tue, 22 Oct 2013)
New Revision: 7211
Added:
SwiftTutorials/swift-cloud-tutorial/part05/simulate.sh
SwiftTutorials/swift-cloud-tutorial/part05/stats.sh
Removed:
SwiftTutorials/swift-cloud-tutorial/scs/get_ip_list.sh
Modified:
SwiftTutorials/swift-cloud-tutorial/part04/apps
SwiftTutorials/swift-cloud-tutorial/part05/apps
SwiftTutorials/swift-cloud-tutorial/part06/apps
Log:
Define site as 'cloud' rather than persistent-coasters
Some cleanup
Modified: SwiftTutorials/swift-cloud-tutorial/part04/apps
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part04/apps 2013-10-22 19:26:47 UTC (rev 7210)
+++ SwiftTutorials/swift-cloud-tutorial/part04/apps 2013-10-22 19:45:17 UTC (rev 7211)
@@ -1 +1 @@
-persistent-coasters sh /bin/bash
+cloud sh /bin/bash
Modified: SwiftTutorials/swift-cloud-tutorial/part05/apps
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part05/apps 2013-10-22 19:26:47 UTC (rev 7210)
+++ SwiftTutorials/swift-cloud-tutorial/part05/apps 2013-10-22 19:45:17 UTC (rev 7211)
@@ -1 +1 @@
-persistent-coasters sh /bin/bash
+cloud sh /bin/bash
Added: SwiftTutorials/swift-cloud-tutorial/part05/simulate.sh
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part05/simulate.sh (rev 0)
+++ SwiftTutorials/swift-cloud-tutorial/part05/simulate.sh 2013-10-22 19:45:17 UTC (rev 7211)
@@ -0,0 +1 @@
+link ../app/simulate.sh
\ No newline at end of file
Property changes on: SwiftTutorials/swift-cloud-tutorial/part05/simulate.sh
___________________________________________________________________
Added: svn:special
+ *
Added: SwiftTutorials/swift-cloud-tutorial/part05/stats.sh
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part05/stats.sh (rev 0)
+++ SwiftTutorials/swift-cloud-tutorial/part05/stats.sh 2013-10-22 19:45:17 UTC (rev 7211)
@@ -0,0 +1 @@
+link ../app/stats.sh
\ No newline at end of file
Property changes on: SwiftTutorials/swift-cloud-tutorial/part05/stats.sh
___________________________________________________________________
Added: svn:special
+ *
Modified: SwiftTutorials/swift-cloud-tutorial/part06/apps
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/part06/apps 2013-10-22 19:26:47 UTC (rev 7210)
+++ SwiftTutorials/swift-cloud-tutorial/part06/apps 2013-10-22 19:45:17 UTC (rev 7211)
@@ -1 +1 @@
-persistent-coasters sh /bin/bash
+cloud sh /bin/bash
Deleted: SwiftTutorials/swift-cloud-tutorial/scs/get_ip_list.sh
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/scs/get_ip_list.sh 2013-10-22 19:26:47 UTC (rev 7210)
+++ SwiftTutorials/swift-cloud-tutorial/scs/get_ip_list.sh 2013-10-22 19:45:17 UTC (rev 7211)
@@ -1,4 +0,0 @@
-#!/bin/bash
-
-nova list |grep ACTIVE|awk '{print ( $(NF-1) )}'|cut -d'=' -f2 | sed ':a;N;$!ba;s/\n/ /g'
-
From davidk at ci.uchicago.edu Tue Oct 22 15:00:04 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 15:00:04 -0500 (CDT)
Subject: [Swift-commit] r7212 - SwiftTutorials/swift-cloud-tutorial/doc
Message-ID: <20131022200004.1D23D9CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 15:00:03 -0500 (Tue, 22 Oct 2013)
New Revision: 7212
Modified:
SwiftTutorials/swift-cloud-tutorial/doc/README
Log:
Update doc with new pool names
Modified: SwiftTutorials/swift-cloud-tutorial/doc/README
===================================================================
--- SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 19:45:17 UTC (rev 7211)
+++ SwiftTutorials/swift-cloud-tutorial/doc/README 2013-10-22 20:00:03 UTC (rev 7212)
@@ -349,7 +349,7 @@
the equivalent python version (simulate.py). The new apps file now looks like this:
-----
-localhost simulate simulate.py
+sys::[cat ../part02/apps]
-----
Swift does not need to know anything about the language an application is written in. The application
@@ -518,16 +518,16 @@
`sim_N.log`. The log files provide data on the runtime environment of
each app invocation. For example:
-FIXME: The output below needs to get recaptured for worker nodes
-
-----
-$ cat output/sim_0.log
-Called as: /home/users/p01532/swift-osdc-tutorial/app/simulate.sh: --timesteps 1 --range 100 --nvalues 5
+$ cat output/sim_0.log
-Start time: Tue Aug 27 12:17:43 CDT 2013
-Running on node: nid00018
-Running as user: uid=61532(p01532) gid=61532 groups=61532
+Called as: simulate.sh: --timesteps 1 --range 100 --nvalues 5
+Start time: Tue Oct 22 14:54:11 CDT 2013
+Running as user: uid=5116(davidk) gid=311(collab) groups=311(collab),104(fuse),1349(swift),45053(swat)
+Running on node: stomp
+Node IP address: 140.221.9.237
+
Simulation parameters:
bias=0
@@ -543,15 +543,15 @@
Environment:
-ALPS_APP_DEPTH=32
-ASSEMBLER_X86_64=/opt/cray/cce/8.2.0.173/cray-binutils/x86_64-unknown-linux-gnu/bin/as
-ASYNCPE_DIR=/opt/cray/xt-asyncpe/5.23.02
-ASYNCPE_VERSION=5.23.02
-...
+EDITOR=vim
+HOME=/homes/davidk
+JAVA_HOME=/nfs/proj-davidk/jdk1.7.0_01
+LANG=C
+....
-----
To tell Swift to run the apps on compute nodes, we specify in the
-`apps` file that the apps should be executed on the `osdc` site
+`apps` file that the apps should be executed on the `cloud` site
(instead of the `localhost` site). We can specify the location of
each app in the third field of the `apps` file, with either an
absolute pathname or the name of an executable to be located in
@@ -559,16 +559,16 @@
-----
$ cat apps
-raven simulate simulate.sh
-raven stats stats.sh
+cloud simulate simulate.sh
+cloud stats stats.sh
-----
You can experiment, for example, with an alternate version of stats.sh by specfying that app's location explicitly:
-----
$ cat apps
-raven simulate simulate.sh
-raven stats /home/users/p01532/bin/my-alt-stats.sh
+cloud simulate simulate.sh
+cloud stats /home/users/p01532/bin/my-alt-stats.sh
-----
We can see that when we run many apps requesting a larger set of nodes (6), we are indeed running on the compute nodes:
From davidk at ci.uchicago.edu Tue Oct 22 15:06:48 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 15:06:48 -0500 (CDT)
Subject: [Swift-commit] r7213 - www/docs
Message-ID: <20131022200648.419339CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 15:06:48 -0500 (Tue, 22 Oct 2013)
New Revision: 7213
Modified:
www/docs/index.php
Log:
Remove link to versioned quickstart
Remove references to 0.93
Modified: www/docs/index.php
===================================================================
--- www/docs/index.php 2013-10-22 20:00:03 UTC (rev 7212)
+++ www/docs/index.php 2013-10-22 20:06:48 UTC (rev 7213)
@@ -27,9 +27,8 @@
This guide describes the steps needed to download, install, configure, and run the basic examples for Swift.
@@ -57,10 +56,6 @@
[html] [pdf]
- Previous (0.93)
- [html] [pdf]
-
-
Trunk
[html] [pdf]
From davidk at ci.uchicago.edu Tue Oct 22 15:29:02 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 15:29:02 -0500 (CDT)
Subject: [Swift-commit] r7214 - in SwiftTutorials/swift-cray-tutorial: app
doc part02
Message-ID: <20131022202902.375199CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 15:29:02 -0500 (Tue, 22 Oct 2013)
New Revision: 7214
Added:
SwiftTutorials/swift-cray-tutorial/app/simulate.py
SwiftTutorials/swift-cray-tutorial/app/stats.py
Modified:
SwiftTutorials/swift-cray-tutorial/doc/README
SwiftTutorials/swift-cray-tutorial/doc/build_docs.sh
SwiftTutorials/swift-cray-tutorial/part02/apps
Log:
Add python examples to cray docs
Added: SwiftTutorials/swift-cray-tutorial/app/simulate.py
===================================================================
--- SwiftTutorials/swift-cray-tutorial/app/simulate.py (rev 0)
+++ SwiftTutorials/swift-cray-tutorial/app/simulate.py 2013-10-22 20:29:02 UTC (rev 7214)
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+import sys
+import os
+import socket
+import time
+import math
+import random
+import getpass
+
+def parse():
+ from optparse import OptionParser
+ parser=OptionParser()
+ parser.add_option("-b", "--bias", type="int", dest="bias", default=0,
+ help="offset bias: add this integer to all results");
+
+ parser.add_option("-B", "--biasfile", type="string", dest="biasfile",
+ default="none", help="file of integer biases to add to results" );
+
+ parser.add_option("-l", "--log", type="string", dest="log", default="yes",
+ help="generate a log in stderr if not nul");
+
+ parser.add_option("-n", "--nvalues", type="int", dest="nvalues",default=1,
+ help="print this many values per simulation" );
+
+ parser.add_option("-s", "--seed", type="int", dest="initseed", default=0,
+ help="use this integer [0..32767] as a seed");
+
+ parser.add_option("-S", "--seedfile", type="string", dest="seedfile",
+ default="none", help="use this file (containing integer seeds [0..32767]) one per line" );
+
+ parser.add_option("-t", "--timesteps", type="int", dest="timesteps",
+ default=0, help='number of simulated "timesteps" in seconds (determines runtime)' );
+
+ parser.add_option("-r", "--range", type="int", dest="range", default=100,
+ help="range (limit) of generated results" );
+
+ parser.add_option("-w", "--width", type="int", dest="width", default=8,
+ help="Width ?" );
+
+ parser.add_option("-x", "--scale", type="int", dest="scale", default=1,
+ help="scale the results by this integer" );
+ # Not implemented yet
+ parser.add_option("-p", "--paramfile", type="string", dest="paramfile", default="none",
+ help="Not implemented yet" );
+ return (parser.parse_args());
+
+def log():
+ import datetime
+ print >> sys.stderr, "Called as: ", str(sys.argv)
+ print >> sys.stderr, "Start time: ", datetime.datetime.now()
+ print >> sys.stderr, "Running on node: ", socket.gethostname()
+ print >> sys.stderr, "Running as user: ", getpass.getuser()
+ print >> sys.stderr, "\nEnvironment:\n\n"
+ print >> sys.stderr, os.environ
+
+def printparams(options):
+ print 'bias =',options.bias
+ print 'biasfile = ',options.biasfile
+ print 'log = ', options.log
+ print 'nvalues = ',options.nvalues
+ print 'seed = ', options.initseed
+ print 'seedfile = ', options.seedfile
+ print 'timesteps = ', options.timesteps
+ print 'range = ', options.range
+ print 'width = ', options.width
+ print 'scale = ', options.scale
+ print 'paramfile = ', options.paramfile
+
+def simulate(options):
+ time.sleep(options.timesteps)
+ bias=[];
+ if (options.biasfile != "none"):
+ try:
+ with open(options.biasfile) as biasfile:
+ lines = biasfile.read().splitlines()
+ for line in lines:
+ bias.append(int(line))
+ except IOError:
+ print "Error accessing content from file: ", options.biasfile
+ bias_count = len(bias)
+
+ for i in range(options.nvalues):
+ value = (random.random() +
+ random.random()*math.pow(2,16) +
+ random.random()*math.pow(2,32) +
+ random.random()*math.pow(2,48))
+ value=( (int(value)%options.range) * options.scale + options.bias)
+ if ( i < bias_count ):
+ value = value + bias[i]
+ elif ( bias_count > 0 ):
+ value = value + bias[bias_count-1]
+
+ print '{num:{fill}{width}}'.format(num=value, fill=' ', width=options.width)
+
+
+def seed(options):
+ if (options.initseed != 0 ):
+ random.seed(options.initseed)
+ if (options.seedfile != "none"):
+ try:
+ with open(options.seedfile) as seedfile:
+ lines=seedfile.read().splitlines()
+ seed = 0
+ for line in lines:
+ seed = seed + int(line)
+ random.seed(seed)
+ except IOError:
+ print "Could not open file: ", options.seedfile
+
+
+if __name__ == "__main__":
+ (options, args) = parse()
+ printparams(options)
+ seed(options)
+ simulate(options)
+ log()
+
+
+
+
+
+
+
+
+
Property changes on: SwiftTutorials/swift-cray-tutorial/app/simulate.py
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/swift-cray-tutorial/app/stats.py
===================================================================
--- SwiftTutorials/swift-cray-tutorial/app/stats.py (rev 0)
+++ SwiftTutorials/swift-cray-tutorial/app/stats.py 2013-10-22 20:29:02 UTC (rev 7214)
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+import socket
+import sys
+import os
+
+def log():
+ import datetime
+ print >> sys.stderr, "Called as: ", str(sys.argv)
+ print >> sys.stderr, "Start time: ", datetime.datetime.now()
+ print >> sys.stderr, "Running on node: ", socket.gethostname()
+ print >> sys.stderr, "Running as user: ",os.getlogin()
+ print >> sys.stderr, "\nEnvironment:\n\n"
+ print >> sys.stderr, os.environ
+
+def stat():
+ total = 0
+ count = 0
+ for f in sys.argv[1:]:
+ try:
+ with open(f) as ifile:
+ lines = ifile.read().splitlines()
+ for line in lines:
+ total += int(line)
+ count += 1
+ except IOError:
+ print "Error accessing content from file: ", options.biasfile
+ print total/count
+
+if __name__ == "__main__":
+ log()
+ stat()
Property changes on: SwiftTutorials/swift-cray-tutorial/app/stats.py
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftTutorials/swift-cray-tutorial/doc/README
===================================================================
--- SwiftTutorials/swift-cray-tutorial/doc/README 2013-10-22 20:06:48 UTC (rev 7213)
+++ SwiftTutorials/swift-cray-tutorial/doc/README 2013-10-22 20:29:02 UTC (rev 7214)
@@ -344,6 +344,16 @@
sys::[cat ../part02/p2.swift]
-----
+In part 2, we also update the apps file. Instead of using shell script (simulate.sh), we use
+the equivalent python version (simulate.py). The new apps file now looks like this:
+
+-----
+sys::[cat ../part02/apps]
+-----
+
+Swift does not need to know anything about the language an application is written in. The application
+can be written in Perl, Python, Java, Fortran, or any other language.
+
The script also shows an
example of naming the output files of an ensemble run. In this case, the output files will be named
`output/sim_N.out`.
Modified: SwiftTutorials/swift-cray-tutorial/doc/build_docs.sh
===================================================================
--- SwiftTutorials/swift-cray-tutorial/doc/build_docs.sh 2013-10-22 20:06:48 UTC (rev 7213)
+++ SwiftTutorials/swift-cray-tutorial/doc/build_docs.sh 2013-10-22 20:29:02 UTC (rev 7214)
@@ -1,4 +1,4 @@
#!/bin/bash -e
-asciidoc -a icons -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o swift-cray-tutorial.html README
+asciidoc -a icons -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o tutorial.html README
Modified: SwiftTutorials/swift-cray-tutorial/part02/apps
===================================================================
--- SwiftTutorials/swift-cray-tutorial/part02/apps 2013-10-22 20:06:48 UTC (rev 7213)
+++ SwiftTutorials/swift-cray-tutorial/part02/apps 2013-10-22 20:29:02 UTC (rev 7214)
@@ -1 +1 @@
-localhost simulate simulate.sh
+localhost simulate simulate.py
From davidk at ci.uchicago.edu Tue Oct 22 15:46:30 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 22 Oct 2013 15:46:30 -0500 (CDT)
Subject: [Swift-commit] r7215 - in SwiftTutorials/OSG-Swift: app doc part02
Message-ID: <20131022204630.9F9199CC83@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-22 15:46:30 -0500 (Tue, 22 Oct 2013)
New Revision: 7215
Added:
SwiftTutorials/OSG-Swift/app/simulate.py
SwiftTutorials/OSG-Swift/app/stats.py
Modified:
SwiftTutorials/OSG-Swift/doc/README
SwiftTutorials/OSG-Swift/doc/build_docs.sh
SwiftTutorials/OSG-Swift/part02/apps
Log:
Python scripts for osgconnect tutorial
Updated build_docs
Updated README
Added: SwiftTutorials/OSG-Swift/app/simulate.py
===================================================================
--- SwiftTutorials/OSG-Swift/app/simulate.py (rev 0)
+++ SwiftTutorials/OSG-Swift/app/simulate.py 2013-10-22 20:46:30 UTC (rev 7215)
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+import sys
+import os
+import socket
+import time
+import math
+import random
+import getpass
+
+def parse():
+ from optparse import OptionParser
+ parser=OptionParser()
+ parser.add_option("-b", "--bias", type="int", dest="bias", default=0,
+ help="offset bias: add this integer to all results");
+
+ parser.add_option("-B", "--biasfile", type="string", dest="biasfile",
+ default="none", help="file of integer biases to add to results" );
+
+ parser.add_option("-l", "--log", type="string", dest="log", default="yes",
+ help="generate a log in stderr if not nul");
+
+ parser.add_option("-n", "--nvalues", type="int", dest="nvalues",default=1,
+ help="print this many values per simulation" );
+
+ parser.add_option("-s", "--seed", type="int", dest="initseed", default=0,
+ help="use this integer [0..32767] as a seed");
+
+ parser.add_option("-S", "--seedfile", type="string", dest="seedfile",
+ default="none", help="use this file (containing integer seeds [0..32767]) one per line" );
+
+ parser.add_option("-t", "--timesteps", type="int", dest="timesteps",
+ default=0, help='number of simulated "timesteps" in seconds (determines runtime)' );
+
+ parser.add_option("-r", "--range", type="int", dest="range", default=100,
+ help="range (limit) of generated results" );
+
+ parser.add_option("-w", "--width", type="int", dest="width", default=8,
+ help="Width ?" );
+
+ parser.add_option("-x", "--scale", type="int", dest="scale", default=1,
+ help="scale the results by this integer" );
+ # Not implemented yet
+ parser.add_option("-p", "--paramfile", type="string", dest="paramfile", default="none",
+ help="Not implemented yet" );
+ return (parser.parse_args());
+
+def log():
+ import datetime
+ print >> sys.stderr, "Called as: ", str(sys.argv)
+ print >> sys.stderr, "Start time: ", datetime.datetime.now()
+ print >> sys.stderr, "Running on node: ", socket.gethostname()
+ print >> sys.stderr, "Running as user: ", getpass.getuser()
+ print >> sys.stderr, "\nEnvironment:\n\n"
+ print >> sys.stderr, os.environ
+
+def printparams(options):
+ print 'bias =',options.bias
+ print 'biasfile = ',options.biasfile
+ print 'log = ', options.log
+ print 'nvalues = ',options.nvalues
+ print 'seed = ', options.initseed
+ print 'seedfile = ', options.seedfile
+ print 'timesteps = ', options.timesteps
+ print 'range = ', options.range
+ print 'width = ', options.width
+ print 'scale = ', options.scale
+ print 'paramfile = ', options.paramfile
+
+def simulate(options):
+ time.sleep(options.timesteps)
+ bias=[];
+ if (options.biasfile != "none"):
+ try:
+ with open(options.biasfile) as biasfile:
+ lines = biasfile.read().splitlines()
+ for line in lines:
+ bias.append(int(line))
+ except IOError:
+ print "Error accessing content from file: ", options.biasfile
+ bias_count = len(bias)
+
+ for i in range(options.nvalues):
+ value = (random.random() +
+ random.random()*math.pow(2,16) +
+ random.random()*math.pow(2,32) +
+ random.random()*math.pow(2,48))
+ value=( (int(value)%options.range) * options.scale + options.bias)
+ if ( i < bias_count ):
+ value = value + bias[i]
+ elif ( bias_count > 0 ):
+ value = value + bias[bias_count-1]
+
+ print '{num:{fill}{width}}'.format(num=value, fill=' ', width=options.width)
+
+
+def seed(options):
+ if (options.initseed != 0 ):
+ random.seed(options.initseed)
+ if (options.seedfile != "none"):
+ try:
+ with open(options.seedfile) as seedfile:
+ lines=seedfile.read().splitlines()
+ seed = 0
+ for line in lines:
+ seed = seed + int(line)
+ random.seed(seed)
+ except IOError:
+ print "Could not open file: ", options.seedfile
+
+
+if __name__ == "__main__":
+ (options, args) = parse()
+ printparams(options)
+ seed(options)
+ simulate(options)
+ log()
+
+
+
+
+
+
+
+
+
Property changes on: SwiftTutorials/OSG-Swift/app/simulate.py
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/OSG-Swift/app/stats.py
===================================================================
--- SwiftTutorials/OSG-Swift/app/stats.py (rev 0)
+++ SwiftTutorials/OSG-Swift/app/stats.py 2013-10-22 20:46:30 UTC (rev 7215)
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+import socket
+import sys
+import os
+
+def log():
+ import datetime
+ print >> sys.stderr, "Called as: ", str(sys.argv)
+ print >> sys.stderr, "Start time: ", datetime.datetime.now()
+ print >> sys.stderr, "Running on node: ", socket.gethostname()
+ print >> sys.stderr, "Running as user: ",os.getlogin()
+ print >> sys.stderr, "\nEnvironment:\n\n"
+ print >> sys.stderr, os.environ
+
+def stat():
+ total = 0
+ count = 0
+ for f in sys.argv[1:]:
+ try:
+ with open(f) as ifile:
+ lines = ifile.read().splitlines()
+ for line in lines:
+ total += int(line)
+ count += 1
+ except IOError:
+ print "Error accessing content from file: ", options.biasfile
+ print total/count
+
+if __name__ == "__main__":
+ log()
+ stat()
Property changes on: SwiftTutorials/OSG-Swift/app/stats.py
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftTutorials/OSG-Swift/doc/README
===================================================================
--- SwiftTutorials/OSG-Swift/doc/README 2013-10-22 20:29:02 UTC (rev 7214)
+++ SwiftTutorials/OSG-Swift/doc/README 2013-10-22 20:46:30 UTC (rev 7215)
@@ -324,6 +324,16 @@
image::part02.png[align="center"]
+In part 2, we also update the apps file. Instead of using shell script (simulate.sh), we use
+the equivalent python version (simulate.py). The new apps file now looks like this:
+
+-----
+sys::[cat ../part02/apps]
+-----
+
+Swift does not need to know anything about the language an application is written in. The application
+can be written in Perl, Python, Java, Fortran, or any other language.
+
.p2.swift
-----
sys::[cat -n ../part02/p2.swift]
Modified: SwiftTutorials/OSG-Swift/doc/build_docs.sh
===================================================================
--- SwiftTutorials/OSG-Swift/doc/build_docs.sh 2013-10-22 20:29:02 UTC (rev 7214)
+++ SwiftTutorials/OSG-Swift/doc/build_docs.sh 2013-10-22 20:46:30 UTC (rev 7215)
@@ -1,13 +1,4 @@
#!/bin/bash -e
-if false; then
- echo skipping
-pushd part11-swift-py-r/code >& /dev/null
-# Strip comments, blank lines; prepend shell prompt ($)
-grep -A 20 stc run-dets.sh | \
- grep -v -e "^$\|#" | \
- sed 's/^/$ /' > run-dets.sh.txt
-popd >& /dev/null
-fi
+asciidoc -a icons -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o tutorial.html README
-asciidoc -a icons -a "src_tab=3 --line-number=' '" -a toc -a toplevels=2 -a stylesheet=$PWD/asciidoc.css -a max-width=800px -o cic-tutorial.html README
Modified: SwiftTutorials/OSG-Swift/part02/apps
===================================================================
--- SwiftTutorials/OSG-Swift/part02/apps 2013-10-22 20:29:02 UTC (rev 7214)
+++ SwiftTutorials/OSG-Swift/part02/apps 2013-10-22 20:46:30 UTC (rev 7215)
@@ -1 +1 @@
-localhost simulate simulate.sh
+localhost simulate simulate.py
From davidk at ci.uchicago.edu Wed Oct 23 09:20:53 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 09:20:53 -0500 (CDT)
Subject: [Swift-commit] r7216 - www/downloads
Message-ID: <20131023142053.76075178884@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-23 09:20:52 -0500 (Wed, 23 Oct 2013)
New Revision: 7216
Modified:
www/downloads/index.php
Log:
Stable release header
Modified: www/downloads/index.php
===================================================================
--- www/downloads/index.php 2013-10-22 20:46:30 UTC (rev 7215)
+++ www/downloads/index.php 2013-10-23 14:20:52 UTC (rev 7216)
@@ -35,7 +35,7 @@
Swift Usage Tracking Policy.
-
+Latest Stable Release
Swift 0.94.1 RC3 - 2013/09/04
For the majority of users, this is the version you will want to download. This package
From swift at ci.uchicago.edu Wed Oct 23 09:25:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 09:25:03 -0500 (CDT)
Subject: [Swift-commit] cog r3812
Message-ID: <20131023142503.A12838D000A5@bridled.ci.uchicago.edu>
------------------------------------------------------------------------
r3812 | jmwozniak | 2013-10-23 09:22:48 -0500 (Wed, 23 Oct 2013) | 1 line
Adding tests/tcl
------------------------------------------------------------------------
From ketan at ci.uchicago.edu Wed Oct 23 11:21:25 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 11:21:25 -0500 (CDT)
Subject: [Swift-commit] r7217 - in SwiftApps/gocat: . log
Message-ID: <20131023162125.A3909178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-23 11:21:25 -0500 (Wed, 23 Oct 2013)
New Revision: 7217
Modified:
SwiftApps/gocat/log/GlobusCatalog-log.txt
SwiftApps/gocat/tagwrap.sh
Log:
'
Modified: SwiftApps/gocat/log/GlobusCatalog-log.txt
===================================================================
--- SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-23 14:20:52 UTC (rev 7216)
+++ SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-23 16:21:25 UTC (rev 7217)
@@ -61,3 +61,17 @@
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 dag9 text
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"taken"}
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 80 {"dag9":"flow"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"shadow"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 parameter1 text
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 81 {"parameter1":"angle49"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_dataset_annotations 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_dataset_annotations 48 81
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_dataset_annotations 48 81
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"/home/ketan/dataset1/id.txt"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 obtained text
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 83 {"obtained":"2003"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_dataset_annotations 48 83
Modified: SwiftApps/gocat/tagwrap.sh
===================================================================
--- SwiftApps/gocat/tagwrap.sh 2013-10-23 14:20:52 UTC (rev 7216)
+++ SwiftApps/gocat/tagwrap.sh 2013-10-23 16:21:25 UTC (rev 7217)
@@ -18,7 +18,7 @@
retstr=$(python $loc/catalog.py create_dataset $catid $exprstr)
echo '==='
- echo $retstr
+ echo CatalogID, DatasetID: $retstr
echo '==='
# 2. Annotate it
@@ -27,7 +27,7 @@
dsetid=`echo $retstr |awk -F, '{print $2}'`
echo '==='
- echo $dsetid
+ echo "Dataset ID: $dsetid"
echo '==='
# b. Add dataset annotation
python $loc/catalog.py add_dataset_annotation $catid $dsetid "{\"$tagname\":\"$tagval\"}"
From swift at ci.uchicago.edu Wed Oct 23 11:45:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 11:45:03 -0500 (CDT)
Subject: [Swift-commit] cog r3815
Message-ID: <20131023164503.E92BF8D000A5@bridled.ci.uchicago.edu>
------------------------------------------------------------------------
r3815 | jmwozniak | 2013-10-23 11:42:09 -0500 (Wed, 23 Oct 2013) | 2 lines
Drop autogenerated file
------------------------------------------------------------------------
Index: modules/provider-coaster-c-client/Makefile.in
===================================================================
--- modules/provider-coaster-c-client/Makefile.in (revision 3814)
+++ modules/provider-coaster-c-client/Makefile.in (working copy)
@@ -1,756 +0,0 @@
-# Makefile.in generated by automake 1.11.6 from Makefile.am.
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-
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-# Foundation, Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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-
- at SET_MAKE@
-VPATH = @srcdir@
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From swift at ci.uchicago.edu Wed Oct 23 11:50:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 11:50:03 -0500 (CDT)
Subject: [Swift-commit] cog r3817
Message-ID: <20131023165003.A1AD68D000A5@bridled.ci.uchicago.edu>
------------------------------------------------------------------------
r3817 | jmwozniak | 2013-10-23 11:47:07 -0500 (Wed, 23 Oct 2013) | 1 line
Set ignores
------------------------------------------------------------------------
Property changes on: modules/provider-coaster-c-client/src
___________________________________________________________________
Added: svn:ignore
+ .deps
Makefile.in
Makefile
CoasterSWIG_wrap.cxx
coaster-client-test
Property changes on: modules/provider-coaster-c-client
___________________________________________________________________
Added: svn:ignore
+ Makefile.in
Makefile
From ketan at ci.uchicago.edu Wed Oct 23 16:47:42 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 16:47:42 -0500 (CDT)
Subject: [Swift-commit] r7218 - in SwiftApps/gocat: . log
Message-ID: <20131023214742.09F03178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-23 16:47:41 -0500 (Wed, 23 Oct 2013)
New Revision: 7218
Modified:
SwiftApps/gocat/log/GlobusCatalog-log.txt
SwiftApps/gocat/tagwrap.sh
Log:
Modified: SwiftApps/gocat/log/GlobusCatalog-log.txt
===================================================================
--- SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-23 16:21:25 UTC (rev 7217)
+++ SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-23 21:47:41 UTC (rev 7218)
@@ -75,3 +75,13 @@
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_datasets 48
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_datasets 48
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_dataset_annotations 48 83
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"shadow"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 85 {"parameter1":"angle49"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py query_datasets 48 name EQUAL shadow
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"shadow"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 86 {"parameter1":"angle49"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text query_datasets 48 name EQUAL shadow
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"shadow"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 87 {"parameter1":"angle49"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_datasets 48
Modified: SwiftApps/gocat/tagwrap.sh
===================================================================
--- SwiftApps/gocat/tagwrap.sh 2013-10-23 16:21:25 UTC (rev 7217)
+++ SwiftApps/gocat/tagwrap.sh 2013-10-23 21:47:41 UTC (rev 7218)
@@ -1,7 +1,13 @@
#!/bin/bash -x
-# Usage: $0 =
+# Usage: $0 =
+if [ $# -ne 2 ]
+then
+ echo "Usage: $0 ="
+ exit 1
+fi
+
loc=/scratch/local/ketan/catalog-client/globusonline/catalog/client/examples
catid=48
dsetname=$1
@@ -11,6 +17,9 @@
tagval=`echo $tagvalpair|awk -F= '{print $2}'`
# 1. Create dataset
+ # a. Check if it already exists
+ python $loc/catalog.py -text query_datasets $catid name EQUAL $dsetname
+
exprstr="{\"name\":\"$dsetname\"}"
echo '==='
echo $exprstr
From ketan at ci.uchicago.edu Wed Oct 23 22:06:29 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Wed, 23 Oct 2013 22:06:29 -0500 (CDT)
Subject: [Swift-commit] r7219 - SwiftApps/Swift-MapRed/blast
Message-ID: <20131024030629.81815178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-23 22:06:29 -0500 (Wed, 23 Oct 2013)
New Revision: 7219
Modified:
SwiftApps/Swift-MapRed/blast/blast.swift
SwiftApps/Swift-MapRed/blast/run.sh
SwiftApps/Swift-MapRed/blast/sequence.seq
SwiftApps/Swift-MapRed/blast/sites.xml
Log:
Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,3 +1,4 @@
+
type fastaseq;
type headerfile;
type indexfile;
@@ -11,46 +12,48 @@
seqfile psq;
}
-string num_partitions=@arg("n", "8");
+string num_partitions = arg("n", "50");
-string program_name=@arg("p", "blastp");
+string program_name = arg("p", "blastp");
-fastaseq dbin ;
+fastaseq dbin ;
-query query_file ;
+query query_file ;
-string expectation_value=@arg("e", "0.1");
+string expectation_value = arg("e", "0.1");
-output blast_output_file ;
+output blast_output_file ;
-string filter_query_sequence=@arg("F", "F");
+string filter_query_sequence = arg("F", "F");
-fastaseq partition[] ;
+fastaseq partition[] ;
-database formatdbout[] ;
-output out[] ;
+database formatdbout[] ;
+output out[] ;
+
app (fastaseq out[]) split_database (fastaseq d, string n){
- fastasplitn @filename(d) n;
+ fastasplitn filename(d) n;
}
app (database out) formatdb (fastaseq i){
- formatdb "-i" @filename(i);
+ formatdb "-i" filename(i);
}
app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db){
- blastall "-p" p "-i" @filename(i) "-d" @filename(d) "-o" @filename(o) "-e" e "-T" "-F" f;
+ blastall "-p" p "-i" filename(i) "-d" filename(d) "-o" filename(o) "-e" e "-T" "-F" f;
}
app (output o) blastmerge(output o_frags[]){
- blastmerge @filename(o) @filenames(o_frags);
+ blastmerge filename(o) filenames(o_frags);
}
+
partition=split_database(dbin, num_partitions);
foreach part,i in partition {
formatdbout[i] = formatdb(part);
- out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
+ out[i] = blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
}
-blast_output_file=blastmerge(out);
+blast_output_file = blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/run.sh
===================================================================
--- SwiftApps/Swift-MapRed/blast/run.sh 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/run.sh 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,3 +1 @@
-#!/bin/bash
-
swift -sites.file sites.xml -config cf tc.file tc.data blast.swift
Modified: SwiftApps/Swift-MapRed/blast/sequence.seq
===================================================================
--- SwiftApps/Swift-MapRed/blast/sequence.seq 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/sequence.seq 2013-10-24 03:06:29 UTC (rev 7219)
@@ -1,4 +1,106 @@
->seq1
-AACGCGTATATACACAGGG
->seq2
-CGTATAGATACA
+>gnl|md5|e0785fc0b8720a5c4d78be370ef19af0
+MEVLESGEQGVLQWDRKLSELSEPGDGEALMYHTHFSELLDEFSQNVLGQLLNDPFLSEK
+SVSMEVEPSPTSPAPLIQAEHSYSLCEEPRAQSPFTHITSDSFNDDEVESEKWYLSTDFP
+STSIKTEPITDEPPPGLVPSVTLTITAISTPLEKEEPPLEMNTGVDSSCQTIIPKIKLEP
+HEVDQFLNFSPKEAPVDHLHLPPTPPSSHGSDSEGSLSPNPRLHPFSLPQTHSPSRAAPR
+APSALSSSPLLTAPHKLQGSGPLVLTEEEKRTLIAEGYPIPTKLPLSKSEEKALKKIRRK
+IKNKISAQESRRKKKEYMDSLEKKVESCSTENLELRKKVEVLENTNRTLLQQLQKLQTLV
+MGKVSRTCKLAGTQTGTCLMVVVLCFAVAFGSFFQGYGPYPSATKMALPSQHSLQEPYTA
+SVVRSRNLLIYEEHSPPEESSSPGSAGELGGWDRGSSLLRVSGLESRPDVDLPHFIISNE
+TSLEKSVLLELQQHLVSAKLEGNETLKVVELDRRVNTTF
+>gnl|md5|f67549f249c59ecd0b48ff02ca209442
+MAEETRQSKLAIAKEKLKEYWQRNSLGVPAGVKRNRKTSGSSPETATSGGCHSPEDSATG
+IHGEGPTSSATLKDLESPCQELAVVLDSRSIKISQLNNTIKSLVIMANILVFVFPKCIVI
+DLNRNVDTEISKMSMG
+>gnl|md5|cd0de5548a14c880425dc87f8486310c
+MNSGAMRIHSKGHFQGGIQVKNEKNRPSLKSLKTDNRPEKSKCKPLWGKVFYLDLPSVTI
+SEKLQKDIKDLGGRVEEFLSKDISYLISNKKEAKFAQTLGRISPVPSPESAYTAETTSPH
+PSHDGSSFKSPDTVCLSRGKLLVEKAIKDHDFIPSNSILSNALSWGVKILHIDDIRYYIE
+QKKKELYLLKKSSTSVRDGGKRVGSGAQKTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMP
+FINYSIQKPCSPFDVDKPSSMQKQTQVKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCL
+QKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYEKDTPKKKRIKYSVGSLSP
+VSASVLKKTEQKEKVELQHISQKDCQEDDTTVKEQNFLYKETQETEKKLLFISEPIPHPS
+NELRGLNEKMSNKCSMLSTAEDDIRQNFTQLPLHKNKQECILDISEHTLSENDLEELRVD
+HYKCNIQASVHVSDFSTDNSGSQPKQKSDTVLFPAKDLKEKDLHSIFTHDSGLITINSSQ
+EHLTVQAKAPFHTPPEEPNECDFKNMDSLPSGKIHRKVKILLGQNRKENLEPNAEFDKRT
+EFITQEENRICSSPVQSLPDLFQTSEEKSEFLGFTSYTEKSGICNVLDIWEEENSDNLLT
+AFFSSPSTSTFTGF
+>gnl|md5|c243d77c83c27dff598d70af18d8ed42
+MGAEQIRLEDRAQCAARQVLGGAGDGEGGVVHQRVDAPQGQRGFGAARHAVLAAQFQVQR
+VEALGAAGLDILGLAAGGDDAPAARPHVPRRVQPDARGTAGDQNGLHARLLAAGVLRQGR
+ALRKPRISGWTGAACGPIHRNMSDDPNVPDPTPPDPSQDQTTSEPLSRAIGERYLTYALS
+TIMNRALPDARDGLKPVHRRILFAMRELRLSPTGAFRKSAKISGDVMGNYHPHGDAAIYD
+AMARLAQPFAMRYPLVDGQGNFGNIDGDNPAASRYTEARLTAAAEALMEGLAENAVDFRP
+NYDGTLEEPIVLPAAFPNLLCNGASGIAVGMATNVPPHNLHEVIDACLHLIKAPDARDDT
+LVSIVPGPDFPTGGVLVESRETIAEAYRTGRGSLRLRARWSVEDLGRGQWQIVVTEIPYQ
+VQKSKLIERLAEVIQLKKVPILADVRDESAEDIRIVLEPRTRAVDAEQLMAALFRVSDLE
+VRFGLNMNVLIDGRVPKVCSLKEVLRAFLDHRREVLVRRSNHRLDKIAARLEVLEGYMIA
+FLNLDRVIEIIRHEDDPKAVMIAEFKLSDVQVEAILNMRLRALRRLEEIELRAEHENLTR
+EREGLAAMLADEGAQWARIAEELRETRAKFGKSASGGQRRTEIGEAGEVAEIDMDAMIER
+EPITVILSKMGWIRAMKGHQPLDAEVKFKDGDGPFMALHAETTDKLMVFAANGRFYTLPA
+NNLPGGRGMGEPLRLMIDLPNDAAVIDMFPWRDGERYLVASKAGDGFVVAGADILAQTRA
+GKQVLNGEAALCRRVTGDHVAVVGQNRKLLVFPLSELPEMARGKGVRLQKYKDGGLSDAV
+CITLAEGLRWQETGGRTRSEPDLTEWLGKRAGAGYMAPRGFPRDNRFN
+>gnl|md5|ccc28dbc1a3ca81c8dd929af669b1173
+MDRAERIGFWVSGFAHAGLLGAALVGGALFRPQPLEAVRMAEVATMSEAEFQSLAAAAAG
+RGPVSDVAATTPAQPRPPADENRLGEVEAVSPPAPDAQAAELSTPSDRPEARPDLSDFQT
+PNRPVAVATDAPRPAEPENTVELAAL
+>gnl|md5|9d3da0729b348bbcaba8c65c444b6fee
+MAGPAHGRAHRGAALMLEVAFRHRFPGLSLEVAFQAPGGVTALFGPSGCGKSTAINAIAG
+LLRPDQGRIALDGRVLFDGATNLSPQARRIGCVFQDARLFPHMTVAANLRYPSRWRRGAA
+RDFDRITEMLALGPLLHRRPGTLSGGERQRVAIGRALLSDPALLVMDEPLAALDEARKAE
+IMPWLERLRDQIRLPILYVSHSVPEVLRLATTVVLMRQGRVTHSGALADILADPELAPQL
+GAREAGALIRATVEAREADGLTRVATAGGPMLLPELDLAPGRVLRLRILAHEVILAREAP
+RGLSALNALPVAVTRIEGGLVQLALGHGAQHERMLAQVTPRSVKALELQPGTACHAIVKS
+VSVLPS
+>gnl|md5|4276fd81078276b607fce4cf16581984
+MPRRRSSCCPRSLAGRPVPRNTRQPSRGSTLPGSPRRWKSPRPHGRSISEGLARPGKGRT
+FIGRPSPSLNIWPGIAGIMPPLAVGSWVAAVEQTYAADAGMRRDEAIRSATPGAAFPIFA
+AQAHGLASCPMVGFDAERLAREFALAADEIPVLLVAVGHAAEGNRPQKPRLPVAQILTTL
+QQPEVDMPKPSDILLTALAPAVWGSTYIVATELLPGAPPLSVAAIRALPTGLILLLLVRQ
+LPKGDWLWRSFVLGALNFTVFWALLFVAAYRLPGGIAATVGAVQPLIVVFAASAVLGTRI
+RVLSVLAAVMGMAGVALLVLQDGAVPDMPGIAAALGGAFSMAFGTVLTRKWRPPVSALVL
+TAWQLTAGGLLLLPLALLLDPPMPPLDAANAAGMGYLVLFTALTYILWFRGVARLEPAAV
+SSLGFLSPLTAILLGWAILGQALSASQMIGAAVVVASIWLSQRATPSRQVHAR
+>gnl|md5|6803c5e1ab1272ec69688700d3c02e0e
+MKVYLANQPVDFRKGPDSQLSLVRDAGSDPFSFELEILAAHVLGEILKGPRVFADETGLP
+TLAPGTGTVNKAWLWAYARDDSTFGGSGPPMVPYRFEDSRSGECVHRHLGGYGGILQVDG
+YAAYNQLVRKDGGNAGPSLAECWAHSRRRFYELHTAGTVRSPPPRSSGWPISGSSNPRFV
+AKTPTFAPPRGRPSPPPPSPDCSPSGNRPCRASRANRSWPRPSAMPSPGATSSSDS
+>gnl|md5|c63587eb43399c568f1164527fc27358
+PFWATPFALAACTPEAPPPPEPETVSVDPCGAARYSHLIGQTSPTISVPEGQMYRIARED
+RPMTMEMIQDRLTFIVDSRGKLLSVSCS
+>gnl|md5|3f0af0be21624a9da7db4d62141deca1
+MSRHRGAKRCRRYGLLGIISLLSPAYLLSVERWPFHSGPPDHYGRLSSLLDLSVLQSGWL
+LPLHSTSDFRPL
+>gnl|md5|bfd0bd685d4ee94a015cd061816ab82d
+RHIRRDALEASVLNGLKKHLMEPELFREFCAEFTREVNRLRMERGADLEVARRELDKIGR
+QISQIIEAITDGMYHPSMKEKMTKLEARKAEATEKLANADEPPPLLHPNMAALYAQRITE
+LSENLQHEDSRAQAAEILRSLVDQVTLLPEEGELAIVLRGDLGAILRFAAGKKDPDFLSE
+AEALDNLLGQMAVSRKPGRTKAKTSALNATEVSQLSLVAGVGFEPTTFRL
+>gnl|md5|458f535dc6b3a85dbf0b50bf0ffae312
+MMMPTARSMTLPRAMNSLNSLNMGLPFPACCACSGRGCHITLTPCNMRQDMTGNDMTALS
+EFPITRRWPPRRPDVIQLYTLNTPNGIKTSVMLEECGLDYDAHRISIGDPEDQFTPEFLS
+LNPNNKIPAMIDPNGPDGKPMGLFETGAMLVYLGDKTGKFLPASGAARYHTIQWLMWQMG
+GVGPMFGQVGYFHRYKGSEIEDARPRTRYYNEARRLLGVLDRQLEGRDWITGEYSIADMA
+VGPWLRTVRVNYEAEKETGMDGFANVQAYLDRFLARPAVQRGIEVGAE
+>gnl|md5|f53520edd5c9ba7e5bed2fd08cb44ad7
+MPSWRRNWAAATRIRPAVRFWPRSGWTDAAGPMRPDPRPAACAAAPAGAEPRHRCTEEPA
+LTESRKINPWLKAALEFGPLILFFLVFMRFRDQTVSLAGRDYSGFILATLAFVPVLALST
+LALWRLTGRLSPMQVATLVLVVVFGGLSVWLNDPKFFKMKPTIIYLIFAALLGTSLALRR
+NWLELVMSEALPMNAEGWRILTLRMALLFLGLAAANEAVWRLMSETAWVNFKTFGLPAIM
+VAFFIANSRLFERHAQPRDGE
+>gnl|md5|68631421ddc36a3fd81617d12227b1dd
+MILHRPDDDSTARRLEIELRNGPALEAKLVDKIGGAWVELNARHERLVRQEVGARLDAER
+DRKAEVILDLLYEEAAEGRLYTSTQFASNFENRAGLGSQHTIQDRLNVLATKGFIKYQRN
+GALYGLPLVRSRFGYMCVEGMRFGRVEQVDPETGEITGQGLAVLPSHYRCASSGAALEVE
+NPSVWVWPEVVDV
+>gnl|md5|04b3fad17b0d40e02b489a48c451ecc3
+MPVACCRPCGAADGGADLGRSGGEGWLHLFPVLLGAGQARTHEALRRQGRIARRTAGTPR
+PWFIVIITAGLLARRSLPLPAFPMPCGTSGVIRRRLAAYSCGGSAGLAPKGAPASLFAFG
+SDRPERTVMPTYRDDEAISVKMLYWPATLCPREEVSPLTTTGAEDLKQADTVLYMQFFRL
+R
+>gnl|md5|0fab0da718e659ed5fb9c7a5f6a3d18e
+MAEHLPFLAHCSPAPRGLARAWGFGRRPGSNDRGNDTLTHNVLRFASGLWRGQPGRVILY
+TIHYKAFTMTASTTMTIRVSPETKQKLERIAGETRRSKSFLAAEAVSAYVERELEIIDGI
+RRGMADAAAGRVVSHEDAMAEIHAVIDAAEATRAGKA
Modified: SwiftApps/Swift-MapRed/blast/sites.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-23 21:47:41 UTC (rev 7218)
+++ SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 03:06:29 UTC (rev 7219)
@@ -2,10 +2,10 @@
- 0
+ 0.06
10000
- /tmp/swift.work
+ swift.work
local
From ketan at ci.uchicago.edu Thu Oct 24 10:24:34 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 24 Oct 2013 10:24:34 -0500 (CDT)
Subject: [Swift-commit] r7220 - SwiftApps/gocat
Message-ID: <20131024152434.ADB03178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-24 10:24:34 -0500 (Thu, 24 Oct 2013)
New Revision: 7220
Modified:
SwiftApps/gocat/tagwrap.sh
Log:
Modified: SwiftApps/gocat/tagwrap.sh
===================================================================
--- SwiftApps/gocat/tagwrap.sh 2013-10-24 03:06:29 UTC (rev 7219)
+++ SwiftApps/gocat/tagwrap.sh 2013-10-24 15:24:34 UTC (rev 7220)
@@ -1,43 +1,30 @@
#!/bin/bash -x
# Usage: $0 =
-
+# Required: Env variable catloc pointing to the directory containing catalog.py
if [ $# -ne 2 ]
then
- echo "Usage: $0 ="
+ echo "Usage: $0 = = ..."
exit 1
fi
-loc=/scratch/local/ketan/catalog-client/globusonline/catalog/client/examples
catid=48
dsetname=$1
-tagvalpair=$2
+shift
-tagname=`echo $tagvalpair|awk -F= '{print $1}'`
-tagval=`echo $tagvalpair|awk -F= '{print $2}'`
+for tagvalpair in "$@"
+do
+ tagname=`echo $tagvalpair|awk -F= '{print $1}'`
+ tagval=`echo $tagvalpair|awk -F= '{print $2}'`
-# 1. Create dataset
- # a. Check if it already exists
- python $loc/catalog.py -text query_datasets $catid name EQUAL $dsetname
+ python $catloc/catalog.py -text query_datasets $catid name EQUAL $dsetname
+ exprstr="{\"name\":\"$dsetname\"}"
+ retstr=$(python $catloc/catalog.py create_dataset $catid $exprstr)
- exprstr="{\"name\":\"$dsetname\"}"
- echo '==='
- echo $exprstr
- echo '==='
- retstr=$(python $loc/catalog.py create_dataset $catid $exprstr)
+ python $catloc/catalog.py create_annotation_def $catid "$tagname" 'text'
+ dsetid=`echo $retstr |awk -F, '{print $2}'`
- echo '==='
- echo CatalogID, DatasetID: $retstr
- echo '==='
+ python $catloc/catalog.py add_dataset_annotation $catid $dsetid "{\"$tagname\":\"$tagval\"}"
-# 2. Annotate it
- # a. create annotation definition
- python $loc/catalog.py create_annotation_def $catid "$tagname" 'text'
+done
- dsetid=`echo $retstr |awk -F, '{print $2}'`
- echo '==='
- echo "Dataset ID: $dsetid"
- echo '==='
- # b. Add dataset annotation
- python $loc/catalog.py add_dataset_annotation $catid $dsetid "{\"$tagname\":\"$tagval\"}"
-
From ketan at ci.uchicago.edu Thu Oct 24 10:26:07 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 24 Oct 2013 10:26:07 -0500 (CDT)
Subject: [Swift-commit] r7221 - in SwiftApps/gocat: . log
Message-ID: <20131024152607.828D4178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-24 10:26:07 -0500 (Thu, 24 Oct 2013)
New Revision: 7221
Modified:
SwiftApps/gocat/log/GlobusCatalog-log.txt
SwiftApps/gocat/tagwrap.sh
Log:
Modified: SwiftApps/gocat/log/GlobusCatalog-log.txt
===================================================================
--- SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-24 15:24:34 UTC (rev 7220)
+++ SwiftApps/gocat/log/GlobusCatalog-log.txt 2013-10-24 15:26:07 UTC (rev 7221)
@@ -85,3 +85,15 @@
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 87 {"parameter1":"angle49"}
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py get_datasets 48
python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text get_datasets 48
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text query_datasets 48 name EQUAL cofeemug
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"cofeemug"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 color text
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 88 {"color":"white"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text query_datasets 48 name EQUAL cofeemug
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"cofeemug"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 size text
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 90 {"size":"16oz"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py -text query_datasets 48 name EQUAL cofeemug
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_dataset 48 {"name":"cofeemug"}
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py create_annotation_def 48 make text
+python /scratch/local/ketan/catalog-client/globusonline/catalog/client/examples/catalog.py add_dataset_annotation 48 92 {"make":"target"}
Modified: SwiftApps/gocat/tagwrap.sh
===================================================================
--- SwiftApps/gocat/tagwrap.sh 2013-10-24 15:24:34 UTC (rev 7220)
+++ SwiftApps/gocat/tagwrap.sh 2013-10-24 15:26:07 UTC (rev 7221)
@@ -2,7 +2,7 @@
# Usage: $0 =
# Required: Env variable catloc pointing to the directory containing catalog.py
-if [ $# -ne 2 ]
+if [ $# -le 2 ]
then
echo "Usage: $0 = = ..."
exit 1
From ketan at ci.uchicago.edu Thu Oct 24 10:27:28 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 24 Oct 2013 10:27:28 -0500 (CDT)
Subject: [Swift-commit] r7222 - SwiftApps/gocat
Message-ID: <20131024152728.C6869178884@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-24 10:27:28 -0500 (Thu, 24 Oct 2013)
New Revision: 7222
Modified:
SwiftApps/gocat/tagwrap.sh
Log:
Modified: SwiftApps/gocat/tagwrap.sh
===================================================================
--- SwiftApps/gocat/tagwrap.sh 2013-10-24 15:26:07 UTC (rev 7221)
+++ SwiftApps/gocat/tagwrap.sh 2013-10-24 15:27:28 UTC (rev 7222)
@@ -1,6 +1,7 @@
#!/bin/bash -x
# Usage: $0 =
+#e.g. sh tagwrap.sh cofeemug color=white size=16oz material=clay
# Required: Env variable catloc pointing to the directory containing catalog.py
if [ $# -le 2 ]
then
From davidk at ci.uchicago.edu Thu Oct 24 11:25:39 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Thu, 24 Oct 2013 11:25:39 -0500 (CDT)
Subject: [Swift-commit] r7223 - in trunk: . lib
Message-ID: <20131024162539.76559178884@svn.ci.uchicago.edu>
Author: davidk
Date: 2013-10-24 11:25:39 -0500 (Thu, 24 Oct 2013)
New Revision: 7223
Added:
trunk/lib/listcoasterurls.jar
Modified:
trunk/build.xml
Log:
Reliable way to list local network interfaces and generate a list of coaster URLs
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2013-10-24 15:27:28 UTC (rev 7222)
+++ trunk/build.xml 2013-10-24 16:25:39 UTC (rev 7223)
@@ -81,6 +81,8 @@
+
+
Added: trunk/lib/listcoasterurls.jar
===================================================================
(Binary files differ)
Property changes on: trunk/lib/listcoasterurls.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
From ketan at ci.uchicago.edu Thu Oct 24 14:39:33 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 24 Oct 2013 14:39:33 -0500 (CDT)
Subject: [Swift-commit] r7224 - SwiftApps/Swift-MapRed/blast
Message-ID: <20131024193933.4EC729CC83@svn.ci.uchicago.edu>
Author: ketan
Date: 2013-10-24 14:39:33 -0500 (Thu, 24 Oct 2013)
New Revision: 7224
Added:
SwiftApps/Swift-MapRed/blast/blast.c++.swift
Modified:
SwiftApps/Swift-MapRed/blast/blast.swift
SwiftApps/Swift-MapRed/blast/cf
SwiftApps/Swift-MapRed/blast/sites.xml
SwiftApps/Swift-MapRed/blast/tc.data
Log:
blast working
Added: SwiftApps/Swift-MapRed/blast/blast.c++.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.c++.swift (rev 0)
+++ SwiftApps/Swift-MapRed/blast/blast.c++.swift 2013-10-24 19:39:33 UTC (rev 7224)
@@ -0,0 +1,59 @@
+
+type fastaseq;
+type headerfile;
+type indexfile;
+type seqfile;
+type query;
+type output;
+
+type database {
+ headerfile phr;
+ indexfile pin;
+ seqfile psq;
+}
+
+string num_partitions = arg("n", "50");
+
+string program_name = arg("p", "blastp");
+
+fastaseq dbin ;
+
+query query_file ;
+
+string expectation_value = arg("e", "0.1");
+
+output blast_output_file ;
+
+string filter_query_sequence = arg("F", "F");
+
+fastaseq partition[] ;
+
+database formatdbout[] ;
+
+output out[] ;
+
+app (fastaseq out[]) split_database (fastaseq d, string n){
+ fastasplitn filename(d) n;
+}
+
+app (database out) formatdb (fastaseq i){
+ formatdb "-dbtype" "prot" "-in" @filename(i);
+ }
+
+app (output o) blastapp(query i, fastaseq d, string e, string f, database db){
+ blastp "-query" @filename(i) "-out" @filename(o) "-db" @filename(d) "-evalue" e "-html" "-outfmt" "1";
+}
+
+app (output o) blastmerge(output o_frags[]){
+ blastmerge filename(o) filenames(o_frags);
+}
+
+
+partition=split_database(dbin, num_partitions);
+
+foreach part,i in partition {
+ formatdbout[i] = formatdb(part);
+ out[i] = blastapp(query_file, part, expectation_value, filter_query_sequence, formatdbout[i]);
+}
+
+blast_output_file = blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 19:39:33 UTC (rev 7224)
@@ -1,59 +1,55 @@
-
type fastaseq;
type headerfile;
type indexfile;
type seqfile;
-type query;
-type output;
-
-type database {
+type database
+{
headerfile phr;
indexfile pin;
seqfile psq;
}
-string num_partitions = arg("n", "50");
+type query;
+type output;
-string program_name = arg("p", "blastp");
+string num_partitions=@arg("n", "8");
+string program_name=@arg("p", "blastp");
+fastaseq dbin ;
+query query_file ;
+string expectation_value=@arg("e", "0.1");
+output blast_output_file ;
+string filter_query_sequence=@arg("F", "F");
-fastaseq dbin ;
+fastaseq partition[] ;
-query query_file ;
-
-string expectation_value = arg("e", "0.1");
-
-output blast_output_file ;
-
-string filter_query_sequence = arg("F", "F");
-
-fastaseq partition[] ;
-
-database formatdbout[] ;
-
-output out[] ;
-
-app (fastaseq out[]) split_database (fastaseq d, string n){
- fastasplitn filename(d) n;
+app (fastaseq out[]) split_database (fastaseq d, string n)
+{
+ fastasplitn @filename(d) n;
}
-app (database out) formatdb (fastaseq i){
- formatdb "-i" filename(i);
+app (database out) formatdb (fastaseq i)
+{
+ formatdb "-i" @filename(i);
}
-app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db){
- blastall "-p" p "-i" filename(i) "-d" filename(d) "-o" filename(o) "-e" e "-T" "-F" f;
+app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db)
+{
+ blastall "-p" p "-i" @filename(i) "-d" @filename(d) "-o" @filename(o) "-e" e "-T" "-F" f;
}
-app (output o) blastmerge(output o_frags[]){
- blastmerge filename(o) filenames(o_frags);
+app (output o) blastmerge(output o_frags[])
+{
+ blastmerge @filename(o) @filenames(o_frags);
}
-
partition=split_database(dbin, num_partitions);
+database formatdbout[] ;
+output out[] ;
+
foreach part,i in partition {
formatdbout[i] = formatdb(part);
- out[i] = blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
+ out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
}
-blast_output_file = blastmerge(out);
+blast_output_file=blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/cf
===================================================================
--- SwiftApps/Swift-MapRed/blast/cf 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/cf 2013-10-24 19:39:33 UTC (rev 7224)
@@ -3,7 +3,7 @@
file.gc.enabled=false
status.mode=provider
execution.retries=0
-lazy.errors=false
-use.provider.staging=true
+lazy.errors=true
+use.provider.staging=false
provider.staging.pin.swiftfiles=true
use.wrapper.staging=false
Modified: SwiftApps/Swift-MapRed/blast/sites.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 19:39:33 UTC (rev 7224)
@@ -5,7 +5,7 @@
0.06
10000
- swift.work
+ /scratch/local/maheshwari/swift.work
local