From ketan at ci.uchicago.edu Mon Jun 3 00:38:55 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 3 Jun 2013 00:38:55 -0500 (CDT) Subject: [Swift-commit] r6528 - trunk/docs/designs Message-ID: <20130603053855.6CD0F9CC8F@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-03 00:38:54 -0500 (Mon, 03 Jun 2013) New Revision: 6528 Modified: trunk/docs/designs/swiftrun.txt Log: Modified: trunk/docs/designs/swiftrun.txt =================================================================== --- trunk/docs/designs/swiftrun.txt 2013-05-31 16:19:44 UTC (rev 6527) +++ trunk/docs/designs/swiftrun.txt 2013-06-03 05:38:54 UTC (rev 6528) @@ -208,7 +208,7 @@ app.beagle.* = * ----- -NOTE: If the form of line in tc is so generic, it could also be considered a default/generate on the fly. Eg. pick site name from swift commandline and generate a tc internally on-the-fly. +NOTE: If the form of line in tc is so generic, it could also be considered a default/generate on the fly. Eg. pick site name from swift commandline and generate a tc internally on-the-fly. In other words, only if user has a special need to define specific path for a specific app, tc should appear otherwise, it should be auto-generated internally. --Ketan. Sites ----- @@ -220,7 +220,7 @@ $ swift -site midway hello.swift ----- -NOTE: Is the -site switch needed? Could we say "swift -local hello.swift" or "swift -midway,beagle hello.swift" +NOTE: Is the -site switch needed? Could we say "swift -local hello.swift" or "swift -midway,beagle hello.swift" --Ketan. To run on multiple sites, separate site names by a comma. @@ -278,6 +278,8 @@ ----- +NOTE: This came up in one or more past discussions: sites file should be less cluttered. Some suggestions: 1) Default values for some attributes be used and should be only visible if a user explicitly wants a new value for them. eg. lowOverAllocation, highOverAllocation, initialscore. 2) One of the walltime and maxwalltime could be done away with. Ditto with depth/ppn and jobspernode. --Ketan + By default in this template, jobsPerNode is set to 24. However, for our application we would like to set this to 12. To do this, we add this line to the Swift configuration file we are using: @@ -313,10 +315,12 @@ Run directories and logs ------------------------ -Every time Swift runs, it should create a directory called called +Every time Swift runs, it should create a directory called $PWD/.swift/runNNN, where NNN is a numeric value that gets incremented with every run. +NOTE: I think the runNNN directory should be created in a visible directory, not a hidden one. It could be simply named runs. --Ketan. + These run directories contain: * kml and swiftx files From ketan at ci.uchicago.edu Mon Jun 3 23:22:05 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 3 Jun 2013 23:22:05 -0500 (CDT) Subject: [Swift-commit] r6529 - branches/release-0.94/docs/userguide Message-ID: <20130604042205.17B3B9CCBD@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-03 23:22:04 -0500 (Mon, 03 Jun 2013) New Revision: 6529 Modified: branches/release-0.94/docs/userguide/coasters branches/release-0.94/docs/userguide/log-processing Log: fixes for bug 1008 Modified: branches/release-0.94/docs/userguide/coasters =================================================================== --- branches/release-0.94/docs/userguide/coasters 2013-06-03 05:38:54 UTC (rev 6528) +++ branches/release-0.94/docs/userguide/coasters 2013-06-04 04:22:04 UTC (rev 6529) @@ -90,3 +90,16 @@ |remoteMonitorEnabled|If true, show a graphical display of the status of the coaster service |================== + +Submitting to a specific job queue +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +In order to submit to a specific job scheduler queue, the +queue+ parameter of +coasters sites file should be used. For example, submitting to the +normal+ +queue of a PBS scheduler, one would use the following sites line: + +---- +normal +---- + + Modified: branches/release-0.94/docs/userguide/log-processing =================================================================== --- branches/release-0.94/docs/userguide/log-processing 2013-06-03 05:38:54 UTC (rev 6528) +++ branches/release-0.94/docs/userguide/log-processing 2013-06-04 04:22:04 UTC (rev 6529) @@ -112,18 +112,22 @@ the "-resume" option. The .rlog file is only for Swift's internal purpose and not to be interpreted by the user. -Each line in the log file is typically made up of three parts. The first part +Each line in the log file typically consists of three parts. The first part is the timestamp, the second is the type of log message and the third is the message itself. The types of log messages follows the java log4j standard types -of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. This section lists the various -Swift log messages and explains the meaning and likely interpretation of those -messages. Please note that the list is not comprehensive at this time. Also -note that we will ignore the timestamps here. +of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. +//// +This section lists the various Swift log messages and explains the meaning and +likely interpretation of those messages. Note that the list is not +comprehensive at this time. Also note that we will ignore the timestamps here. + . _DEBUG Loader arguments: [-sites.file, sites.xml, -config, cf, -tc.file, tc, postproc-gridftp.swift]_ + Swift commandline arguments . _DEBUG Loader Max heap: 5592449024_ + The java runtime heap size . _DEBUG textfiles BEGIN_ -. _DEBUG Loader kmlversion is_ + A dump of config and source files associated with this run . _DEBUG VDL2ExecutionContext Stack dump_ . _INFO SetFieldValue Set_ . _INFO get__site STARTCOMPOUND thread=0-8 name=get__site_ @@ -142,7 +146,9 @@ . _INFO ThrottleManager mem=113.54 MB, heap=482.88 MB, maxHeap=5.21 GB_ . _INFO ThrottleManager I maxBuffers=512, crtBuffers=0, allowedTransfers=256, active=0, suspended=0_ . _INFO PerformanceDiagnosticInputStream [MEM] Heap total: 482.88 MB, Heap used: 118.58 MB_ +Heap sizes for performance . _INFO vdl:execute END_SUCCESS thread=0-8-0 tr=getsite_ +The job ended successfully . _INFO WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854_ . _ - +//// From ketan at ci.uchicago.edu Mon Jun 3 23:22:38 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 3 Jun 2013 23:22:38 -0500 (CDT) Subject: [Swift-commit] r6530 - trunk/docs/userguide Message-ID: <20130604042238.4D2D59CCBD@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-03 23:22:38 -0500 (Mon, 03 Jun 2013) New Revision: 6530 Modified: trunk/docs/userguide/coasters trunk/docs/userguide/log-processing Log: fixes for bug 1008 Modified: trunk/docs/userguide/coasters =================================================================== --- trunk/docs/userguide/coasters 2013-06-04 04:22:04 UTC (rev 6529) +++ trunk/docs/userguide/coasters 2013-06-04 04:22:38 UTC (rev 6530) @@ -91,21 +91,16 @@ the coaster service |================== +//// Submitting to a specific job queue ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In order to submit to a specific job schedular queue, the +queue+ parameter of coasters sites file should be used. For example, submitting to the +normal+ queue of a PBS schedular, one would use the following sites line: +In order to submit to a specific job scheduler queue, the +queue+ parameter of +coasters sites file should be used. For example, submitting to the +normal+ +queue of a PBS scheduler, one would use the following sites line: ---- normal ---- +//// -Jobs and Coasters Parameters Equation -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -The parameters provided in the coasters specification affect jobs submitted by Swift to the scheduling system. - ----- -Jobs Submitted = slots X jobsPerNode X nodeGranularity X maxNodes ----- - Modified: trunk/docs/userguide/log-processing =================================================================== --- trunk/docs/userguide/log-processing 2013-06-04 04:22:04 UTC (rev 6529) +++ trunk/docs/userguide/log-processing 2013-06-04 04:22:38 UTC (rev 6530) @@ -115,11 +115,13 @@ Each line in the log file typically consists of three parts. The first part is the timestamp, the second is the type of log message and the third is the message itself. The types of log messages follows the java log4j standard types -of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. This section lists the various -Swift log messages and explains the meaning and likely interpretation of those -messages. Note that the list is not comprehensive at this time. Also -note that we will ignore the timestamps here. +of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. +//// +This section lists the various Swift log messages and explains the meaning and +likely interpretation of those messages. Note that the list is not +comprehensive at this time. Also note that we will ignore the timestamps here. + . _DEBUG Loader arguments: [-sites.file, sites.xml, -config, cf, -tc.file, tc, postproc-gridftp.swift]_ Swift commandline arguments . _DEBUG Loader Max heap: 5592449024_ @@ -149,4 +151,4 @@ The job ended successfully . _INFO WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854_ . _ - +//// From ketan at ci.uchicago.edu Fri Jun 7 18:15:10 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Fri, 7 Jun 2013 18:15:10 -0500 (CDT) Subject: [Swift-commit] r6531 - branches/release-0.94/docs/userguide Message-ID: <20130607231510.88F2C9CCA5@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-07 18:15:10 -0500 (Fri, 07 Jun 2013) New Revision: 6531 Modified: branches/release-0.94/docs/userguide/coasters Log: remove queue selection section from coasters Modified: branches/release-0.94/docs/userguide/coasters =================================================================== --- branches/release-0.94/docs/userguide/coasters 2013-06-04 04:22:38 UTC (rev 6530) +++ branches/release-0.94/docs/userguide/coasters 2013-06-07 23:15:10 UTC (rev 6531) @@ -91,15 +91,3 @@ the coaster service |================== -Submitting to a specific job queue -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -In order to submit to a specific job scheduler queue, the +queue+ parameter of -coasters sites file should be used. For example, submitting to the +normal+ -queue of a PBS scheduler, one would use the following sites line: - ----- -normal ----- - - From ketan at ci.uchicago.edu Fri Jun 7 19:15:43 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Fri, 7 Jun 2013 19:15:43 -0500 (CDT) Subject: [Swift-commit] r6532 - branches/release-0.94/docs/userguide Message-ID: <20130608001544.0075C9CCA5@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-07 19:15:43 -0500 (Fri, 07 Jun 2013) New Revision: 6532 Modified: branches/release-0.94/docs/userguide/coasters Log: update coaster parameters and jobs relationship Modified: branches/release-0.94/docs/userguide/coasters =================================================================== --- branches/release-0.94/docs/userguide/coasters 2013-06-07 23:15:10 UTC (rev 6531) +++ branches/release-0.94/docs/userguide/coasters 2013-06-08 00:15:43 UTC (rev 6532) @@ -91,3 +91,35 @@ the coaster service |================== +Coaster config parameters and Job Quantities +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This section presents information on coaster configuration parameters and their effect on application and scheduler jobs submitted by Swift. In order to achieve optimal performance, the number of application tasks must correspond to the total number of coaster workers. Coaster configuration parameters influence both application tasks and the LRM (Local Resource Manager) jobs that are submitted by Swift. Specifically, the following quantities are influenced by coasters configuration parameters: + +* Number of application tasks Swift will pack in one "wave" to be executed in parallel depends on the +foreach.max.threads+ and the +throttle+ parameters. Furthermore, the number of +foreach+ loops in a Swift script influences the aggregate +foreach.max.threads+. The relation between application tasks and the above mentioned quantities could be explained as follows: +---- +app_tasks = min{nforeach X foreach.max.threads), (throttle X 100 +1)} +---- + +Where +nforeach+ is the number of independent foreach loops appearing in a Swift script. + +* Number of jobs Swift will submit via the LRM interface is determined by the +slots+ configuration parameter in sites file. + +---- +LRM jobs = slots +---- + +* Size of each LRM job in terms of number of compute nodes per job is determined by the +maxnodes+ and +nodegranularity+ parameters. LRM jobs submitted by Swift will be of size spread between +nodegranularity+ and +maxnodes+ values. + +---- +nodegranularity <= LRM job size <= maxnodes +---- + +* Number of coaster workers to be run per LRM job on a target cluster is determined by the +jobspernode+ parameter. + +Considering the above factors, the following paramter expressions must match in order for a Swift run to be optimal: + +---- +min{nforeach X foreach.max.threads), (throttle X 100 +1)} ~= + slots X avg(nodegranularity,maxnodes) X jobspernode +---- From davidk at ci.uchicago.edu Tue Jun 11 06:56:22 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Tue, 11 Jun 2013 06:56:22 -0500 (CDT) Subject: [Swift-commit] r6533 - branches/release-0.94/docs/siteguide Message-ID: <20130611115622.D8F819CCB6@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-11 06:56:21 -0500 (Tue, 11 Jun 2013) New Revision: 6533 Added: branches/release-0.94/docs/siteguide/ssh Modified: branches/release-0.94/docs/siteguide/siteguide.txt Log: SSH example Modified: branches/release-0.94/docs/siteguide/siteguide.txt =================================================================== --- branches/release-0.94/docs/siteguide/siteguide.txt 2013-06-08 00:15:43 UTC (rev 6532) +++ branches/release-0.94/docs/siteguide/siteguide.txt 2013-06-11 11:56:21 UTC (rev 6533) @@ -26,6 +26,8 @@ include::midway[] +include::ssh[] + include::stampede[] include::uc3[] Added: branches/release-0.94/docs/siteguide/ssh =================================================================== --- branches/release-0.94/docs/siteguide/ssh (rev 0) +++ branches/release-0.94/docs/siteguide/ssh 2013-06-11 11:56:21 UTC (rev 6533) @@ -0,0 +1,91 @@ +SSH +--- +This section describes how to use the SSH provider to connect to remote sites +and to handle data transfer. + +Generate a unique SSH key +~~~~~~~~~~~~~~~~~~~~~~~~~ +It is recommended that you create a new SSH key exclusively for this purpose. +In order to avoid being prompted for passwords/passphrases, your SSH passphrase +will be stored in a read protected file. Instead of using your real SSH key and +passphrase for this purpose, create a new one. Run this command on the machine +where you will be running Swift: + +----- +ssh-keygen -t dsa -f $HOME/.ssh/id_dsa-swift +----- + +You will be prompted to create a passphrase. This will create two files: +$HOME/.ssh/id_dsa-swift and $HOME/.ssh/id_dsa-swift.pub. + +Add your public key to the remote host +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +On the remote host where you will be running, edit or create the file +$HOME/.ssh/authorized_keys. Paste in the contents of the newly created +$HOME/.ssh/id_dsa-swift.pub from the previous step to the end of the file. + +Verify your new key works +~~~~~~~~~~~~~~~~~~~~~~~~~ +From the host where you will be running Swift, run the following +command to verify your keys are working: + +----- +ssh -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu +----- + +You should be able to connect without being asked for a password or passphrase. + +Create auth.defaults +~~~~~~~~~~~~~~~~~~~~ +Once you verify your keys are working, create a file called +$HOME/.ssh/auth.defaults by running the following commands + +----- +touch $HOME/.ssh/auth.defaults +chmod 600 $HOME/.ssh/auth.defaults +----- + +Next, edit $HOME/.ssh/auth.defaults and add the following lines: +------ +login.remotehost.edu.type=key +login.remotehost.edu.username=your_remote_username +login.remotehost.edu.key=/your/home/.ssh/id_dsa-swift +login.remotehost.edu.passphrase=your_passphrase +----- + +Replace the values for "your_remote_username", "your_passphrase", and the path +to the private key you generated. + +Create a sites.xml file +~~~~~~~~~~~~~~~~~~~~~~~ +Here is an example sites.xml file that will allow you to connect and transfer +data to a remote host: + +----- + + + + + 0 + 10000 + /path/to/remote/workdirectory + + +----- + +NOTE: This example will run work directly on login.remotehost.edu. In most +cases you will not want to do this. You'll like want to modify your sites.xml +to use a remote scheduler, by setting jobmanager to ssh:pbs or ssh:slurm, for +example. This usually requires also setting things like queues and walltimes. +This example is provided for simplicity and testing. + +Setting your properties +~~~~~~~~~~~~~~~~~~~~~~~ +Since you want to data transfer via ssh, you'll want to verify that you're not +using any other file transfer mechanisms. Make sure you have the following +swift properties defined in your configuration file: + +----- +use.provider.staging=false +use.wrapper.staging=false +----- From davidk at ci.uchicago.edu Tue Jun 11 07:27:37 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Tue, 11 Jun 2013 07:27:37 -0500 (CDT) Subject: [Swift-commit] r6534 - branches/release-0.94/docs/siteguide Message-ID: <20130611122737.CF3D09CCB6@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-11 07:27:37 -0500 (Tue, 11 Jun 2013) New Revision: 6534 Modified: branches/release-0.94/docs/siteguide/ssh Log: Some minor updates for formatting Modified: branches/release-0.94/docs/siteguide/ssh =================================================================== --- branches/release-0.94/docs/siteguide/ssh 2013-06-11 11:56:21 UTC (rev 6533) +++ branches/release-0.94/docs/siteguide/ssh 2013-06-11 12:27:37 UTC (rev 6534) @@ -7,8 +7,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~ It is recommended that you create a new SSH key exclusively for this purpose. In order to avoid being prompted for passwords/passphrases, your SSH passphrase -will be stored in a read protected file. Instead of using your real SSH key and -passphrase for this purpose, create a new one. Run this command on the machine +will be stored in a read protected file. Run this command on the machine where you will be running Swift: ----- @@ -37,12 +36,12 @@ Create auth.defaults ~~~~~~~~~~~~~~~~~~~~ -Once you verify your keys are working, create a file called -$HOME/.ssh/auth.defaults by running the following commands +Create a file called $HOME/.ssh/auth.defaults on the host where you are running Swift. +Use the following commands to create this file: ----- -touch $HOME/.ssh/auth.defaults -chmod 600 $HOME/.ssh/auth.defaults +$ touch $HOME/.ssh/auth.defaults +$ chmod 600 $HOME/.ssh/auth.defaults ----- Next, edit $HOME/.ssh/auth.defaults and add the following lines: @@ -53,8 +52,9 @@ login.remotehost.edu.passphrase=your_passphrase ----- -Replace the values for "your_remote_username", "your_passphrase", and the path -to the private key you generated. +Replace login.remotehost.edu with the hostname you want to use, replace the +values for "your_remote_username", "your_passphrase", and set the correct path +of private key you generated. Create a sites.xml file ~~~~~~~~~~~~~~~~~~~~~~~ @@ -73,7 +73,7 @@ ----- -NOTE: This example will run work directly on login.remotehost.edu. In most +NOTE: This example will run work directly on login.remotehost.edu. In many cases you will not want to do this. You'll like want to modify your sites.xml to use a remote scheduler, by setting jobmanager to ssh:pbs or ssh:slurm, for example. This usually requires also setting things like queues and walltimes. From swift at ci.uchicago.edu Tue Jun 11 15:20:03 2013 From: swift at ci.uchicago.edu (swift at ci.uchicago.edu) Date: Tue, 11 Jun 2013 15:20:03 -0500 (CDT) Subject: [Swift-commit] cog r3671 Message-ID: <20130611202003.B0A2E8D00087@bridled.ci.uchicago.edu> ------------------------------------------------------------------------ r3671 | davidkelly999 | 2013-06-11 15:17:32 -0500 (Tue, 11 Jun 2013) | 2 lines Condor leave in queue fix for trunk ------------------------------------------------------------------------ Index: modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java =================================================================== --- modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java (revision 3670) +++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java (working copy) @@ -150,7 +150,7 @@ } wr.write("notification = Never\n"); - wr.write("leave_in_queue = TRUE\n"); + wr.write("leave_in_queue = FALSE\n"); wr.write("queue\n"); wr.close(); } From wilde at ci.uchicago.edu Tue Jun 11 15:25:17 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Tue, 11 Jun 2013 15:25:17 -0500 (CDT) Subject: [Swift-commit] r6535 - SwiftTutorials Message-ID: <20130611202517.750D49CCC0@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-11 15:25:17 -0500 (Tue, 11 Jun 2013) New Revision: 6535 Added: SwiftTutorials/OHBM_2013-06-16/ Log: Initial dir for new tutorial. From davidk at ci.uchicago.edu Tue Jun 11 15:56:11 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Tue, 11 Jun 2013 15:56:11 -0500 (CDT) Subject: [Swift-commit] r6536 - branches/release-0.94/docs/quickstart Message-ID: <20130611205611.5A4619CCB6@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-11 15:56:11 -0500 (Tue, 11 Jun 2013) New Revision: 6536 Modified: branches/release-0.94/docs/quickstart/quickstart.txt Log: Updates to checkout procedure Modified: branches/release-0.94/docs/quickstart/quickstart.txt =================================================================== --- branches/release-0.94/docs/quickstart/quickstart.txt 2013-06-11 20:25:17 UTC (rev 6535) +++ branches/release-0.94/docs/quickstart/quickstart.txt 2013-06-11 20:56:11 UTC (rev 6536) @@ -46,13 +46,13 @@ and http://www.oracle.com/technetwork/java/javase/downloads/index.html[Java JDK]. Once built, the dist/swift-svn directory will contain your build. -To download and build Swift 0.93, follow these instructions: +To download and build Swift 0.94, follow these instructions: ----- -$ mkdir swift-0.93 -$ cd swift-0.93 -$ svn co https://cogkit.svn.sourceforge.net/svnroot/cogkit/branches/4.1.9/src/cog +$ mkdir swift-0.94 +$ cd swift-0.94 +$ svn co https://svn.code.sf.net/p/cogkit/svn/branches/4.1.10/src/cog $ cd cog/modules -$ svn co https://svn.ci.uchicago.edu/svn/vdl2/branches/release-0.93 swift +$ svn co https://svn.ci.uchicago.edu/svn/vdl2/branches/release-0.94 swift $ cd swift $ ant redist ----- @@ -62,9 +62,9 @@ Once Swift is installed, it is useful to add the swift binary to your PATH environment variable. To do this, first determine where the Swift bin directory is located. If you installed Swift from a binary release, it will -be in the swift-0.93/bin directory where you installed it. If you followed +be in the swift-0.94/bin directory where you installed it. If you followed the instructions above for installing Swift from a source repository, it -will be located in swift-0.93/cog/modules/swift/dist/swift-svn/bin. +will be located in swift-0.94/cog/modules/swift/dist/swift-svn/bin. Add the following line to the bottom of ~/.bashrc: @@ -98,4 +98,4 @@ Swift script! More documentation on how to run Swift can be found at -http://www.ci.uchicago.edu/swift/docs/index.php, +http://www.ci.uchicago.edu/swift/docs/index.php. From wilde at ci.uchicago.edu Tue Jun 11 17:23:37 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Tue, 11 Jun 2013 17:23:37 -0500 (CDT) Subject: [Swift-commit] r6537 - in SwiftTutorials/OHBM_2013-06-16: . data original Message-ID: <20130611222337.550F59CCB6@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-11 17:23:37 -0500 (Tue, 11 Jun 2013) New Revision: 6537 Added: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/align.sh SwiftTutorials/OHBM_2013-06-16/apps SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere SwiftTutorials/OHBM_2013-06-16/clean.sh SwiftTutorials/OHBM_2013-06-16/data/ SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img SwiftTutorials/OHBM_2013-06-16/data/reference.hdr SwiftTutorials/OHBM_2013-06-16/data/reference.img SwiftTutorials/OHBM_2013-06-16/genatlas.swift SwiftTutorials/OHBM_2013-06-16/original/ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh SwiftTutorials/OHBM_2013-06-16/output/ SwiftTutorials/OHBM_2013-06-16/sites.xml SwiftTutorials/OHBM_2013-06-16/swift.properties SwiftTutorials/OHBM_2013-06-16/volmapper SwiftTutorials/OHBM_2013-06-16/work/ Log: Initial revision. Added: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,24 @@ + +fMRI Data Processing demo for OHBM 2013 + +Setup + + # Get the scripts from svn + + svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftTutorials/OHBM_2013-06-16 + cd OHBM_2013-06-16 + + # Set default swift.properties in $HOME/.swift. Points to "." for apps (tc) and sites.xml + + mkdir -p ~/.swift + cp ~/.swift/swift.properties ~/.swift/save.swift.properties # If needed, as needed. + cp swift.properties ~/.swift + + # Get swift + + module load swift + +To run: + + swift genatlas.swift + Added: SwiftTutorials/OHBM_2013-06-16/align.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/align.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/align.sh 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,52 @@ +#!/bin/sh + +AIR5=/home/wilde/software/AIR5.3.0 +fsl=/project/wilde/software/fsl-5.0.4/fsl + +# Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out) + +ref=$1 +anat=$2 +resliced=$3 + +time $AIR5/bin/alignlinear $ref $anat init.warp \ + -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 +time $AIR5/bin/align_warp $ref $anat refined.warp \ + -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01 +time $AIR5/bin/reslice refined.warp $resliced -a $anat + +exit + + + + + + + +clean=y + +if [ $clean = y ]; then + rm *warp atlas* resliced* +fi + + + +if true; then + + warp 1 + warp 2 + warp 3 + warp 4 + + time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img +fi + +export FSLOUTPUTTYPE=NIFTI + +time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm +time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm +time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm + +time convert atlas-x.pgm atlas-x.gif +time convert atlas-y.pgm atlas-y.gif +time convert atlas-z.pgm atlas-z.gif Property changes on: SwiftTutorials/OHBM_2013-06-16/align.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/OHBM_2013-06-16/apps =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/apps 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,4 @@ +localhost sh /bin/sh +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Added: SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,4 @@ +westmere sh /bin/sh +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Added: SwiftTutorials/OHBM_2013-06-16/clean.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/clean.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/clean.sh 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,4 @@ +#! /bin/sh + +rm -rf _concurrent work/* output/* *.log *.rlog *.d *.kml *.swiftx + Property changes on: SwiftTutorials/OHBM_2013-06-16/clean.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/reference.hdr =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/reference.hdr ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/data/reference.img =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/data/reference.img ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/OHBM_2013-06-16/genatlas.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/genatlas.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,77 @@ +type file; + +type Volume { + file header; + file image; +}; + +app (Volume alignedVol) align (file alignScript, Volume reference, Volume input) +{ + sh @alignScript @filename(reference.image) @filename(input.image) @filename(alignedVol.image); +} + +app (Volume atlas) softmean (Volume v[]) +{ + softmean @filename(atlas.header) "y" "null" imageNames(v); +} + +app (Volume atlas) softmeanORIG (Volume v[]) +{ + softmean @filename(atlas.header) "y" "null" @filenames(v); +} + +app (file pgm) slicer (Volume v, string axis) +{ + slicer @filename(v.header) @strcat("-",axis) .5 @filename(pgm); +} + +app (file o) convert (file i) +{ + convert @i @o; +} + +Volume referenceVolume; +Volume inputVolumes []; +Volume outputVolumes[]; + +file alignScript<"align.sh">; + +foreach v, i in inputVolumes { + Volume aligned; + aligned = align(alignScript,referenceVolume, v); + outputVolumes[i] = aligned; +} + +Volume atlasVolume; +atlasVolume = softmean(outputVolumes); + +file xSlice<"output/atlas-x.png">; +file ySlice<"output/atlas-y.png">; +file zSlice<"output/atlas-z.png">; + +xSlice = convert(slicer(atlasVolume,"x")); +ySlice = convert(slicer(atlasVolume,"y")); +zSlice = convert(slicer(atlasVolume,"z")); + + + + + + +string testNames[] = imageNames(outputVolumes); +foreach n, i in testNames { + tracef("testNames[%i] = %s\n", i, n); +} + + +(string onames[]) imageNames (Volume v[]) +{ + string names[] = @filenames(v); + foreach n, i in names { + if ( i %% 2 == 0) { + // tracef("n[%i] = %s\n", i, n); + onames[i] = n; + } + } +} + Added: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,30 @@ +#!/bin/sh + +AIR5=$HOME/software/AIR5.3.0 +fsl=/project/wilde/software/fsl-5.0.4/fsl + +if true; then + +#time $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -j # -q + +time $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -s 1024 2 2 -c .01 -f out # -q -s 1024 2 2 -c .01 + + +time $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/reslice warp1.warp resliced1 +time $AIR5/bin/reslice warp2.warp resliced2 +time $AIR5/bin/reslice warp3.warp resliced3 +time $AIR5/bin/reslice warp4.warp resliced4 +time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img +fi + +export FSLOUTPUTTYPE=NIFTI + +time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm +time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm +time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm +time convert atlas-x.pgm atlas-x.gif +time convert atlas-y.pgm atlas-y.gif +time convert atlas-z.pgm atlas-z.gif Property changes on: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,40 @@ +#!/bin/sh + +AIR5=$HOME/software/AIR5.3.0 + + +clean=y + +if [ $clean = y ]; then + rm *warp atlas* resliced* +fi + +warp() +{ +time $AIR5/bin/alignlinear reference.img anatomy$1.img initwarp$1.warp -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 +time $AIR5/bin/align_warp reference.img anatomy$1.img warp$1.warp -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -s 1024 2 2 -c .01 -f initwarp$1.warp # -q -s 1024 2 2 -c .01 +} + +if true; then + +warp 1 +warp 2 +warp 3 +warp 4 + +time $AIR5/bin/reslice warp1.warp resliced1 -a anatomy1 +time $AIR5/bin/reslice warp2.warp resliced2 -a anatomy2 +time $AIR5/bin/reslice warp3.warp resliced3 -a anatomy3 +time $AIR5/bin/reslice warp4.warp resliced4 -a anatomy4 + +time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img +fi + +export FSLOUTPUTTYPE=NIFTI + +time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm +time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm +time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm +time convert atlas-x.pgm atlas-x.gif +time convert atlas-y.pgm atlas-y.gif +time convert atlas-z.pgm atlas-z.gif Property changes on: SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/OHBM_2013-06-16/sites.xml =================================================================== --- SwiftTutorials/OHBM_2013-06-16/sites.xml (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,41 @@ + + + + + 10000 + + /scratch/midway/{env.USER}/swiftwork + .03 + + + + + + + westmere + 12 + + + + 1 + 1 + 1 + 12 + .11 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + Added: SwiftTutorials/OHBM_2013-06-16/swift.properties =================================================================== --- SwiftTutorials/OHBM_2013-06-16/swift.properties (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,14 @@ + +sites.file=sites.xml +tc.file=apps + +status.mode=provider +use.provider.staging=false +use.wrapper.staging=false +wrapperlog.always.transfer=true +execution.retries=0 +lazy.errors=false +provider.staging.pin.swiftfiles=false +sitedir.keep=true +file.gc.enabled=false +#tcp.port.range=50000,51000 Added: SwiftTutorials/OHBM_2013-06-16/volmapper =================================================================== --- SwiftTutorials/OHBM_2013-06-16/volmapper (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/volmapper 2013-06-11 22:23:37 UTC (rev 6537) @@ -0,0 +1,29 @@ +#! /bin/sh + +case $1 in + + -prefix) + + prefix=$2 + names=$(echo ${prefix}*.img) + + for n in $names; do + name=$(echo $n | sed -e 's,\..*,,') + num=$(echo $n | sed -e 's,\..*,,' -e "s,${prefix},,") + echo "[$num].header $name.hdr" + echo "[$num].image $name.img" + done + ;; + + -name) + + echo 'header' $2.hdr + echo 'image ' $2.img + ;; + + *) + echo error in external mapper $0 + ;; +esac + + Property changes on: SwiftTutorials/OHBM_2013-06-16/volmapper ___________________________________________________________________ Added: svn:executable + * From wilde at ci.uchicago.edu Tue Jun 11 17:25:47 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Tue, 11 Jun 2013 17:25:47 -0500 (CDT) Subject: [Swift-commit] r6538 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130611222547.ABCB59CCB6@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-11 17:25:47 -0500 (Tue, 11 Jun 2013) New Revision: 6538 Added: SwiftTutorials/OHBM_2013-06-16/apps.midway Removed: SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere Modified: SwiftTutorials/OHBM_2013-06-16/README Log: Add instructions and minor tweak for miway execution. Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-11 22:23:37 UTC (rev 6537) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-11 22:25:47 UTC (rev 6538) @@ -20,5 +20,10 @@ To run: + # On localhost: + swift genatlas.swift + # With most parallel work on midway westmere parition: + + swift -tc.file apps.midway genatlas.swift Copied: SwiftTutorials/OHBM_2013-06-16/apps.midway (from rev 6537, SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere) =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.midway (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/apps.midway 2013-06-11 22:25:47 UTC (rev 6538) @@ -0,0 +1,4 @@ +westmere sh /bin/sh +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Deleted: SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere 2013-06-11 22:23:37 UTC (rev 6537) +++ SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere 2013-06-11 22:25:47 UTC (rev 6538) @@ -1,4 +0,0 @@ -westmere sh /bin/sh -localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean -localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI -localhost convert convert From wilde at ci.uchicago.edu Tue Jun 11 17:50:42 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Tue, 11 Jun 2013 17:50:42 -0500 (CDT) Subject: [Swift-commit] r6539 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130611225042.DED6D9CCC0@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-11 17:50:42 -0500 (Tue, 11 Jun 2013) New Revision: 6539 Modified: SwiftTutorials/OHBM_2013-06-16/README Log: Update README Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-11 22:25:47 UTC (rev 6538) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-11 22:50:42 UTC (rev 6539) @@ -27,3 +27,29 @@ # With most parallel work on midway westmere parition: swift -tc.file apps.midway genatlas.swift + +The output files of the workflow are placed under output/, +intermediate files under work/. + +The 3 final png output files (a "slice" of the final atlas) should +look like this: + + http://www.ci.uchicago.edu/~wilde/atlas-x.png + http://www.ci.uchicago.edu/~wilde/atlas-y.png + http://www.ci.uchicago.edu/~wilde/atlas-z.png + +Notes: + + The "aligin" initial stage runs 3 AIR tools under as a single shell + script, to reduce staging between these steps. + +TODO + + Show the workflow with the 3 AIR tools expanded as separate workflow + steps, and as a Swift procedure. + + Run on other sites and Multisite + + Add performance monitoring and plotting + + From wilde at ci.uchicago.edu Thu Jun 13 08:02:23 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Thu, 13 Jun 2013 08:02:23 -0500 (CDT) Subject: [Swift-commit] r6540 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130613130223.DDAE09CCA7@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-13 08:02:22 -0500 (Thu, 13 Jun 2013) New Revision: 6540 Added: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx Log: Initial revision of OHBM talk. Added: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx =================================================================== (Binary files differ) Property changes on: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From wilde at ci.uchicago.edu Thu Jun 13 08:43:03 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Thu, 13 Jun 2013 08:43:03 -0500 (CDT) Subject: [Swift-commit] r6541 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130613134303.4466D9CCA7@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-13 08:43:03 -0500 (Thu, 13 Jun 2013) New Revision: 6541 Modified: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx Log: Update title/speaker and fix formats in OHBM talk. Modified: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx =================================================================== (Binary files differ) From wilde at ci.uchicago.edu Thu Jun 13 10:13:05 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Thu, 13 Jun 2013 10:13:05 -0500 (CDT) Subject: [Swift-commit] r6542 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130613151305.AA9109CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-13 10:13:05 -0500 (Thu, 13 Jun 2013) New Revision: 6542 Added: SwiftTutorials/OHBM_2013-06-16/TODO SwiftTutorials/OHBM_2013-06-16/apps.beagle SwiftTutorials/OHBM_2013-06-16/makedata.sh Modified: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/align.sh SwiftTutorials/OHBM_2013-06-16/apps SwiftTutorials/OHBM_2013-06-16/genatlas.swift SwiftTutorials/OHBM_2013-06-16/sites.xml SwiftTutorials/OHBM_2013-06-16/swift.properties Log: Misc changes; updated README; add beagle and midway site defs; adjust properties. Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-13 15:13:05 UTC (rev 6542) @@ -18,16 +18,30 @@ module load swift +To generate test data directories: + + ./makedata data_100 100 # create 100 anatomical image volumes in directory data_100 + To run: # On localhost: - swift genatlas.swift + swift genatlas.swift # processes data/ directory by default + swift genatlas.swift -d=data_100 # process data_100/ directory # With most parallel work on midway westmere parition: swift -tc.file apps.midway genatlas.swift + # Choices for -tc.file are: + + apps # default, runs on localhost + apps.beagle # on beagle, 8 nodes + apps.midway # on midway westmere, 1 node + apps.amazon # on Amazon EC2 - needs start-coaster-service, see below + apps.UC3 # submits to UC3, needs apps to be sent. + + The output files of the workflow are placed under output/, intermediate files under work/. Added: SwiftTutorials/OHBM_2013-06-16/TODO =================================================================== --- SwiftTutorials/OHBM_2013-06-16/TODO (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/TODO 2013-06-13 15:13:05 UTC (rev 6542) @@ -0,0 +1,5 @@ +timeseries: + +/scratch/midway/wilde/ds107/ds107/sub001/model/model001 + + Modified: SwiftTutorials/OHBM_2013-06-16/align.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/align.sh 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/align.sh 2013-06-13 15:13:05 UTC (rev 6542) @@ -1,7 +1,6 @@ #!/bin/sh -AIR5=/home/wilde/software/AIR5.3.0 -fsl=/project/wilde/software/fsl-5.0.4/fsl +#AIR5=/home/wilde/software/AIR5.3.0 # Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out) @@ -23,6 +22,8 @@ +fsl=/project/wilde/software/fsl-5.0.4/fsl + clean=y if [ $clean = y ]; then Modified: SwiftTutorials/OHBM_2013-06-16/apps =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/apps 2013-06-13 15:13:05 UTC (rev 6542) @@ -1,4 +1,5 @@ -localhost sh /bin/sh +localhost sh /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0 +#localhost sh /bin/sh localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI localhost convert convert Added: SwiftTutorials/OHBM_2013-06-16/apps.beagle =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.beagle (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/apps.beagle 2013-06-13 15:13:05 UTC (rev 6542) @@ -0,0 +1,4 @@ +beagle sh /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0 +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-13 15:13:05 UTC (rev 6542) @@ -5,18 +5,13 @@ file image; }; -app (Volume alignedVol) align (file alignScript, Volume reference, Volume input) +app (Volume alignedVol) align (file script, Volume reference, Volume input) { - sh @alignScript @filename(reference.image) @filename(input.image) @filename(alignedVol.image); + sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); } app (Volume atlas) softmean (Volume v[]) { - softmean @filename(atlas.header) "y" "null" imageNames(v); -} - -app (Volume atlas) softmeanORIG (Volume v[]) -{ softmean @filename(atlas.header) "y" "null" @filenames(v); } @@ -30,12 +25,13 @@ convert @i @o; } +string dataDir = @arg("d","data"); +file alignScript<"align.sh">; + Volume referenceVolume; -Volume inputVolumes []; +Volume inputVolumes []; Volume outputVolumes[]; -file alignScript<"align.sh">; - foreach v, i in inputVolumes { Volume aligned; aligned = align(alignScript,referenceVolume, v); @@ -54,16 +50,19 @@ zSlice = convert(slicer(atlasVolume,"z")); +/******* The following code to be removed - - - string testNames[] = imageNames(outputVolumes); foreach n, i in testNames { tracef("testNames[%i] = %s\n", i, n); } +app (Volume atlas) softmeanALT (Volume v[]) # A better version +{ + softmean @filename(atlas.header) "y" "null" imageNames(v); # puts only the .img on command line +} + (string onames[]) imageNames (Volume v[]) { string names[] = @filenames(v); @@ -75,3 +74,4 @@ } } +*******/ \ No newline at end of file Added: SwiftTutorials/OHBM_2013-06-16/makedata.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/makedata.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/makedata.sh 2013-06-13 15:13:05 UTC (rev 6542) @@ -0,0 +1,24 @@ +#! /bin/sh + +datadir=${1:-data_10} +nfiles=${2:-10} + +rm -rf $datadir +mkdir $datadir +cp data/anatomy1.{hdr,img} $datadir + +n=0 +( cd $datadir + mv anatomy1.hdr s.hdr + mv anatomy1.img s.img + for id in $(seq -w 000 999); do + n=$((n+1)) + if [ $n -gt $nfiles ]; then + break; + else + ln s.img anatomy$id.img + ln s.hdr anatomy$id.hdr + fi + done + rm s.{img,hdr} +) Property changes on: SwiftTutorials/OHBM_2013-06-16/makedata.sh ___________________________________________________________________ Added: svn:executable + * Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml =================================================================== --- SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-13 15:13:05 UTC (rev 6542) @@ -5,6 +5,7 @@ 10000 /scratch/midway/{env.USER}/swiftwork + file .03 @@ -38,4 +39,24 @@ 10000 + + + 24 + 100 + 100 + pbs.aprun;pbs.mpp;depth=24 + + 3600 + 00:05:00 + /lustre/beagle/{env.USER}/swiftwork + 20 + 1 + 1 + 4.80 + 10000 + /tmp/{env.USER}/swiftwork + + Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties =================================================================== --- SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-13 13:43:03 UTC (rev 6541) +++ SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-13 15:13:05 UTC (rev 6542) @@ -3,12 +3,12 @@ tc.file=apps status.mode=provider -use.provider.staging=false +use.provider.staging=true use.wrapper.staging=false wrapperlog.always.transfer=true execution.retries=0 lazy.errors=false -provider.staging.pin.swiftfiles=false +provider.staging.pin.swiftfiles=true sitedir.keep=true file.gc.enabled=false #tcp.port.range=50000,51000 From ketan at ci.uchicago.edu Thu Jun 13 11:31:22 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 11:31:22 -0500 (CDT) Subject: [Swift-commit] r6543 - trunk/docs/siteguide Message-ID: <20130613163122.A2E3C9CCA7@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 11:31:22 -0500 (Thu, 13 Jun 2013) New Revision: 6543 Added: trunk/docs/siteguide/ec2 Log: first cut for running Swift on EC2 resources Added: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 (rev 0) +++ trunk/docs/siteguide/ec2 2013-06-13 16:31:22 UTC (rev 6543) @@ -0,0 +1,116 @@ +Amazon EC2 Cloud +---------------- +Amazon EC2 offers virtualized resources on demand from its cloud data centers. +This section describes how to use Swift to run applications on EC2 resources. +More information on EC2 can be found link:https://aws.amazon.com/ec2[here]. + +Getting Access +~~~~~~~~~~~~~~ + +==Users with EC2 Allocation + +If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources. + +Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000. + +Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows: +---- +export AWS_ACCESS_KEY= +export AWS_SECRET_KEY= +---- + +A public AMI for Swift user is available with id: ami-332e585a. + +Create instances from the above AMI as follows: + +---- +ec2run -k -g -n ami-332e585a +---- + +==Users without EC2 Allocation + +Configuring coaster-service.conf +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +To run on EC2, you will need a file called coaster-service.conf. +This file contains many options to control how things run. Here is +an example of a working coaster-service.conf for EC2. + +----- +# Where to copy worker.pl on the remote machine for sites.xml +export WORKER_LOCATION=/tmp + +# How to launch workers: local, ssh, cobalt +export WORKER_MODE=ssh + +# Do all the worker nodes you're using have a shared filesystem? (yes/no) +export SHARED_FILESYSTEM=no + +# Username to use on worker nodes +export WORKER_USERNAME=root + +# Enable SSH tunneling? (yes/no) +export SSH_TUNNELING=yes + +# Directory to keep log files, relative to working directory when launching start-coaster-service +export LOG_DIR=logs + +# Swift information for creating sites.xml +export WORK=/tmp + +# Application locations for tc.data +#app convert=/usr/bin/convert +----- + +Add a list of any applications you want to run in the format "#app myapp=/path/to/app". + +Starting the Coaster Service Script +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Now that everything is configured, change to the location of the coaster-service.conf file +and run this command to start the coaster service: + +----- +$ start-coaster-service +----- + +This command will start the VMs, start the required processes on the worker nodes, +and generate Swift configuration files for you to use. The configuration files +will be generated in your current directory. These files are sites.xml, tc.data, +and cf. + +Running Swift +~~~~~~~~~~~~~ +Now that you have all of your configuration files generated, run the following command: + +----- +$ swift -sites.file sites.xml -tc.file tc.data -config cf +----- + +If you like to create a custom tc and/or cf file for repeated use, rename it to something other +than tc.data/cf to prevent it from being overwritten. The sites.xml however will need to be +regenerated every time you start the coaster service. If you need to repeatedly modify some +sites.xml options, you may edit the template in Swift's etc/sites/persistent-coasters. You +may also create your own custom tc files with the hostname of persistent-coasters. More +information about this can be found in the Swift userguide at +http://www.ci.uchicago.edu/swift/guides/trunk/userguide/userguide.html. + +Stopping the Coaster Service Script +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +To stop the coaster service, run the following command: +----- +$ stop-coaster-service +----- + +This will kill the coaster service, kill the worker scripts on remote systems. + +Terminate the virtual machines that were created for this work as follows: + +---- +ec2din|grep running|awk '{print $2}'|xargs ec2kill +---- + +More Help +~~~~~~~~~ +The best place for additional help is the Swift user mailing list. You can subscribe to this list at +http://mail.ci.uchicago.edu/mailman/listinfo/swift-user. When submitting information, send +your sites.xml file, your tc.data, and any error messages you run into. + From ketan at ci.uchicago.edu Thu Jun 13 11:37:12 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 11:37:12 -0500 (CDT) Subject: [Swift-commit] r6544 - trunk/docs/siteguide Message-ID: <20130613163712.B081F9CCA7@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 11:37:12 -0500 (Thu, 13 Jun 2013) New Revision: 6544 Modified: trunk/docs/siteguide/ec2 Log: updates Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 16:31:22 UTC (rev 6543) +++ trunk/docs/siteguide/ec2 2013-06-13 16:37:12 UTC (rev 6544) @@ -36,31 +36,46 @@ an example of a working coaster-service.conf for EC2. ----- -# Where to copy worker.pl on the remote machine for sites.xml -export WORKER_LOCATION=/tmp +#Location of SWIFT. If empty, PATH is referenced +export SWIFT= -# How to launch workers: local, ssh, cobalt +# Where to place/launch worker.pl on the remote machine for sites.xml +export WORKER_LOCATION=/root + +# How to launch workers: local, ssh, or cobalt export WORKER_MODE=ssh -# Do all the worker nodes you're using have a shared filesystem? (yes/no) -export SHARED_FILESYSTEM=no +# Worker logging setting passed to worker.pl for sites.xml +export WORKER_LOGGING_LEVEL=DEBUG -# Username to use on worker nodes +export SSH_TUNNELING=yes + +# User name to use for all systems export WORKER_USERNAME=root -# Enable SSH tunneling? (yes/no) -export SSH_TUNNELING=yes +# Worker host names for ssh +# export WORKER_HOSTS="crush thwomp stomp crank grind churn trounce thrash vanquish" # Directory to keep log files, relative to working directory when launching start-coaster-service export LOG_DIR=logs +export WORKER_LOG_DIR=/root -# Swift information for creating sites.xml -export WORK=/tmp +# Manually define ports. If not specified, ports will be automatically generated +export LOCAL_PORT=50100 +export SERVICE_PORT=50200 -# Application locations for tc.data -#app convert=/usr/bin/convert +# Set shared filesystem to no since work will be done in local /sandbox directory +export SHARED_FILESYSTEM=no + +# Below are various settings to give information about how to create sites.xml +export WORK=/tmp/swift.work +export JOBSPERNODE=4 +export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS | wc -w ))/100 - 0.00001"|bc ) + +# Swift applications +#app cat=/bin/cat +#app bash=/bin/bash ----- - Add a list of any applications you want to run in the format "#app myapp=/path/to/app". Starting the Coaster Service Script From ketan at ci.uchicago.edu Thu Jun 13 12:00:02 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 12:00:02 -0500 (CDT) Subject: [Swift-commit] r6545 - trunk/docs/siteguide Message-ID: <20130613170002.9D8CD9CCA7@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 12:00:02 -0500 (Thu, 13 Jun 2013) New Revision: 6545 Modified: trunk/docs/siteguide/ec2 Log: Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 16:37:12 UTC (rev 6544) +++ trunk/docs/siteguide/ec2 2013-06-13 17:00:02 UTC (rev 6545) @@ -29,6 +29,17 @@ ==Users without EC2 Allocation +Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov. + +Log in to the swift.rcc.uchicago.edu and copy the swift_cloud directory to your home: + +---- +cp -r ~maheshwari/swift_cloud $HOME/ +---- + +Replace the hosts.txt by adding the address/DNS of instances. + + Configuring coaster-service.conf ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To run on EC2, you will need a file called coaster-service.conf. From davidk at ci.uchicago.edu Thu Jun 13 12:07:15 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Thu, 13 Jun 2013 12:07:15 -0500 (CDT) Subject: [Swift-commit] r6546 - branches/release-0.94/docs/siteguide Message-ID: <20130613170715.EDBA39CCA7@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-13 12:07:15 -0500 (Thu, 13 Jun 2013) New Revision: 6546 Modified: branches/release-0.94/docs/siteguide/ssh Log: Fix error in verification step Modified: branches/release-0.94/docs/siteguide/ssh =================================================================== --- branches/release-0.94/docs/siteguide/ssh 2013-06-13 17:00:02 UTC (rev 6545) +++ branches/release-0.94/docs/siteguide/ssh 2013-06-13 17:07:15 UTC (rev 6546) @@ -29,10 +29,10 @@ command to verify your keys are working: ----- -ssh -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu +$ ssh -o IdentitiesOnly=true -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu ----- -You should be able to connect without being asked for a password or passphrase. +You should be prompted for your new passphrase and be able to connect. Create auth.defaults ~~~~~~~~~~~~~~~~~~~~ From ketan at ci.uchicago.edu Thu Jun 13 13:51:24 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 13:51:24 -0500 (CDT) Subject: [Swift-commit] r6547 - trunk/docs/siteguide Message-ID: <20130613185124.B6E579CC82@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 13:51:24 -0500 (Thu, 13 Jun 2013) New Revision: 6547 Modified: trunk/docs/siteguide/ec2 trunk/docs/siteguide/siteguide.txt Log: refinements Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 17:07:15 UTC (rev 6546) +++ trunk/docs/siteguide/ec2 2013-06-13 18:51:24 UTC (rev 6547) @@ -7,39 +7,40 @@ Getting Access ~~~~~~~~~~~~~~ -==Users with EC2 Allocation + ==Users with EC2 Allocation If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources. Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000. Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows: + ---- export AWS_ACCESS_KEY= export AWS_SECRET_KEY= ---- -A public AMI for Swift user is available with id: ami-332e585a. +Command-line tools are pre-installed on +swift.rcc.uchicago.edu+. In order to use them add the following lines to your .bashrc: +---- +export EC2_HOME=/home/maheshwari/.ec2 +export PATH=$PATH:$EC2_HOME/bin +---- + +A public AMI on EC2 is available to create instance. The id of this AMI is: ami-332e585a. + Create instances from the above AMI as follows: ---- ec2run -k -g -n ami-332e585a ---- -==Users without EC2 Allocation + ==Users without EC2 Allocation Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov. -Log in to the swift.rcc.uchicago.edu and copy the swift_cloud directory to your home: ----- -cp -r ~maheshwari/swift_cloud $HOME/ ----- -Replace the hosts.txt by adding the address/DNS of instances. - - Configuring coaster-service.conf ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To run on EC2, you will need a file called coaster-service.conf. @@ -91,24 +92,32 @@ Starting the Coaster Service Script ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Now that everything is configured, change to the location of the coaster-service.conf file -and run this command to start the coaster service: +Now that everything is configured, run this command to start the coaster service: ----- -$ start-coaster-service +source setup ----- -This command will start the VMs, start the required processes on the worker nodes, -and generate Swift configuration files for you to use. The configuration files -will be generated in your current directory. These files are sites.xml, tc.data, -and cf. +This command will add the instances to coaster configuration, start the +required processes on the worker nodes, and generate Swift configuration files +for you to use. The configuration files will be generated in your current +directory. These files are sites.xml, tc.data, and cf. Running Swift ~~~~~~~~~~~~~ + +Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home: + +---- +cp -r ~maheshwari/swift_cloud $HOME/ +---- + +Replace the hosts.txt by adding the address/DNS of instances. + Now that you have all of your configuration files generated, run the following command: ----- -$ swift -sites.file sites.xml -tc.file tc.data -config cf +$ swift -sites.file sites.xml -tc.file tc.data -config cf catsn.swift ----- If you like to create a custom tc and/or cf file for repeated use, rename it to something other Modified: trunk/docs/siteguide/siteguide.txt =================================================================== --- trunk/docs/siteguide/siteguide.txt 2013-06-13 17:07:15 UTC (rev 6546) +++ trunk/docs/siteguide/siteguide.txt 2013-06-13 18:51:24 UTC (rev 6547) @@ -28,5 +28,7 @@ include::stampede[] +include::ec2[] + link:http://www.ci.uchicago.edu/swift/docs/index.php[home] From ketan at ci.uchicago.edu Thu Jun 13 14:01:38 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 14:01:38 -0500 (CDT) Subject: [Swift-commit] r6548 - trunk/docs/siteguide Message-ID: <20130613190138.7EECB9CC82@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 14:01:38 -0500 (Thu, 13 Jun 2013) New Revision: 6548 Modified: trunk/docs/siteguide/ec2 Log: cleanup Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 18:51:24 UTC (rev 6547) +++ trunk/docs/siteguide/ec2 2013-06-13 19:01:38 UTC (rev 6548) @@ -11,7 +11,11 @@ If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources. -Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000. +Before using EC2 for Swift you must create a security group in order to allow +Swift communicate with EC2 instances via open ports. In order to create a +security group, follow instructions +link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. +Preferably, open ports between 50000 and 51000. Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows: @@ -66,9 +70,10 @@ export WORKER_USERNAME=root # Worker host names for ssh -# export WORKER_HOSTS="crush thwomp stomp crank grind churn trounce thrash vanquish" +# export WORKER_HOSTS="crush thwomp" -# Directory to keep log files, relative to working directory when launching start-coaster-service +# Directory to keep log files, +#relative to working directory when launching start-coaster-service export LOG_DIR=logs export WORKER_LOG_DIR=/root @@ -82,7 +87,7 @@ # Below are various settings to give information about how to create sites.xml export WORK=/tmp/swift.work export JOBSPERNODE=4 -export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS | wc -w ))/100 - 0.00001"|bc ) +export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS|wc -w ))/100 - 0.00001"|bc ) # Swift applications #app cat=/bin/cat From ketan at ci.uchicago.edu Thu Jun 13 17:29:27 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 17:29:27 -0500 (CDT) Subject: [Swift-commit] r6549 - in trunk/docs: siteguide userguide Message-ID: <20130613222927.EA58F9CC82@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 17:29:27 -0500 (Thu, 13 Jun 2013) New Revision: 6549 Modified: trunk/docs/siteguide/ec2 trunk/docs/userguide/coasters Log: structure of doc Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 19:01:38 UTC (rev 6548) +++ trunk/docs/siteguide/ec2 2013-06-13 22:29:27 UTC (rev 6549) @@ -7,7 +7,8 @@ Getting Access ~~~~~~~~~~~~~~ - ==Users with EC2 Allocation +Users with EC2 Allocation +^^^^^^^^^^^^^^^^^^^^^^^^^ If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources. @@ -31,7 +32,8 @@ export PATH=$PATH:$EC2_HOME/bin ---- -A public AMI on EC2 is available to create instance. The id of this AMI is: ami-332e585a. +A public AMI on EC2 is available to create instance. Everything needed to run +Swift is preinstalled on this image. The id of this AMI is: ami-332e585a. Create instances from the above AMI as follows: @@ -39,12 +41,12 @@ ec2run -k -g -n ami-332e585a ---- - ==Users without EC2 Allocation +Users without EC2 Allocation +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov. - Configuring coaster-service.conf ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ To run on EC2, you will need a file called coaster-service.conf. Modified: trunk/docs/userguide/coasters =================================================================== --- trunk/docs/userguide/coasters 2013-06-13 19:01:38 UTC (rev 6548) +++ trunk/docs/userguide/coasters 2013-06-13 22:29:27 UTC (rev 6549) @@ -91,16 +91,4 @@ the coaster service |================== -//// -Submitting to a specific job queue -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In order to submit to a specific job scheduler queue, the +queue+ parameter of -coasters sites file should be used. For example, submitting to the +normal+ -queue of a PBS scheduler, one would use the following sites line: - ----- -normal ----- -//// - From swift at ci.uchicago.edu Thu Jun 13 18:25:03 2013 From: swift at ci.uchicago.edu (swift at ci.uchicago.edu) Date: Thu, 13 Jun 2013 18:25:03 -0500 (CDT) Subject: [Swift-commit] cog r3672 Message-ID: <20130613232504.2D4758D00087@bridled.ci.uchicago.edu> ------------------------------------------------------------------------ r3672 | hategan | 2013-06-13 18:20:18 -0500 (Thu, 13 Jun 2013) | 1 line fixed heartbeat to 30s; the wrongly set 300s could cause channel timeouts ------------------------------------------------------------------------ Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java =================================================================== --- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java (revision 3671) +++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java (working copy) @@ -371,7 +371,7 @@ protected RemoteConfiguration.Entry getChannelConfiguration(String contact) { return new RemoteConfiguration.Entry( contact.replaceAll("\\.", "\\."), - "KEEPALIVE, RECONNECT(8), HEARTBEAT(300)"); + "KEEPALIVE, RECONNECT(8), HEARTBEAT(30)"); } public static void main(String[] args) { From ketan at ci.uchicago.edu Thu Jun 13 23:07:57 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 13 Jun 2013 23:07:57 -0500 (CDT) Subject: [Swift-commit] r6550 - trunk/docs/siteguide Message-ID: <20130614040757.49FA09CCA7@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-13 23:07:57 -0500 (Thu, 13 Jun 2013) New Revision: 6550 Modified: trunk/docs/siteguide/ec2 Log: adding ec2 command to obtain instance ips Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-13 22:29:27 UTC (rev 6549) +++ trunk/docs/siteguide/ec2 2013-06-14 04:07:57 UTC (rev 6550) @@ -99,6 +99,21 @@ Starting the Coaster Service Script ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home: + +---- +cp -r ~maheshwari/swift_cloud $HOME/ +---- + +Replace the hosts.txt found in +swift_cloud+ directory by adding the address/DNS of instances. + +With the ec2 commandline, the list of ip addresses of running instances can be obtained and added to hosts.txt as follows: + +---- +ec2din | grep running | awk '{print $15}' > hosts.txt +---- + Now that everything is configured, run this command to start the coaster service: ----- @@ -113,14 +128,8 @@ Running Swift ~~~~~~~~~~~~~ -Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home: ----- -cp -r ~maheshwari/swift_cloud $HOME/ ----- -Replace the hosts.txt by adding the address/DNS of instances. - Now that you have all of your configuration files generated, run the following command: ----- From wilde at ci.uchicago.edu Fri Jun 14 08:52:12 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 08:52:12 -0500 (CDT) Subject: [Swift-commit] r6551 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130614135212.756EA9CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 08:52:11 -0500 (Fri, 14 Jun 2013) New Revision: 6551 Added: SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp SwiftTutorials/OHBM_2013-06-16/auth.defaults.example SwiftTutorials/OHBM_2013-06-16/setup.sh SwiftTutorials/OHBM_2013-06-16/swift.properties.ps Modified: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/TODO SwiftTutorials/OHBM_2013-06-16/genatlas.swift SwiftTutorials/OHBM_2013-06-16/sites.xml SwiftTutorials/OHBM_2013-06-16/swift.properties Log: Demo updates; includes provider staging config for midway-to-beagle. Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-14 04:07:57 UTC (rev 6550) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-14 13:52:11 UTC (rev 6551) @@ -1,7 +1,7 @@ fMRI Data Processing demo for OHBM 2013 -Setup +* Setup # Get the scripts from svn @@ -11,37 +11,59 @@ # Set default swift.properties in $HOME/.swift. Points to "." for apps (tc) and sites.xml mkdir -p ~/.swift - cp ~/.swift/swift.properties ~/.swift/save.swift.properties # If needed, as needed. - cp swift.properties ~/.swift + cp ~/.swift/swift.properties ~/.swift/swift.properties.save # Backup yours, if needed + cp swift.properties ~/.swift # for ssh staging (see + cp swift.propertes.ps ~/.swift # for provider staging below) + + # for scp staging, set your auth.defaults: + + mv auth.defaults.example auth.defaults # AND EDIT to set your login and ssh key + cp $HOME/.ssh/auth.defaults $HOME/.ssh/auth.defaults.save # Backup as needed + cp auth.defaults $HOME/.ssh/auth.defaults + # Get swift - module load swift + module load swift # or set PATH as below -To generate test data directories: + # NOTE: CURRENT TESTING SHOULD USE THIS SWIFT: (with the latest provider-staging fixes) - ./makedata data_100 100 # create 100 anatomical image volumes in directory data_100 + PATH=/project/wilde/swift/src/0.94/cog/modules/swift/dist/swift-svn/bin:$PATH -To run: + # Run setup: sets env var(s) and ensures java is loaded # <== DONT FORGET !!! - # On localhost: + source setup.sh - swift genatlas.swift # processes data/ directory by default - swift genatlas.swift -d=data_100 # process data_100/ directory +* Generate test data directories (example): - # With most parallel work on midway westmere parition: + ./makedata data_100 100 # creates 100 anatomical image volumes in directory data_100 - swift -tc.file apps.midway genatlas.swift +The generated data consists of links to a single file, for ease of setup and demo. - # Choices for -tc.file are: - apps # default, runs on localhost - apps.beagle # on beagle, 8 nodes - apps.midway # on midway westmere, 1 node - apps.amazon # on Amazon EC2 - needs start-coaster-service, see below - apps.UC3 # submits to UC3, needs apps to be sent. +* To run: + # On localhost: + swift genatlas.swift # processes data/ directory by default + swift genatlas.swift -d=data_100 # process data_100/ directory + + # With most parallel work on midway westmere parition: + + swift -tc.file apps.midway genatlas.swift + + # From midway to beagle using provider staging: + + swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100 + + # Choices for -tc.file are: + + apps # default, runs on localhost + apps.beagle # on beagle, 8 nodes + apps.midway # on midway westmere, 1 node + apps.amazon # on Amazon EC2 - needs start-coaster-service, see below + apps.UC3 # submits to UC3, needs apps to be sent. + The output files of the workflow are placed under output/, intermediate files under work/. @@ -52,18 +74,10 @@ http://www.ci.uchicago.edu/~wilde/atlas-y.png http://www.ci.uchicago.edu/~wilde/atlas-z.png -Notes: +* Notes: The "aligin" initial stage runs 3 AIR tools under as a single shell script, to reduce staging between these steps. -TODO - Show the workflow with the 3 AIR tools expanded as separate workflow - steps, and as a Swift procedure. - Run on other sites and Multisite - - Add performance monitoring and plotting - - Modified: SwiftTutorials/OHBM_2013-06-16/TODO =================================================================== --- SwiftTutorials/OHBM_2013-06-16/TODO 2013-06-14 04:07:57 UTC (rev 6550) +++ SwiftTutorials/OHBM_2013-06-16/TODO 2013-06-14 13:52:11 UTC (rev 6551) @@ -2,4 +2,17 @@ /scratch/midway/wilde/ds107/ds107/sub001/model/model001 +Show nested studies + +Show the workflow with the 3 AIR tools (align.sh) expanded as separate workflow +steps, and as a Swift procedure. + +Run on other sites and Multisite + +Add performance monitoring and plotting + + +--- + + Added: SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp 2013-06-14 13:52:11 UTC (rev 6551) @@ -0,0 +1,4 @@ +beagle-scp sh /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0 +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Added: SwiftTutorials/OHBM_2013-06-16/auth.defaults.example =================================================================== --- SwiftTutorials/OHBM_2013-06-16/auth.defaults.example (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/auth.defaults.example 2013-06-14 13:52:11 UTC (rev 6551) @@ -0,0 +1,4 @@ +login.beagle.ci.uchicago.edu.type=key +login.beagle.ci.uchicago.edu.username=wilde +login.beagle.ci.uchicago.edu.key=/home/wilde/.ssh/id_rsa-swift +login.beagle.ci.uchicago.edu.PROMPT_FOR_passphrase=this is the key Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 04:07:57 UTC (rev 6550) +++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 13:52:11 UTC (rev 6551) @@ -1,10 +1,14 @@ type file; +# import fMRIdefs + type Volume { file header; file image; }; +# import AIRdefs + app (Volume alignedVol) align (file script, Volume reference, Volume input) { sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); @@ -25,6 +29,8 @@ convert @i @o; } +# Start code here + string dataDir = @arg("d","data"); file alignScript<"align.sh">; Added: SwiftTutorials/OHBM_2013-06-16/setup.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/setup.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/setup.sh 2013-06-14 13:52:11 UTC (rev 6551) @@ -0,0 +1,7 @@ +export GLOBUS_HOSTNAME=swift.rcc.uchicago.edu +module load java + +if [ $(hostname) != midway001 ]; then + echo ERROR: this neesd to run from swift.rcc.uchicago.edu + return +fi Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml =================================================================== --- SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-14 04:07:57 UTC (rev 6550) +++ SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-14 13:52:11 UTC (rev 6551) @@ -45,13 +45,13 @@ 100 100 pbs.aprun;pbs.mpp;depth=24 - 3600 00:05:00 /lustre/beagle/{env.USER}/swiftwork - 20 + 8 1 1 4.80 @@ -59,4 +59,36 @@ /tmp/{env.USER}/swiftwork + + + 24 + 100 + 100 + pbs.aprun;pbs.mpp;depth=24 + + 3600 + 00:05:00 + /lustre/beagle/{env.USER}/swiftwork + 4 + 1 + 1 + 1.00 + 10000 + + + /lustre/beagle/{env.USER}/swiftwork + + + + + 0 + 10000 + + + /lustre/beagle/wilde/swiftwork + + + Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties =================================================================== --- SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-14 04:07:57 UTC (rev 6550) +++ SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-14 13:52:11 UTC (rev 6551) @@ -2,13 +2,94 @@ sites.file=sites.xml tc.file=apps +use.provider.staging=false +provider.staging.pin.swiftfiles=true + +use.wrapper.staging=false status.mode=provider -use.provider.staging=true -use.wrapper.staging=false wrapperlog.always.transfer=true -execution.retries=0 -lazy.errors=false -provider.staging.pin.swiftfiles=true +execution.retries=3 +lazy.errors=true sitedir.keep=true file.gc.enabled=false #tcp.port.range=50000,51000 + +########################################################################### +# Throttling options # +########################################################################### +# +# For the throttling parameters, valid values are either a positive integer +# or "off" (without the quotes). +# + +# +# Limits the number of concurrent submissions for a workflow instance. This +# throttle only limits the number of concurrent tasks (jobs) that are being +# sent to sites, not the total number of concurrent jobs that can be run. +# The submission stage in GRAM is one of the most CPU expensive stages (due +# mostly to the mutual authentication and delegation). Having too many +# concurrent submissions can overload either or both the submit host CPU +# and the remote host/head node causing degraded performance. +# +# Default: 4 +# + +throttle.submit=4 +#throttle.submit=off + +# +# Limits the number of concurrent submissions for any of the sites Swift will +# try to send jobs to. In other words it guarantees that no more than the +# value of this throttle jobs sent to any site will be concurrently in a state +# of being submitted. +# +# Default: 2 +# + +### throttle.host.submit=2 +#throttle.host.submit=off + +# +# The Swift scheduler has the ability to limit the number of concurrent jobs +# allowed on a site based on the performance history of that site. Each site +# is assigned a score (initially 1), which can increase or decrease based +# on whether the site yields successful or faulty job runs. The score for a +# site can take values in the (0.1, 100) interval. The number of allowed jobs +# is calculated using the following formula: +# 2 + score*throttle.score.job.factor +# This means a site will always be allowed at least two concurrent jobs and +# at most 2 + 100*throttle.score.job.factor. With a default of 4 this means +# at least 2 jobs and at most 402. +# +# Default: 4 +# + +### throttle.score.job.factor=0.2 +#throttle.score.job.factor=off + + +# +# Limits the total number of concurrent file transfers that can happen at any +# given time. File transfers consume bandwidth. Too many concurrent transfers +# can cause the network to be overloaded preventing various other signalling +# traffic from flowing properly. +# +# Default: 4 +# + +throttle.transfers=1 +#throttle.transfers=off + +# Limits the total number of concurrent file operations that can happen at any +# given time. File operations (like transfers) require an exclusive connection +# to a site. These connections can be expensive to establish. A large number +# of concurrent file operations may cause Swift to attempt to establish many +# such expensive connections to various sites. Limiting the number of concurrent +# file operations causes Swift to use a small number of cached connections and +# achieve better overall performance. +# +# Default: 8 +# + +throttle.file.operations=1 +#throttle.file.operations=off Added: SwiftTutorials/OHBM_2013-06-16/swift.properties.ps =================================================================== --- SwiftTutorials/OHBM_2013-06-16/swift.properties.ps (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/swift.properties.ps 2013-06-14 13:52:11 UTC (rev 6551) @@ -0,0 +1,95 @@ + +sites.file=sites.xml +tc.file=apps + +use.provider.staging=true +provider.staging.pin.swiftfiles=true + +use.wrapper.staging=false +status.mode=provider +wrapperlog.always.transfer=true +execution.retries=3 +lazy.errors=true +sitedir.keep=true +file.gc.enabled=false +#tcp.port.range=50000,51000 + +########################################################################### +# Throttling options # +########################################################################### +# +# For the throttling parameters, valid values are either a positive integer +# or "off" (without the quotes). +# + +# +# Limits the number of concurrent submissions for a workflow instance. This +# throttle only limits the number of concurrent tasks (jobs) that are being +# sent to sites, not the total number of concurrent jobs that can be run. +# The submission stage in GRAM is one of the most CPU expensive stages (due +# mostly to the mutual authentication and delegation). Having too many +# concurrent submissions can overload either or both the submit host CPU +# and the remote host/head node causing degraded performance. +# +# Default: 4 +# + +throttle.submit=4 +#throttle.submit=off + +# +# Limits the number of concurrent submissions for any of the sites Swift will +# try to send jobs to. In other words it guarantees that no more than the +# value of this throttle jobs sent to any site will be concurrently in a state +# of being submitted. +# +# Default: 2 +# + +### throttle.host.submit=2 +#throttle.host.submit=off + +# +# The Swift scheduler has the ability to limit the number of concurrent jobs +# allowed on a site based on the performance history of that site. Each site +# is assigned a score (initially 1), which can increase or decrease based +# on whether the site yields successful or faulty job runs. The score for a +# site can take values in the (0.1, 100) interval. The number of allowed jobs +# is calculated using the following formula: +# 2 + score*throttle.score.job.factor +# This means a site will always be allowed at least two concurrent jobs and +# at most 2 + 100*throttle.score.job.factor. With a default of 4 this means +# at least 2 jobs and at most 402. +# +# Default: 4 +# + +### throttle.score.job.factor=0.2 +#throttle.score.job.factor=off + + +# +# Limits the total number of concurrent file transfers that can happen at any +# given time. File transfers consume bandwidth. Too many concurrent transfers +# can cause the network to be overloaded preventing various other signalling +# traffic from flowing properly. +# +# Default: 4 +# + +throttle.transfers=1 +#throttle.transfers=off + +# Limits the total number of concurrent file operations that can happen at any +# given time. File operations (like transfers) require an exclusive connection +# to a site. These connections can be expensive to establish. A large number +# of concurrent file operations may cause Swift to attempt to establish many +# such expensive connections to various sites. Limiting the number of concurrent +# file operations causes Swift to use a small number of cached connections and +# achieve better overall performance. +# +# Default: 8 +# + +throttle.file.operations=1 +#throttle.file.operations=off From ketan at ci.uchicago.edu Fri Jun 14 12:13:55 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Fri, 14 Jun 2013 12:13:55 -0500 (CDT) Subject: [Swift-commit] r6552 - trunk/docs/siteguide Message-ID: <20130614171355.585A49CC82@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-14 12:13:55 -0500 (Fri, 14 Jun 2013) New Revision: 6552 Modified: trunk/docs/siteguide/ec2 Log: updates based on Justin feedback Modified: trunk/docs/siteguide/ec2 =================================================================== --- trunk/docs/siteguide/ec2 2013-06-14 13:52:11 UTC (rev 6551) +++ trunk/docs/siteguide/ec2 2013-06-14 17:13:55 UTC (rev 6552) @@ -106,6 +106,16 @@ cp -r ~maheshwari/swift_cloud $HOME/ ---- +Make sure Swift module is loaded and your credentials are added as follows: + +---- +module load swift +---- + +---- +ssh-add +---- + Replace the hosts.txt found in +swift_cloud+ directory by adding the address/DNS of instances. With the ec2 commandline, the list of ip addresses of running instances can be obtained and added to hosts.txt as follows: From wilde at ci.uchicago.edu Fri Jun 14 16:19:58 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 16:19:58 -0500 (CDT) Subject: [Swift-commit] r6553 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130614211958.1CA4F9CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 16:19:57 -0500 (Fri, 14 Jun 2013) New Revision: 6553 Modified: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/apps SwiftTutorials/OHBM_2013-06-16/apps.beagle SwiftTutorials/OHBM_2013-06-16/apps.midway SwiftTutorials/OHBM_2013-06-16/genatlas.swift SwiftTutorials/OHBM_2013-06-16/sites.xml SwiftTutorials/OHBM_2013-06-16/swift.properties Log: updates for swift version of align() function. Older function is now align_sh(). Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-14 21:19:57 UTC (rev 6553) @@ -48,13 +48,13 @@ swift genatlas.swift # processes data/ directory by default swift genatlas.swift -d=data_100 # process data_100/ directory - # With most parallel work on midway westmere parition: + # With most parallel work on a midway parition (edit sites.xml to set partition) swift -tc.file apps.midway genatlas.swift # From midway to beagle using provider staging: - swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100 + swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100 # Choices for -tc.file are: @@ -62,7 +62,7 @@ apps.beagle # on beagle, 8 nodes apps.midway # on midway westmere, 1 node apps.amazon # on Amazon EC2 - needs start-coaster-service, see below - apps.UC3 # submits to UC3, needs apps to be sent. + apps.beagle+midway # both of these The output files of the workflow are placed under output/, intermediate files under work/. @@ -79,5 +79,5 @@ The "aligin" initial stage runs 3 AIR tools under as a single shell script, to reduce staging between these steps. + A swift version of this function is included as well - Modified: SwiftTutorials/OHBM_2013-06-16/apps =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/apps 2013-06-14 21:19:57 UTC (rev 6553) @@ -1,5 +1,9 @@ -localhost sh /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0 -#localhost sh /bin/sh -localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean -localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI -localhost convert convert +midway sh /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0 +#localhost sh /bin/sh + +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear +localhost align_warp /home/wilde/software/AIR5.3.0/bin/align_warp +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Modified: SwiftTutorials/OHBM_2013-06-16/apps.beagle =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.beagle 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/apps.beagle 2013-06-14 21:19:57 UTC (rev 6553) @@ -1,4 +1,8 @@ -beagle sh /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0 -localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean -localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI -localhost convert convert +beagle sh /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0 +beagle alignlinear /lustre/beagle/wilde/software/AIR5.3.0/bin/alignlinear +beagle align_warp /lustre/beagle/wilde/software/AIR5.3.0/bin/align_warp +beagle reslice /lustre/beagle/wilde/software/AIR5.3.0/bin/reslice + +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert Modified: SwiftTutorials/OHBM_2013-06-16/apps.midway =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps.midway 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/apps.midway 2013-06-14 21:19:57 UTC (rev 6553) @@ -1,4 +1,11 @@ -westmere sh /bin/sh -localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean -localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI -localhost convert convert +midway sh /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0 +midway alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear +midway align_warp /home/wilde/software/AIR5.3.0/bin/align_warp +midway reslice /home/wilde/software/AIR5.3.0/bin/reslice + +localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean +localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI +localhost convert convert + + + Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 21:19:57 UTC (rev 6553) @@ -7,13 +7,10 @@ file image; }; -# import AIRdefs -app (Volume alignedVol) align (file script, Volume reference, Volume input) -{ - sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); -} +# import AIR + app (Volume atlas) softmean (Volume v[]) { softmean @filename(atlas.header) "y" "null" @filenames(v); @@ -29,10 +26,53 @@ convert @i @o; } +app (file warp) alignlinear (Volume ref, Volume subject, string params[]) +{ + alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params; +} + +app (file warp) alignwarp (Volume ref, Volume subject, file initWarp, string params[]) +{ + align_warp @filename(ref.header) @filename(subject.header) @filename(warp) "-f" @filename(initWarp) params; +} + +app (Volume v) reslice (file warp, Volume subject) +{ + reslice @filename(warp) @filename(v.header) "-a" @filename(subject.header); +} + + + +# start of genatlas workflow + +file alignScript<"align.sh">; + /* This script does: + time $AIR5/bin/alignlinear $ref $anat init.warp \ + -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 + time $AIR5/bin/align_warp $ref $anat refined.warp \ + -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01 + time $AIR5/bin/reslice refined.warp $resliced -a $anat + */ + +app (Volume alignedVol) align_sh (file script, Volume reference, Volume input) +{ + sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); +} + +(Volume alignedVol) native_align (Volume ref, Volume subject) +{ + file firstwarp = alignlinear(ref, subject, + ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]); + file refinedWarp = alignwarp(ref, subject, firstwarp, + ["-m","1","12","-b1",".1",".1",".1","-b2",".1",".1",".1", + "-h","10000","-s","1024","2","2","-c",".01"]); + alignedVol = reslice(refinedWarp,subject); +} + + # Start code here string dataDir = @arg("d","data"); -file alignScript<"align.sh">; Volume referenceVolume; Volume inputVolumes []; @@ -40,7 +80,8 @@ foreach v, i in inputVolumes { Volume aligned; - aligned = align(alignScript,referenceVolume, v); + // aligned = align(alignScript,referenceVolume, v); + aligned = native_align(referenceVolume, v); outputVolumes[i] = aligned; } @@ -56,6 +97,12 @@ zSlice = convert(slicer(atlasVolume,"z")); + + + + + + /******* The following code to be removed string testNames[] = imageNames(outputVolumes); Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml =================================================================== --- SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/sites.xml 2013-06-14 21:19:57 UTC (rev 6553) @@ -9,11 +9,11 @@ .03 - + - westmere + bigmem 12 Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties =================================================================== --- SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-14 17:13:55 UTC (rev 6552) +++ SwiftTutorials/OHBM_2013-06-16/swift.properties 2013-06-14 21:19:57 UTC (rev 6553) @@ -3,7 +3,7 @@ tc.file=apps use.provider.staging=false -provider.staging.pin.swiftfiles=true +provider.staging.pin.swiftfiles=false use.wrapper.staging=false status.mode=provider From wilde at ci.uchicago.edu Fri Jun 14 16:27:01 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 16:27:01 -0500 (CDT) Subject: [Swift-commit] r6554 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130614212701.B064A9CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 16:27:01 -0500 (Fri, 14 Jun 2013) New Revision: 6554 Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift Log: Adjust names for align() Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 21:19:57 UTC (rev 6553) +++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift 2013-06-14 21:27:01 UTC (rev 6554) @@ -45,13 +45,12 @@ # start of genatlas workflow -file alignScript<"align.sh">; - /* This script does: - time $AIR5/bin/alignlinear $ref $anat init.warp \ +file alignScript<"align.sh">; /* This script does: + alignlinear $ref $anat init.warp \ -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 - time $AIR5/bin/align_warp $ref $anat refined.warp \ - -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01 - time $AIR5/bin/reslice refined.warp $resliced -a $anat + align_warp $ref $anat refined.warp \ + -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 + reslice refined.warp $resliced -a $anat */ app (Volume alignedVol) align_sh (file script, Volume reference, Volume input) @@ -59,7 +58,7 @@ sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); } -(Volume alignedVol) native_align (Volume ref, Volume subject) +(Volume alignedVol) align (Volume ref, Volume subject) { file firstwarp = alignlinear(ref, subject, ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]); @@ -80,8 +79,8 @@ foreach v, i in inputVolumes { Volume aligned; - // aligned = align(alignScript,referenceVolume, v); - aligned = native_align(referenceVolume, v); + // aligned = align_sh(alignScript,referenceVolume, v); + aligned = align(referenceVolume, v); outputVolumes[i] = aligned; } @@ -100,9 +99,6 @@ - - - /******* The following code to be removed string testNames[] = imageNames(outputVolumes); From wilde at ci.uchicago.edu Fri Jun 14 19:01:57 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 19:01:57 -0500 (CDT) Subject: [Swift-commit] r6555 - in SwiftTutorials/OHBM_2013-06-16: . lib original Message-ID: <20130615000157.30FED9CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 19:01:57 -0500 (Fri, 14 Jun 2013) New Revision: 6555 Added: SwiftTutorials/OHBM_2013-06-16/atlas00.swift SwiftTutorials/OHBM_2013-06-16/atlas01.swift SwiftTutorials/OHBM_2013-06-16/atlas02.swift SwiftTutorials/OHBM_2013-06-16/atlas03.swift SwiftTutorials/OHBM_2013-06-16/lib/ SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift SwiftTutorials/OHBM_2013-06-16/lib/types.swift SwiftTutorials/OHBM_2013-06-16/original/workflow.sh SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh Removed: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh Modified: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/align.sh SwiftTutorials/OHBM_2013-06-16/apps Log: Checkpoint edits for all 4 demo phases building up to full script: atlas0{0,1,2,3}.swift Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-14 21:27:01 UTC (rev 6554) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-15 00:01:57 UTC (rev 6555) @@ -48,6 +48,10 @@ swift genatlas.swift # processes data/ directory by default swift genatlas.swift -d=data_100 # process data_100/ directory + # While above are running, do this in another window to view its activity: + + watch ps -u $USER -H + # With most parallel work on a midway parition (edit sites.xml to set partition) swift -tc.file apps.midway genatlas.swift Modified: SwiftTutorials/OHBM_2013-06-16/align.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/align.sh 2013-06-14 21:27:01 UTC (rev 6554) +++ SwiftTutorials/OHBM_2013-06-16/align.sh 2013-06-15 00:01:57 UTC (rev 6555) @@ -1,53 +1,11 @@ #!/bin/sh -#AIR5=/home/wilde/software/AIR5.3.0 +ref=$1 # Input: reference volume +anat=$2 # Input: subject volume +resliced=$3 # Ouput: rrealigned and resliced volume -# Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out) - -ref=$1 -anat=$2 -resliced=$3 - time $AIR5/bin/alignlinear $ref $anat init.warp \ -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 time $AIR5/bin/align_warp $ref $anat refined.warp \ - -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01 + -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 time $AIR5/bin/reslice refined.warp $resliced -a $anat - -exit - - - - - - - -fsl=/project/wilde/software/fsl-5.0.4/fsl - -clean=y - -if [ $clean = y ]; then - rm *warp atlas* resliced* -fi - - - -if true; then - - warp 1 - warp 2 - warp 3 - warp 4 - - time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img -fi - -export FSLOUTPUTTYPE=NIFTI - -time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm -time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm -time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm - -time convert atlas-x.pgm atlas-x.gif -time convert atlas-y.pgm atlas-y.gif -time convert atlas-z.pgm atlas-z.gif Modified: SwiftTutorials/OHBM_2013-06-16/apps =================================================================== --- SwiftTutorials/OHBM_2013-06-16/apps 2013-06-14 21:27:01 UTC (rev 6554) +++ SwiftTutorials/OHBM_2013-06-16/apps 2013-06-15 00:01:57 UTC (rev 6555) @@ -1,9 +1,9 @@ midway sh /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0 #localhost sh /bin/sh -localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean localhost alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear localhost align_warp /home/wilde/software/AIR5.3.0/bin/align_warp +localhost reslice /home/wilde/software/AIR5.3.0/bin/reslice localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI localhost convert convert Added: SwiftTutorials/OHBM_2013-06-16/atlas00.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/atlas00.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/atlas00.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,17 @@ + +import "lib/types"; + +app (file warp) alignlinear (file rh, file ri, file sh, file si) +{ + alignlinear @rh @sh @warp "-m" "12" "-q"; +} + +file refhdr <"data/reference.hdr">; // Reference volume +file refimg <"data/reference.img">; + +file subhdr <"data/anatomy4.hdr">; // One subject volume +file subimg <"data/anatomy4.img">; + +file output <"warp.out">; // Output alignment + +output = alignlinear(refhdr,refimg,subhdr,subimg); Added: SwiftTutorials/OHBM_2013-06-16/atlas01.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/atlas01.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/atlas01.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,24 @@ + +import "lib/types"; + +type Volume { + file header; + file image; +}; + +app (file warp) alignlinear (Volume ref, Volume subject, string params[]) +{ + alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params; +} + +string dataDir = @arg("d","data"); // Get a command-line argument, -d + +file alignment; + +Volume refVolume ; +Volume subjects[] ; +file warps[] ; + +foreach subjectVolume, i in subjects { + warps[i] = alignlinear(refVolume, subjectVolume, ["-m","12","-q"]); +} Added: SwiftTutorials/OHBM_2013-06-16/atlas02.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/atlas02.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/atlas02.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,49 @@ + +import "lib/types"; +import "lib/fMRI"; +import "lib/AIR"; +import "lib/FSL"; +import "lib/ImageMagick"; + +# Full version of align() function + +(Volume alignedVol) align (Volume ref, Volume subject) +{ + file firstwarp = alignlinear(ref, subject, + ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]); + file refinedWarp = alignwarp(ref, subject, firstwarp, + ["-m","1","12","-b1",".1",".1",".1","-b2",".1",".1",".1", + "-h","10000","-s","1024","2","2","-c",".01"]); + alignedVol = reslice(refinedWarp,subject); +} + +string dataDir = @arg("d","data"); + +Volume referenceVolume ; +Volume inputVolumes [] ; +Volume outputVolumes[]; + +# Align all subjects + +foreach v, i in inputVolumes { + Volume aligned ; + aligned = align(referenceVolume, v); + outputVolumes[i] = aligned; +} + +# Create the "averaged" atlas + +Volume atlasVolume ; +atlasVolume = softmean(outputVolumes); + +# Extract x, y, z slices for inspection + +file xSlice<"output/atlas-x.png">; +file ySlice<"output/atlas-y.png">; +file zSlice<"output/atlas-z.png">; + +# Convert x, y, z planes to viewable files + +xSlice = convert(slicer(atlasVolume,"x")); +ySlice = convert(slicer(atlasVolume,"y")); +zSlice = convert(slicer(atlasVolume,"z")); Added: SwiftTutorials/OHBM_2013-06-16/atlas03.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/atlas03.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/atlas03.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,38 @@ + +import "lib/types"; +import "lib/fMRI"; +import "lib/AIR"; +import "lib/FSL"; +import "lib/ImageMagick"; + +# Perform align() function in an external shell script + +file alignScript<"align.sh">; + +app (Volume alignedVol) align_sh (file script, Volume reference, Volume input) +{ + sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image); +} + +string dataDir = @arg("d","data"); + +Volume referenceVolume ; +Volume inputVolumes [] ; +Volume outputVolumes[]; + +foreach v, i in inputVolumes { + Volume aligned ; + aligned = align_sh(alignScript,referenceVolume, v); + outputVolumes[i] = aligned; +} + +Volume atlasVolume ; +atlasVolume = softmean(outputVolumes); + +file xSlice<"output/atlas-x.png">; +file ySlice<"output/atlas-y.png">; +file zSlice<"output/atlas-z.png">; + +xSlice = convert(slicer(atlasVolume,"x")); +ySlice = convert(slicer(atlasVolume,"y")); +zSlice = convert(slicer(atlasVolume,"z")); Added: SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,20 @@ + +app (Volume atlas) softmean (Volume v[]) +{ + softmean @filename(atlas.header) "y" "null" @filenames(v); +} + +app (file warp) alignlinear (Volume ref, Volume subject, string params[]) +{ + alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params; +} + +app (file warp) alignwarp (Volume ref, Volume subject, file initWarp, string params[]) +{ + align_warp @filename(ref.header) @filename(subject.header) @filename(warp) "-f" @filename(initWarp) params; +} + +app (Volume v) reslice (file warp, Volume subject) +{ + reslice @filename(warp) @filename(v.header) "-a" @filename(subject.header); +} Added: SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,5 @@ + +app (file pgm) slicer (Volume v, string axis) +{ + slicer @filename(v.header) @strcat("-",axis) .5 @filename(pgm); +} Added: SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,6 @@ + +app (file o) convert (file i) +{ + convert @i @o; +} + Added: SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,5 @@ + +type Volume { + file header; + file image; +}; Added: SwiftTutorials/OHBM_2013-06-16/lib/types.swift =================================================================== --- SwiftTutorials/OHBM_2013-06-16/lib/types.swift (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/lib/types.swift 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,2 @@ + +type file; Deleted: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh 2013-06-14 21:27:01 UTC (rev 6554) +++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh 2013-06-15 00:01:57 UTC (rev 6555) @@ -1,30 +0,0 @@ -#!/bin/sh - -AIR5=$HOME/software/AIR5.3.0 -fsl=/project/wilde/software/fsl-5.0.4/fsl - -if true; then - -#time $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -j # -q - -time $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -s 1024 2 2 -c .01 -f out # -q -s 1024 2 2 -c .01 - - -time $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q -time $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q -time $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q -time $AIR5/bin/reslice warp1.warp resliced1 -time $AIR5/bin/reslice warp2.warp resliced2 -time $AIR5/bin/reslice warp3.warp resliced3 -time $AIR5/bin/reslice warp4.warp resliced4 -time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img -fi - -export FSLOUTPUTTYPE=NIFTI - -time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm -time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm -time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm -time convert atlas-x.pgm atlas-x.gif -time convert atlas-y.pgm atlas-y.gif -time convert atlas-z.pgm atlas-z.gif Added: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,25 @@ +#!/bin/sh + +# +# Original workflow from PC1 and DBIC +# + +AIR5.2.5/bin/align_warp anatomy1.img reference.img warp1.warp -m 12 -q +AIR5.2.5/bin/align_warp anatomy2.img reference.img warp2.warp -m 12 -q +AIR5.2.5/bin/align_warp anatomy3.img reference.img warp3.warp -m 12 -q +AIR5.2.5/bin/align_warp anatomy4.img reference.img warp4.warp -m 12 -q + +AIR5.2.5/bin/reslice warp1.warp resliced1 +AIR5.2.5/bin/reslice warp2.warp resliced2 +AIR5.2.5/bin/reslice warp3.warp resliced3 +AIR5.2.5/bin/reslice warp4.warp resliced4 + +AIR5.2.5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img + +fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm +fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm +fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm + +convert atlas-x.pgm atlas-x.gif +convert atlas-y.pgm atlas-y.gif +convert atlas-z.pgm atlas-z.gif Copied: SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh (from rev 6550, SwiftTutorials/OHBM_2013-06-16/original/workflow.sh) =================================================================== --- SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh (rev 0) +++ SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh 2013-06-15 00:01:57 UTC (rev 6555) @@ -0,0 +1,30 @@ +#!/bin/sh + +AIR5=$HOME/software/AIR5.3.0 +fsl=/project/wilde/software/fsl-5.0.4/fsl + +if true; then + +#time $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -j # -q + +time $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12 -b1 .1 .1 .1 -b2 .1 .1 .1 -h 10000 -v -s 1024 2 2 -c .01 -f out # -q -s 1024 2 2 -c .01 + + +time $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1 # -q +time $AIR5/bin/reslice warp1.warp resliced1 +time $AIR5/bin/reslice warp2.warp resliced2 +time $AIR5/bin/reslice warp3.warp resliced3 +time $AIR5/bin/reslice warp4.warp resliced4 +time $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img +fi + +export FSLOUTPUTTYPE=NIFTI + +time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm +time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm +time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm +time convert atlas-x.pgm atlas-x.gif +time convert atlas-y.pgm atlas-y.gif +time convert atlas-z.pgm atlas-z.gif From wilde at ci.uchicago.edu Fri Jun 14 19:14:45 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 19:14:45 -0500 (CDT) Subject: [Swift-commit] r6556 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130615001445.1787E9CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 19:14:44 -0500 (Fri, 14 Jun 2013) New Revision: 6556 Modified: SwiftTutorials/OHBM_2013-06-16/README SwiftTutorials/OHBM_2013-06-16/clean.sh Log: Edit README, adjust clean.sh Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-15 00:01:57 UTC (rev 6555) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-15 00:14:44 UTC (rev 6556) @@ -43,6 +43,18 @@ * To run: + # Latest demo code versions: + + atlas00.swift: Just run one app, no Volume struct types + atlas01.swift: Run a loop with volume struct types + atlas02.swift: The fill workflow, with align() as a Swift function (for local execution) + atlas03.swift: Full wowrkflow with align.sh, suitable for remote execution + + genatlas.swift: The original workflow, now obsolete. + + In the examples below, use atlas00.swift through atlas02.swift, + and atlas03.swift for all runs on beagle and cloud. + # On localhost: swift genatlas.swift # processes data/ directory by default Modified: SwiftTutorials/OHBM_2013-06-16/clean.sh =================================================================== --- SwiftTutorials/OHBM_2013-06-16/clean.sh 2013-06-15 00:01:57 UTC (rev 6555) +++ SwiftTutorials/OHBM_2013-06-16/clean.sh 2013-06-15 00:14:44 UTC (rev 6556) @@ -1,4 +1,4 @@ #! /bin/sh -rm -rf _concurrent work/* output/* *.log *.rlog *.d *.kml *.swiftx +rm -rf _concurrent work/* output/* warps *.log *.rlog *.d *.kml *.swiftx From wilde at ci.uchicago.edu Fri Jun 14 19:29:02 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Fri, 14 Jun 2013 19:29:02 -0500 (CDT) Subject: [Swift-commit] r6557 - SwiftTutorials/OHBM_2013-06-16 Message-ID: <20130615002902.637749CC82@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-14 19:29:02 -0500 (Fri, 14 Jun 2013) New Revision: 6557 Modified: SwiftTutorials/OHBM_2013-06-16/README Log: Add suggested demo sequence to README Modified: SwiftTutorials/OHBM_2013-06-16/README =================================================================== --- SwiftTutorials/OHBM_2013-06-16/README 2013-06-15 00:14:44 UTC (rev 6556) +++ SwiftTutorials/OHBM_2013-06-16/README 2013-06-15 00:29:02 UTC (rev 6557) @@ -55,15 +55,61 @@ In the examples below, use atlas00.swift through atlas02.swift, and atlas03.swift for all runs on beagle and cloud. + # APPROXIMATE *SUGGESTED* DEMO SEQUENCE + + # Show first Swift script: + + ./clean.sh + swift atlas00.swift + + # Show struct data types for fMRI "ANALYZE 7.5" Volumes, @arg, and parallel foreach loop + + ./clean.sh + ./makedata.sh data_10 10 + swift atlas01.swift -d=data_10 + + # While above are running, do this in another window to view its activity: + + watch ps -u $USER -H + + # Show same script running on a cluster + + ./clean.sh + ./makedata.sh data_50 50 + swift -tc.file apps.midway atlas01.swift -d=data_50 + + # Show compound functions, imported libs, and full workflow + + ./clean.sh + swift atlas02.swift -d=data_2 + + ./clean.sh + swift -tc.file apps.midway atlas02.swift -d=data_50 + + # Show full script, optimized for remote exec, running on beagle + + ./clean.sh + swift -tc.file apps.beagle atlas02.swift -d=data_20 + + # Show full script running on Amazon EC2 + + ./clean.sh + # Start cloud resources and services here (document!) + swift -tc.file apps.amazon atlas02.swift -d=data_20 + + # Grand finale: show full script running on multiple resources + + ./clean.sh + swift -tc.file apps.everywhere atlas02.swift -d=data_20 + +### Obsolete below this line.... clean up vvvvvv + + # On localhost: swift genatlas.swift # processes data/ directory by default swift genatlas.swift -d=data_100 # process data_100/ directory - # While above are running, do this in another window to view its activity: - - watch ps -u $USER -H - # With most parallel work on a midway parition (edit sites.xml to set partition) swift -tc.file apps.midway genatlas.swift From swift at ci.uchicago.edu Sat Jun 15 18:50:03 2013 From: swift at ci.uchicago.edu (swift at ci.uchicago.edu) Date: Sat, 15 Jun 2013 18:50:03 -0500 (CDT) Subject: [Swift-commit] cog r3673 Message-ID: <20130615235003.DD7528D0008D@bridled.ci.uchicago.edu> ------------------------------------------------------------------------ r3673 | hategan | 2013-06-15 18:48:32 -0500 (Sat, 15 Jun 2013) | 1 line prevent log configuration warnings when running along with something that replaces the file appender with an async appender (such as swift) ------------------------------------------------------------------------ Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java =================================================================== --- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java (revision 3672) +++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java (working copy) @@ -405,11 +405,8 @@ } public static void configureLogName() { - FileAppender fa = (FileAppender) getAppender(FileAppender.class); - if (fa == null) { - logger.warn("Failed to configure log file name"); - } - else { + FileAppender fa = (FileAppender) getFileAppender(); + if (fa != null) { fa.setFile(Bootstrap.LOG_DIR + File.separator + makeLogFileName()); fa.activateOptions(); @@ -430,16 +427,23 @@ root.addAppender(aa); } - @SuppressWarnings({ "rawtypes", "unchecked" }) - protected static Appender getAppender(Class cls) { + @SuppressWarnings("rawtypes") + protected static Appender getFileAppender() { Logger root = Logger.getRootLogger(); Enumeration e = root.getAllAppenders(); while (e.hasMoreElements()) { Appender a = (Appender) e.nextElement(); - if (cls.isAssignableFrom(a.getClass())) { + if (a instanceof FileAppender) { return a; } + if (a instanceof AsyncAppender) { + // likely this is running in a JVM in which + // the file appender has been replaced with + // an async appender, so don't mess with things + return null; + } } + logger.warn("Could not find a file appender to configure"); return null; } From wilde at ci.uchicago.edu Sun Jun 16 00:11:42 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 00:11:42 -0500 (CDT) Subject: [Swift-commit] r6558 - SwiftTutorials Message-ID: <20130616051142.6F30B178884@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 00:11:42 -0500 (Sun, 16 Jun 2013) New Revision: 6558 Added: SwiftTutorials/CMTS_2013-06-17/ Log: Initial dir for CMTS Workshop tutorial 2013. From wilde at ci.uchicago.edu Sun Jun 16 11:52:26 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 11:52:26 -0500 (CDT) Subject: [Swift-commit] r6560 - in SwiftTutorials/CMTS_2013-06-17/basic_swift: part01 part02 part03 part04 part05 part06 part07 Message-ID: <20130616165226.51B439CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 11:52:26 -0500 (Sun, 16 Jun 2013) New Revision: 6560 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps Removed: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README Log: Initial revisions for CMTS workshop. Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -4,37 +4,41 @@ Verify that random.sh is in your path, and that it works: -$ which random.sh -$ random.sh + $ which random.sh + $ random.sh Study the Swift program: -$ cat p1.swift + $ cat p1.swift -Examine the tool catalog file: +Examine the app location file, telling swift which apps are installed +and where to find them (e.g., from $PATH or a specific pathname): -$ cat tc + $ cat apps Run the program: -$ swift -tc.file tc p1.swift + $ swift p1.swift Look at the output: -$ cat _concurrent/* + $ cat _concurrent/* Look at the other files generated: -$ ls -l + $ ls -l We'll talk more about these files later -$ cleanup +This will remove log and temp files, first prompting you for +confirmation: -Then test the sript a few more times. + $ cleanup -$ swift -tc.file tc p1.swift; cat _concurrent/* +Then test the sript a few more times: -$ swift -tc.file tc p1.swift; cat _concurrent/* + $ swift -tc.file tc p1.swift; cat _concurrent/* -$ swift -tc.file tc p1.swift; cat _concurrent/* + $ swift -tc.file tc p1.swift; cat _concurrent/* + + $ swift -tc.file tc p1.swift; cat _concurrent/* Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1 +0,0 @@ -localhost random random.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,33 +1,36 @@ -TOPIC: specifying the output filenames +TOPIC: Specifying the output filenames + Study the Swift program: -$ cat p2.swift + $ cat p2.swift Examine the tool catalog file: -$ cat tc + $ cat tc Run the program: -$ swift -tc.file tc p2.swift + $ swift -tc.file tc p2.swift Look at the output: -$ cat sim.out + $ cat sim.out Then test the sript a few more times. -$ swift -tc.file tc p1.swift; cat sim.out + $ swift -tc.file tc p1.swift; cat sim.out -$ swift -tc.file tc p1.swift; cat sim.out + $ swift -tc.file tc p1.swift; cat sim.out -$ swift -tc.file tc p1.swift; cat sim.out + $ swift -tc.file tc p1.swift; cat sim.out Things to try: -- change the output filename + o change the output filename -- add a dir component to the output filename + o add a directory component to the output filename + o try using fully qualified file names + Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1 +0,0 @@ -localhost random random.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,20 +1,23 @@ -TOPIC: run many instances of a "simulation" program in a foreach() loop +TOPIC: Run many instances of a "simulation" program in parallel + with a foreach() loop Run the program: -$ swift -tc.file tc p3.swift + $ swift p3.swift Look at the output: -$ cd _concurrent -$ ls -l -$ cat * + $ cd _concurrent + $ ls -l + $ cat * Look at the order in which the files were written: -$ ls -lt + $ ls -lt -We'll come back to this... +Run p3.swift a few more times, noting how the order changes. +Swift runs the apps in a foreach loop with high concurrency: +you cant count on what order they run in! Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1 +0,0 @@ -localhost random random.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,42 +1,59 @@ -TOPIC: run a program in a foreach() loop with explicitly named output files. +TOPIC: Run a program in a foreach() loop with explicitly named output files. Study the program: -- @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins) + @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins) -- Note that @strcat() coerces numeric args to strings + Note that @strcat() coerces numeric args to strings -- <"filename"> was a shorthand for but the latter is more flexible. + <"filename"> was a shorthand for but the latter is more flexible. + Run the program: -$ swift -tc.file tc p4.swift + $ swift -tc.file tc p4.swift Look at the output: -$ cd output -$ ls -l -$ cat * + $ cd output + $ ls -l + $ cat * -Try: +Try these exercises: -- Adjust the script to take the number of simulations to do from the command line + o Adjust the script to take the number of simulations to do from the command line - @arg("argname") returns arguments after the .swift script on the swift command line: + @arg("argname") returns arguments after the .swift script on the swift command line: - swift -tc.file tc p4.swift -myarg1=value1 ... + swift -tc.file tc p4.swift -myarg1=value1 ... - @arg("argname","default") returns "default" if the argname is not given on the command line + @arg("argname","default") returns "default" if the argname is not given on the command line - @toInt() converts strings to integers: + @toInt() converts strings to integers: - @toInt(@arg("myArg1")) + @toInt(@arg("myArg1")) -- trace(expr1,...) traces expressions on stdout. + o Add some output tracing. - Try inserting a few traces. But remember: Swift is *very* concurrent! + trace(expr1,...) traces expressions on stdout. + tracef() allows some simple formatting ala printf (but with slighly different codes) + see: http://www.swiftlang.org/guides/trunk/userguide/userguide.html#_tracef + + Try inserting a few traces. But remember: Swift is *very* concurrent! + + o Use readData() to read the output files back in to the Swift script and print their values. + + o Use readData() to read both a scalar and an array + + o create a version of Random that prints pairs, and read these into arrays + + o Experiment with sparse arrays + + o Experiment with string-indexed arrays (hash tables) + + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,51 +1,39 @@ +TOPIC: Add a program that "analyzes" the output the parallel simulations -TOPIC: Add a program that "analyzes" the output the parallel simulations - Study the program: -We added a new app to "analyze" all the simulation outputs: + We added a new app to "analyze" all the simulation outputs: -app (file o) analyze (file s[]) -{ - average @filenames(s) stdout=@filename(o); -} + app (file o) analyze (file s[]) + { + average @filenames(s) stdout=@filename(o); + } Nots that it expects an array of files as its input, and that it uses @filenames() to place the names of all the files on the command line to the "average" program. Average does: --------------------- -#! /bin/sh -awk ' - -{ sum += $1} - -END { print sum/NR } -' $* -------------------- - - + awk ' { sum += $1} + END { print sum/NR } ' $* + At the end of the script we insert: -file stats<"output/average.out">; -stats = analyze(sims); + file stats<"output/average.out">; + stats = analyze(sims); ...which runs the analysis *after* all the simulations complete. - Run the program: -$ swift -tc.file tc p5.swift + $ swift p5.swift -Look at the output: +Inspect the output: -$ cd output -$ ls -l -$ cat sim*.out -$ cat average.out - - + $ cd output + $ ls -l + $ cat sim*.out + $ cat average.out Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,2 @@ +localhost random random.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,2 +0,0 @@ -localhost random random.sh -localhost average avg.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,28 +1,42 @@ -TOPIC: add arguments to the "simulation" program -(to control number of steps, range of output, and number of output lines) +TOPIC: Add arguments to the "simulation" program + (to control number of steps, range of output, and number of output lines) -Test new versions of the "simulation" program: +Test these new versions of the "simulation" program: random.sh # original random2.sh [runtime] # runtime in seconds; defaults to 1 sec random3.sh [runtime] [range] # requests random numbers in {0:range-1} random4.sh [runtime] [range] [count] # requests "count" random numbers in {0:range} -p6.swift changes to random2 for the simulation program and adds an argument. +p6.swift uses random2 for the simulation program and adds an argument. Run the program: -$ swift -tc.file tc p6.swift -steps=3 # each simulation takes 3 seconds + $ swift p6.swift -steps=3 # each simulation takes 3 seconds Next we need to use the parallel cluster for our simulations! -Try: +Try these exercises: -- change to random3.sh and add the extra argument "range" + o Change to random3.sh and add the extra command line argument " -range= " -- change to random4.sh and add yet another argument "count" + o Change to random4.sh and add yet another argument " -count= " +Also try adjusting the runtime concurrency throttle for "localhost" + $ cp sites.xml faster.xml + $ vi faster.xml + # Add these lines before the closing tag + 10000 + .03 + + $ swift -sites.file faster.xml p6.swift +Note the increased number of active jobs + + + + + Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,2 @@ +localhost random2 random2.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,9 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,2 +0,0 @@ -localhost random2 random2.sh -localhost average avg.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,9 +1,8 @@ -TOPIC: Run the "simulations" on the parallel cluster +TOPIC: Run the "simulations" on the parallel cluster -Til now we've been running our "simulations" on the local login host. - +So far we've been running our "simulations" on the local login host. Now we'll run them on the parallel cluster. The script will be the same as previous, but we change the tool catalog to @@ -12,20 +11,20 @@ We changed file "tc" from: -localhost random4 random4.sh -localhost average avg.sh + localhost random4 random4.sh + localhost average avg.sh to: -westmere random4 random4.sh -localhost average avg.sh + cmtsworkshop random4 random4.sh + localhost average avg.sh -And we added the "sites.xml" file which specifies two "pools" of resources, -the "local host" pool (which we've been using till now) and the "westmere" pool. +And we added a pool entry to "sites.xml" file which specifies two "pools" of resources, +the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool. -To run, we now add the sites.xml file to the swift command line: +To run: -$ swift -tc.file tc -sites.file sites.xml p7.swift -steps=10 -range=1000 -count=6 -nsim=100 + $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100 Note that we're now asking for 100 simulations to be run, each of which is to run for 10 steps (ie 10 seconds). @@ -40,20 +39,20 @@ /scratch/midway/{env.USER}/swiftwork - + - westmere - 12 - + cmtsworkshop + 8 + cmtsworkshop --> 1 1 1 - 12 - .11 + 8 + .07 00:15:00 @@ -74,8 +73,8 @@ Try: -- running more app() calls at once: change jobsPerNode and jobThrottle + o running more app() calls at once: change jobsPerNode and jobThrottle -- requesting more than 1 slurm job at once: change slots + o requesting more than 1 slurm job at once: change slots -- requesting nodes in units greater than 1: change maxnodes and nodeGranularity + o requesting nodes in units greater than 1: change maxnodes and nodeGranularity Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps 2013-06-16 16:52:26 UTC (rev 6560) @@ -0,0 +1,2 @@ +westmere random4 random4.sh +localhost average avg.sh Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc 2013-06-16 13:30:27 UTC (rev 6559) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc 2013-06-16 16:52:26 UTC (rev 6560) @@ -1,2 +0,0 @@ -westmere random4 random4.sh -localhost average avg.sh From wilde at ci.uchicago.edu Sun Jun 16 12:46:23 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 12:46:23 -0500 (CDT) Subject: [Swift-commit] r6561 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part07 Message-ID: <20130616174623.EC0FC9CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 12:46:23 -0500 (Sun, 16 Jun 2013) New Revision: 6561 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml Log: Adjust apps and sites for cmtsworkshop. Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps 2013-06-16 16:52:26 UTC (rev 6560) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps 2013-06-16 17:46:23 UTC (rev 6561) @@ -1,2 +1,2 @@ -westmere random4 random4.sh -localhost average avg.sh +cmtsworkshop random4 random4.sh +localhost average avg.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml 2013-06-16 16:52:26 UTC (rev 6560) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml 2013-06-16 17:46:23 UTC (rev 6561) @@ -6,20 +6,20 @@ /scratch/midway/{env.USER}/swiftwork - + - westmere - 12 - + cmtsworkshop + 8 + cmtsworkshop - 1 + 4 1 1 - 12 - .11 + 8 + .31 00:15:00 From wilde at ci.uchicago.edu Sun Jun 16 12:50:27 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 12:50:27 -0500 (CDT) Subject: [Swift-commit] r6562 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part02 Message-ID: <20130616175027.8F7809CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 12:50:27 -0500 (Sun, 16 Jun 2013) New Revision: 6562 Removed: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift Log: Remove this one answer file. Add answers for all 'eercises' later in a uniform way. Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift 2013-06-16 17:46:23 UTC (rev 6561) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift 2013-06-16 17:50:27 UTC (rev 6562) @@ -1,9 +0,0 @@ -type file; - -app (file o) mysim () -{ - random stdout=@filename(o); -} - -file f<"output/sim.out">; -f = mysim(); From wilde at ci.uchicago.edu Sun Jun 16 13:09:49 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 13:09:49 -0500 (CDT) Subject: [Swift-commit] r6563 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130616180949.E65AC9CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 13:09:49 -0500 (Sun, 16 Jun 2013) New Revision: 6563 Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps Removed: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl Log: Initial adaptations of rmsd exercise (namd sweep). Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 18:09:49 UTC (rev 6563) @@ -13,5 +13,11 @@ data in a gnuplot 2D plot data format. This script also prints to screen the minimum RMSD and the parameter values corresponding to that value. --Frank X. Vazquez fxv at uchicago.edu -7-13-2012 +-Frank X. Vazquez fxv at uchicago.edu 7-13-2012 + +To Run: + + PATH=$PATH:$PWD # Note: must use $PWD, not "." !!! + + swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5 + Copied: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc) =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps 2013-06-16 18:09:49 UTC (rev 6563) @@ -0,0 +1,5 @@ + +localhost gensweep sweep_pd.pl null null null +localhost analyze analyze_pd.pl null null null + +cmtsworkshop rmsd rmsd.sh null null null Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 18:09:49 UTC (rev 6563) @@ -1,3 +1,3 @@ #!/bin/bash -rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/* +rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/ RMSD/ VMD/ CONF/ OUT/ Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 18:09:49 UTC (rev 6563) @@ -1,7 +0,0 @@ -PATH=$PATH:$PWD - -# export SBATCH_RESERVATION=swift_test - -mkdir -p CONF PAR VMD RMSD OUT - -swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5} Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 18:09:49 UTC (rev 6563) @@ -1,11 +1,42 @@ - + /scratch/midway/{env.USER}/swiftwork + + + + + cmtsworkshop + 8 + cmtsworkshop + + + 1 + 2 + 2 + .03 + + + 00:15:00 + 1800 + + + true + single + 1 + 100 + 100 + 10000 + + + + /scratch/midway/{env.USER}/swiftwork + + Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 18:09:49 UTC (rev 6563) @@ -10,6 +10,10 @@ chdir($ARGV[0]); +# Create dirs + +system("mkdir -p CONF PAR VMD RMSD OUT"); + # Bead names my $b1name = "PX"; Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 17:50:27 UTC (rev 6562) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 18:09:49 UTC (rev 6563) @@ -1,8 +0,0 @@ - -local gensweep sweep_pd.pl null null null -local analyze analyze_pd.pl null null null - -#bigmem rmsd rmsd.sh null null null -#sandyb rmsd rmsd.sh null null null -#trestles rmsd rmsd.sh null null null -westmere rmsd rmsd.sh null null null From wilde at ci.uchicago.edu Sun Jun 16 13:15:26 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 13:15:26 -0500 (CDT) Subject: [Swift-commit] r6564 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130616181526.B71FC9CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 13:15:26 -0500 (Sun, 16 Jun 2013) New Revision: 6564 Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift Log: Update README with run instructions; pretty up the trace. Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 18:09:49 UTC (rev 6563) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 18:15:26 UTC (rev 6564) @@ -19,5 +19,8 @@ PATH=$PATH:$PWD # Note: must use $PWD, not "." !!! - swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5 + swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5 # 1 param set + swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5 # 9 param sets (3 x 3) + + Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift 2013-06-16 18:09:49 UTC (rev 6563) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift 2013-06-16 18:15:26 UTC (rev 6564) @@ -26,7 +26,6 @@ string beadids[] = readData(genConfigs(sweepMax, sweepDelta)); -trace("Processing these bead IDs:", beadids); foreach beadid, i in beadids { file conf ; @@ -36,6 +35,8 @@ file log ; file dat ; + tracef("Processing bead ID %s\n", beadid); + (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid); rmsds[i] = dat; } From davidk at ci.uchicago.edu Mon Jun 17 10:25:19 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 10:25:19 -0500 (CDT) Subject: [Swift-commit] r6565 - in SwiftTutorials/CMTS_2013-06-17/basic_swift: part01 part02 part04 part07 Message-ID: <20130617152520.047399CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 10:25:18 -0500 (Mon, 17 Jun 2013) New Revision: 6565 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift Log: Fix some inconsistencies with tc/app files, fix scope warning in p7.swift Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-16 18:15:26 UTC (rev 6564) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-17 15:25:18 UTC (rev 6565) @@ -37,8 +37,8 @@ Then test the sript a few more times: - $ swift -tc.file tc p1.swift; cat _concurrent/* + $ swift p1.swift; cat _concurrent/* - $ swift -tc.file tc p1.swift; cat _concurrent/* + $ swift p1.swift; cat _concurrent/* - $ swift -tc.file tc p1.swift; cat _concurrent/* + $ swift p1.swift; cat _concurrent/* Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-16 18:15:26 UTC (rev 6564) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-17 15:25:18 UTC (rev 6565) @@ -8,11 +8,11 @@ Examine the tool catalog file: - $ cat tc + $ cat apps Run the program: - $ swift -tc.file tc p2.swift + $ swift p2.swift Look at the output: @@ -20,11 +20,11 @@ Then test the sript a few more times. - $ swift -tc.file tc p1.swift; cat sim.out + $ swift p2.swift; cat sim.out - $ swift -tc.file tc p1.swift; cat sim.out + $ swift p2.swift; cat sim.out - $ swift -tc.file tc p1.swift; cat sim.out + $ swift p2.swift; cat sim.out Things to try: Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-16 18:15:26 UTC (rev 6564) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-17 15:25:18 UTC (rev 6565) @@ -13,7 +13,7 @@ Run the program: - $ swift -tc.file tc p4.swift + $ swift p4.swift Look at the output: Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-16 18:15:26 UTC (rev 6564) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-17 15:25:18 UTC (rev 6565) @@ -9,7 +9,7 @@ indicate that our "simulation app" (random4.sh) should be run on the "westmere" partition of the Midway cluster using the "slurm" scheduler: -We changed file "tc" from: +We changed file "apps" from: localhost random4 random4.sh localhost average avg.sh Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift 2013-06-16 18:15:26 UTC (rev 6564) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift 2013-06-17 15:25:18 UTC (rev 6565) @@ -1,8 +1,8 @@ type file; -app (file o) mysim4 (int timesteps, int range, int count) +app (file o) mysim4 (int timesteps, int range_value, int count_value) { - random4 timesteps range count stdout=@filename(o); + random4 timesteps range_value count_value stdout=@filename(o); } app (file o) analyze (file s[]) @@ -12,7 +12,6 @@ file sims[]; int nsim = @toInt(@arg("nsim", "10")); - int steps = @toInt(@arg("steps", "1")); int range = @toInt(@arg("range", "100")); int count = @toInt(@arg("count", "10")); From davidk at ci.uchicago.edu Mon Jun 17 10:44:26 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 10:44:26 -0500 (CDT) Subject: [Swift-commit] r6566 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part04 Message-ID: <20130617154426.9D6069CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 10:44:26 -0500 (Mon, 17 Jun 2013) New Revision: 6566 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps Log: apps Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps 2013-06-17 15:44:26 UTC (rev 6566) @@ -0,0 +1 @@ +localhost random random.sh From davidk at ci.uchicago.edu Mon Jun 17 10:44:54 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 10:44:54 -0500 (CDT) Subject: [Swift-commit] r6567 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part04 Message-ID: <20130617154454.502DC9CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 10:44:54 -0500 (Mon, 17 Jun 2013) New Revision: 6567 Removed: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc Log: Remove tc Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc 2013-06-17 15:44:26 UTC (rev 6566) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc 2013-06-17 15:44:54 UTC (rev 6567) @@ -1 +0,0 @@ -localhost random random.sh From ketan at ci.uchicago.edu Mon Jun 17 10:48:16 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 17 Jun 2013 10:48:16 -0500 (CDT) Subject: [Swift-commit] r6568 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part05 Message-ID: <20130617154816.05F589CC45@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-17 10:48:15 -0500 (Mon, 17 Jun 2013) New Revision: 6568 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README Log: small typo Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-17 15:44:54 UTC (rev 6567) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-17 15:48:15 UTC (rev 6568) @@ -11,7 +11,7 @@ average @filenames(s) stdout=@filename(o); } -Nots that it expects an array of files as its input, and that +Note that it expects an array of files as its input, and that it uses @filenames() to place the names of all the files on the command line to the "average" program. From wilde at ci.uchicago.edu Mon Jun 17 13:10:43 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Mon, 17 Jun 2013 13:10:43 -0500 (CDT) Subject: [Swift-commit] r6569 - SwiftTutorials/CMTS_2013-06-17 Message-ID: <20130617181043.83D2A9CC45@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-17 13:10:43 -0500 (Mon, 17 Jun 2013) New Revision: 6569 Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx Log: Presented version of Swift lecture. Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx =================================================================== (Binary files differ) From davidk at ci.uchicago.edu Mon Jun 17 13:42:31 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 13:42:31 -0500 (CDT) Subject: [Swift-commit] r6570 - in SwiftTutorials/CMTS_2013-06-17/basic_swift: . part08 Message-ID: <20130617184231.684AF9CC45@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 13:42:31 -0500 (Mon, 17 Jun 2013) New Revision: 6570 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml Log: Part08 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 18:42:31 UTC (rev 6570) @@ -0,0 +1,80 @@ + +TOPIC: Example pipelines + + +So far we've been running our "simulations" on the local login host. +Now we'll run them on the parallel cluster. + +The script will be the same as previous, but we change the tool catalog to +indicate that our "simulation app" (random4.sh) should be run on the +"westmere" partition of the Midway cluster using the "slurm" scheduler: + +We changed file "apps" from: + + localhost random4 random4.sh + localhost average avg.sh + +to: + + cmtsworkshop random4 random4.sh + localhost average avg.sh + +And we added a pool entry to "sites.xml" file which specifies two "pools" of resources, +the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool. + +To run: + + $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100 + +Note that we're now asking for 100 simulations to be run, each of which +is to run for 10 steps (ie 10 seconds). + +The sites file looks like this: + + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + cmtsworkshop + 8 + cmtsworkshop --> + + + 1 + 1 + 1 + 8 + .07 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + + +Try: + + o running more app() calls at once: change jobsPerNode and jobThrottle + + o requesting more than 1 slurm job at once: change slots + + o requesting nodes in units greater than 1: change maxnodes and nodeGranularity Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps 2013-06-17 18:42:31 UTC (rev 6570) @@ -0,0 +1,2 @@ +cmtsworkshop random4 random4.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift 2013-06-17 18:42:31 UTC (rev 6570) @@ -0,0 +1,36 @@ +type file; + +app (file o) mysim4 (int timesteps, int range_value, int count_value) +{ + random4 timesteps range_value count_value stdout=@filename(o); +} + +app (file o) mysim4_filename (int timesteps, file range_value, int count_value) +{ + random4 timesteps @filename(range_value) count_value stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; +int nsim = @toInt(@arg("nsim", "10")); +int steps = @toInt(@arg("steps", "1")); +int range = @toInt(@arg("range", "100")); +int count = @toInt(@arg("count", "10")); + +foreach i in [0:nsim-1] { + + file simout ; + simout = mysim4(steps, range, 1); + + file simout2 ; + simout2 = mysim4_filename(steps, simout, nsim); + + sims[i] = simout2; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml 2013-06-17 18:42:31 UTC (rev 6570) @@ -0,0 +1,39 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + cmtsworkshop + 8 + cmtsworkshop + + + 4 + 1 + 1 + 8 + .31 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + From davidk at ci.uchicago.edu Mon Jun 17 13:48:50 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 13:48:50 -0500 (CDT) Subject: [Swift-commit] r6571 - SwiftTutorials/CMTS_2013-06-17/bin Message-ID: <20130617184850.2023C9CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 13:48:50 -0500 (Mon, 17 Jun 2013) New Revision: 6571 Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh Log: updated random4 Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-17 18:42:31 UTC (rev 6570) +++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-17 18:48:50 UTC (rev 6571) @@ -4,6 +4,10 @@ range=${2:-30000} n=${3:-10} +if [ -f "$2" ]; then + range=$( cat $2 ) +fi + sleep $runtime for ((i=0;i Author: ketan Date: 2013-06-17 14:14:57 -0500 (Mon, 17 Jun 2013) New Revision: 6572 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml Log: TJ Lane's example Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,25 @@ + +TOPIC: Example illustrating readData from a file with multiple fields + +To run: + + $ swift p10.swift + +In this example, multiple fields from a file are read into a Swift struct +variable. The file particles.dat contains eight fields corresponding to eight +members in the struct type defined in p10.swift as follows: + +type shootargs{ + string coords; + string qvals; + int numphi; + int numshots; + int nummolec; + float photons; + int parallel; + string output_filename; +} + +Note that the first row in the particles.dat corresponds to the member names in +the shootargs type which is how Swift assigns values to structure member +variables. Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,3 @@ +cmtsworkshop random4 random4.sh +cmtsworkshop echo echo +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,3 @@ +==== +Test. +==== Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,3 @@ +===== +Hello +===== Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,30 @@ +type qvalfile; +type coordfile; +type shotfile; + +type shootargs{ + string coords; + string qvals; + int numphi; + int numshots; + int nummolec; + float photons; + int parallel; + string output_filename; +} + +app (shotfile outfile) shootsim (shootargs args, coordfile coords, qvalfile qvals) { + echo "polshoot" "-s" @coords "-f" @qvals "-x" args.numphi "-n" args.numshots + "-m" args.nummolec "-g" args.photons "-p" args.parallel "-o" @outfile + stdout=@outfile; # Note double use of outfile, just for testing/demo +} + +shootargs myargs[] = readData("particles.dat"); + +foreach a in myargs { + shotfile output ; + coordfile coords ; + qvalfile qvals ; + output = shootsim(a, coords, qvals); +} + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,6 @@ +coords qvals numphi numshots nummolec photons parallel output_filename +gold_5nm.coor gold_qvals.txt 3600 10 1 0.25 12 out0.ring +gold_5nm.coor gold_qvals.txt 3600 10 2 0.5 12 out1.ring +gold_5nm.coor gold_qvals.txt 3600 10 4 1.0 12 out2.ring +gold_5nm.coor gold_qvals.txt 3600 10 8 2.0 12 out3.ring +gold_5nm.coor gold_qvals.txt 3600 10 16 4.0 12 out4.ring Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml 2013-06-17 19:14:57 UTC (rev 6572) @@ -0,0 +1,39 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + cmtsworkshop + 8 + cmtsworkshop + + + 4 + 1 + 1 + 8 + .31 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + From ketan at ci.uchicago.edu Mon Jun 17 14:16:19 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:16:19 -0500 (CDT) Subject: [Swift-commit] r6573 - SwiftTutorials/CMTS_2013-06-17/basic_swift Message-ID: <20130617191619.B9F109CC43@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-17 14:16:19 -0500 (Mon, 17 Jun 2013) New Revision: 6573 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/ Removed: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/ Log: renamed for consistency From ketan at ci.uchicago.edu Mon Jun 17 14:18:14 2013 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:18:14 -0500 (CDT) Subject: [Swift-commit] r6574 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part10 Message-ID: <20130617191814.957F29CC43@svn.ci.uchicago.edu> Author: ketan Date: 2013-06-17 14:18:14 -0500 (Mon, 17 Jun 2013) New Revision: 6574 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README Log: Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README 2013-06-17 19:16:19 UTC (rev 6573) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README 2013-06-17 19:18:14 UTC (rev 6574) @@ -23,3 +23,4 @@ Note that the first row in the particles.dat corresponds to the member names in the shootargs type which is how Swift assigns values to structure member variables. + From davidk at ci.uchicago.edu Mon Jun 17 14:19:36 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:19:36 -0500 (CDT) Subject: [Swift-commit] r6575 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part08 Message-ID: <20130617191936.3219D9CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 14:19:36 -0500 (Mon, 17 Jun 2013) New Revision: 6575 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift Log: Use random number to determine how many random numbers to generate. Updated README. Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 19:18:14 UTC (rev 6574) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 19:19:36 UTC (rev 6575) @@ -1,80 +1,14 @@ -TOPIC: Example pipelines +TOPIC: Example pipeline +This example shows combining two app calls in a pipeline. There are two apps +defined in this script: mysim4, and mysim4_filename. -So far we've been running our "simulations" on the local login host. -Now we'll run them on the parallel cluster. +mysim4 takes integer to determine the number of random numbers to generate. +mysim4_filename reads a file to determine the number of random numbers to generate -The script will be the same as previous, but we change the tool catalog to -indicate that our "simulation app" (random4.sh) should be run on the -"westmere" partition of the Midway cluster using the "slurm" scheduler: +In this example, we use mysim4 to generate a random number. The output of mysim4 +get passed as input to mysim4_filename. -We changed file "apps" from: - - localhost random4 random4.sh - localhost average avg.sh - -to: - - cmtsworkshop random4 random4.sh - localhost average avg.sh - -And we added a pool entry to "sites.xml" file which specifies two "pools" of resources, -the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool. - -To run: - - $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100 - -Note that we're now asking for 100 simulations to be run, each of which -is to run for 10 steps (ie 10 seconds). - -The sites file looks like this: - - - - - - - /scratch/midway/{env.USER}/swiftwork - - - - - - - cmtsworkshop - 8 - cmtsworkshop --> - - - 1 - 1 - 1 - 8 - .07 - - - 00:15:00 - 1800 - - - - /scratch/midway/{env.USER}/swiftwork - - - false - 100 - 100 - 10000 - - - - -Try: - - o running more app() calls at once: change jobsPerNode and jobThrottle - - o requesting more than 1 slurm job at once: change slots - - o requesting nodes in units greater than 1: change maxnodes and nodeGranularity +To run +$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift 2013-06-17 19:18:14 UTC (rev 6574) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift 2013-06-17 19:19:36 UTC (rev 6575) @@ -5,9 +5,9 @@ random4 timesteps range_value count_value stdout=@filename(o); } -app (file o) mysim4_filename (int timesteps, file range_value, int count_value) +app (file o) mysim4_filename (int timesteps, int range_value, file count_value) { - random4 timesteps @filename(range_value) count_value stdout=@filename(o); + random4 timesteps range_value @filename(count_value) stdout=@filename(o); } app (file o) analyze (file s[]) @@ -23,13 +23,13 @@ foreach i in [0:nsim-1] { - file simout ; - simout = mysim4(steps, range, 1); + file random ; + random = mysim4(steps, range, 1); - file simout2 ; - simout2 = mysim4_filename(steps, simout, nsim); + file simout ; + simout = mysim4_filename(steps, range, random); - sims[i] = simout2; + sims[i] = simout; } file stats<"output/average.out">; From davidk at ci.uchicago.edu Mon Jun 17 14:21:41 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:21:41 -0500 (CDT) Subject: [Swift-commit] r6576 - SwiftTutorials/CMTS_2013-06-17/bin Message-ID: <20130617192141.E20EB9CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 14:21:41 -0500 (Mon, 17 Jun 2013) New Revision: 6576 Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh Log: Updated random4.sh for checking for files Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-17 19:19:36 UTC (rev 6575) +++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-17 19:21:41 UTC (rev 6576) @@ -4,8 +4,8 @@ range=${2:-30000} n=${3:-10} -if [ -f "$2" ]; then - range=$( cat $2 ) +if [ -f "$3" ]; then + n=$( cat $3 ) fi sleep $runtime From wilde at ci.uchicago.edu Mon Jun 17 14:37:38 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:37:38 -0500 (CDT) Subject: [Swift-commit] r6579 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130617193738.38FFC9CC43@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-17 14:37:38 -0500 (Mon, 17 Jun 2013) New Revision: 6579 Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml Log: Updates for faster namd runs with correct vmd extraction. Changes initfrm and drops minimize. Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf 2013-06-17 19:37:11 UTC (rev 6578) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf 2013-06-17 19:37:38 UTC (rev 6579) @@ -84,7 +84,7 @@ #langevinTemp $temperature -minimize 10000 +#minimize 10000 #reinitvels $temperature #run 1000000 desired, 200000 min to get non-zero RMSDs -run 20000 +run 10000 Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl 2013-06-17 19:37:11 UTC (rev 6578) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl 2013-06-17 19:37:38 UTC (rev 6579) @@ -13,6 +13,7 @@ # Set the initial frame set inifrm 200 +set inifrm 1 set psf cg_clath_cage.psf set pdb cg_clath_cage.pdb Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-17 19:37:11 UTC (rev 6578) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-17 19:37:38 UTC (rev 6579) @@ -16,9 +16,9 @@ 1 - 2 - 2 - .03 + 1 + 1 + .15 00:15:00 From wilde at ci.uchicago.edu Mon Jun 17 14:55:09 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:55:09 -0500 (CDT) Subject: [Swift-commit] r6581 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130617195509.3A9729CC43@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-17 14:55:09 -0500 (Mon, 17 Jun 2013) New Revision: 6581 Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps Log: minor edits Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-17 19:40:34 UTC (rev 6580) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-17 19:55:09 UTC (rev 6581) @@ -21,6 +21,8 @@ swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5 # 1 param set + swift rmsd.swift -cwd=$PWD -max=0.5 -delta=0.5 # 4 param sets (2 x 2) + swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5 # 9 param sets (3 x 3) Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps 2013-06-17 19:40:34 UTC (rev 6580) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps 2013-06-17 19:55:09 UTC (rev 6581) @@ -1,5 +1,6 @@ +localhost sh /bin/bash +localhost gensweep sweep_pd.pl +localhost analyze analyze_pd.pl -localhost gensweep sweep_pd.pl null null null -localhost analyze analyze_pd.pl null null null +cmtsworkshop rmsd rmsd.sh -cmtsworkshop rmsd rmsd.sh null null null From davidk at ci.uchicago.edu Mon Jun 17 14:55:12 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 14:55:12 -0500 (CDT) Subject: [Swift-commit] r6582 - SwiftTutorials/CMTS_2013-06-17/basic_swift Message-ID: <20130617195512.52F2D9CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 14:55:12 -0500 (Mon, 17 Jun 2013) New Revision: 6582 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README Log: Updating list of applications Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-17 19:55:09 UTC (rev 6581) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-17 19:55:12 UTC (rev 6582) @@ -50,3 +50,10 @@ part06: Add arguments to the "simulation" program part07: Run the "simulations" on the parallel cluster + +part08: Example of pipeline - sending output of one app to the input of another app + +part09: Example pipeline using readData + +part10: Example readData to read file with multiple fields into a struct + From davidk at ci.uchicago.edu Mon Jun 17 15:17:58 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Mon, 17 Jun 2013 15:17:58 -0500 (CDT) Subject: [Swift-commit] r6584 - in SwiftTutorials/CMTS_2013-06-17/basic_swift: . part08 part11 Message-ID: <20130617201758.AF1979CC43@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-17 15:17:58 -0500 (Mon, 17 Jun 2013) New Revision: 6584 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README Log: Part11 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-17 20:01:51 UTC (rev 6583) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-17 20:17:58 UTC (rev 6584) @@ -57,3 +57,4 @@ part10: Example readData to read file with multiple fields into a struct +part11: Example using composite functions Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 20:01:51 UTC (rev 6583) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 20:17:58 UTC (rev 6584) @@ -10,3 +10,4 @@ To run $ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1 + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README 2013-06-17 20:17:58 UTC (rev 6584) @@ -0,0 +1,16 @@ + +TOPIC: Example pipeline showing composite functions + +This example shows composite functions. The function called generate_randoms +combines two app calls and returns only the result we care about. + +(file o) generate_randoms (int timesteps, int range_value, int count_value) +{ + file tmp; + tmp = mysim4(timesteps, range_value, 1); + int rand = readData(tmp); + o = mysim4(timesteps, range_value, rand); +} + +To run +$ swift p11.swift -steps=10 -range=100 -count=6 -nsim=1 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps 2013-06-17 20:17:58 UTC (rev 6584) @@ -0,0 +1,2 @@ +cmtsworkshop random4 random4.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift 2013-06-17 20:17:58 UTC (rev 6584) @@ -0,0 +1,35 @@ +type file; + +app (file o) mysim4 (int timesteps, int range_value, int count_value) +{ + random4 timesteps range_value count_value stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +(file o) generate_randoms (int timesteps, int range_value, int count_value) +{ + file tmp; + tmp = mysim4(timesteps, range_value, 1); + int rand = readData(tmp); + o = mysim4(timesteps, range_value, rand); +} + + +file sims[]; +int nsim = @toInt(@arg("nsim", "10")); +int steps = @toInt(@arg("steps", "1")); +int range = @toInt(@arg("range", "100")); +int count = @toInt(@arg("count", "10")); + +foreach i in [0:nsim-1] { + file simout ; + simout = generate_randoms(steps, range, count); + sims[i] = simout; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml 2013-06-17 20:17:58 UTC (rev 6584) @@ -0,0 +1,39 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + cmtsworkshop + 8 + cmtsworkshop + + + 4 + 1 + 1 + 8 + .31 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + From wilde at ci.uchicago.edu Mon Jun 17 15:23:15 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Mon, 17 Jun 2013 15:23:15 -0500 (CDT) Subject: [Swift-commit] r6585 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130617202315.2FEAB9CC43@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-17 15:23:15 -0500 (Mon, 17 Jun 2013) New Revision: 6585 Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift Log: new example. Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift 2013-06-17 20:23:15 UTC (rev 6585) @@ -0,0 +1,56 @@ +type file; + +global string cwd = @arg("cwd","."); + +app (file blist) genConfigs (dir, string max, string delta) +{ + gensweep dir max delta stdout=@blist; +} + +app (file rmsdout, file rmsd) rmsd (file i[], string id) +{ + rmsd id; +} + +app (file plot_data) analyze (file[] rmsdfiles) +{ + analyze @filenames(rmsdfiles) stdout=@plot_data; +} + +global file pdb <"cg_clath_cage.pdb">; +global file psf <"cg_clath_cage.psf">; + +string sweepMax=@arg("max","0.6"), sweepDelta=@arg("delta","0.5"); + +sweep(string beads[],string set) +{ + file rmsds[]; + foreach beadid, i in beads { + file conf ; + file inp ; + file vmdtcl ; + + file log ; + file dat ; + + tracef("Processing bead ID %s\n", beadid); + + (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid); + rmsds[i] = dat; + } + + file plot_out ; + plot_out = analyze(rmsds); +} + + +string bead_set_1[] = readData(genConfigs("0.2", "0.1")); + +# string bead_set_2[] = readData(genConfigs("0.5", "0.5")); + +sweep(bead_set_1,"set1"); + + + + + From swift at ci.uchicago.edu Thu Jun 20 02:15:02 2013 From: swift at ci.uchicago.edu (swift at ci.uchicago.edu) Date: Thu, 20 Jun 2013 02:15:02 -0500 (CDT) Subject: [Swift-commit] cog r3674 Message-ID: <20130620071502.E91E28D0009E@bridled.ci.uchicago.edu> ------------------------------------------------------------------------ r3674 | hategan | 2013-06-20 02:11:48 -0500 (Thu, 20 Jun 2013) | 1 line expose cwd as a global variable ------------------------------------------------------------------------ Index: modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java =================================================================== --- modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java (revision 3673) +++ modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java (working copy) @@ -147,6 +147,7 @@ stack.setVar("user.home", System.getProperty("user.home")); stack.setVar("user.name", System.getProperty("user.name")); stack.setVar(CMDLINE_ARGS, arguments); + stack.setVar("cwd", cwd); setEnvironmentVariables(stack); } From wilde at ci.uchicago.edu Tue Jun 25 15:06:02 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Tue, 25 Jun 2013 15:06:02 -0500 (CDT) Subject: [Swift-commit] r6588 - SwiftTutorials/CMTS_2013-06-17 Message-ID: <20130625200602.C3F9A9CCC2@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-25 15:06:02 -0500 (Tue, 25 Jun 2013) New Revision: 6588 Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx Log: Final presentation, for web posting. Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx =================================================================== (Binary files differ) From davidk at ci.uchicago.edu Thu Jun 27 15:45:29 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Thu, 27 Jun 2013 15:45:29 -0500 (CDT) Subject: [Swift-commit] r6589 - SwiftApps Message-ID: <20130627204529.8595D9CCC2@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-27 15:45:29 -0500 (Thu, 27 Jun 2013) New Revision: 6589 Added: SwiftApps/FitPosOrStrains/ Log: FitPosOrStrains From davidk at ci.uchicago.edu Thu Jun 27 15:54:53 2013 From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu) Date: Thu, 27 Jun 2013 15:54:53 -0500 (CDT) Subject: [Swift-commit] r6590 - SwiftApps Message-ID: <20130627205453.606A29CC92@svn.ci.uchicago.edu> Author: davidk Date: 2013-06-27 15:54:53 -0500 (Thu, 27 Jun 2013) New Revision: 6590 Added: SwiftApps/strains/ Removed: SwiftApps/FitPosOrStrains/ Log: Rename - directory can't have a capital 'S' in it From wilde at ci.uchicago.edu Sun Jun 16 08:30:30 2013 From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu) Date: Sun, 16 Jun 2013 13:30:30 -0000 Subject: [Swift-commit] r6559 - in SwiftTutorials/CMTS_2013-06-17: . basic_swift basic_swift/data basic_swift/part01 basic_swift/part02 basic_swift/part03 basic_swift/part04 basic_swift/part05 basic_swift/part06 basic_swift/part07 bin namd_sweep Message-ID: <20130616133029.069F09CC8F@svn.ci.uchicago.edu> Author: wilde Date: 2013-06-16 08:30:27 -0500 (Sun, 16 Jun 2013) New Revision: 6559 Added: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx SwiftTutorials/CMTS_2013-06-17/basic_swift/ SwiftTutorials/CMTS_2013-06-17/basic_swift/README SwiftTutorials/CMTS_2013-06-17/basic_swift/data/ SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc SwiftTutorials/CMTS_2013-06-17/bin/ SwiftTutorials/CMTS_2013-06-17/bin/avg.sh SwiftTutorials/CMTS_2013-06-17/bin/cleanup SwiftTutorials/CMTS_2013-06-17/bin/highest.sh SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh SwiftTutorials/CMTS_2013-06-17/bin/makeinput SwiftTutorials/CMTS_2013-06-17/bin/myapp SwiftTutorials/CMTS_2013-06-17/bin/random.sh SwiftTutorials/CMTS_2013-06-17/bin/random2.sh SwiftTutorials/CMTS_2013-06-17/bin/random3.sh SwiftTutorials/CMTS_2013-06-17/bin/random4.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc SwiftTutorials/CMTS_2013-06-17/setup.csh SwiftTutorials/CMTS_2013-06-17/setup.sh Log: Initial revision for this tutorial. Added: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx =================================================================== (Binary files differ) Property changes on: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,52 @@ + +INTRODUCTION TO SWIFT + +SETUP + +Obtain the tutorial package + +Change directory into the created directory called "tutorial" + +This directory contains: + +bin: script tools for the tutorial +scripts: Swift scripts for the tutorial + +TO START, do: + +$ source setup.sh # to add tutorial programs to your PATH + +...and then verify: + +$ random.sh # should be found in your PATH now + + + +The tutorial is arranged in parts. To begin: + +$ cd part01 +$ cat README + +When finished: + +$ cd ../part02 # etc + +In each part, you can type "cleanup" after running a few swift scripts +to remove the old logs that build up, and (usually) the output files. + + +The topics of the tutorial parts are: + +part01: First Swift script - run a "simulation" program, random.sh + +part02: Specifying the output filenames + +part03: Run many instances of a "simulation" program in a foreach() loop + +part04: run a program in a foreach() loop with explicitly named output files. + +part05: Add a program that "analyzes" the output the parallel simulations + +part06: Add arguments to the "simulation" program + +part07: Run the "simulations" on the parallel cluster Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1 @@ +Hi Swift! Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,40 @@ + +TOPIC: First Swift script - run a "simulation" program, random.sh + + +Verify that random.sh is in your path, and that it works: + +$ which random.sh +$ random.sh + +Study the Swift program: + +$ cat p1.swift + +Examine the tool catalog file: + +$ cat tc + +Run the program: + +$ swift -tc.file tc p1.swift + +Look at the output: + +$ cat _concurrent/* + +Look at the other files generated: + +$ ls -l + +We'll talk more about these files later + +$ cleanup + +Then test the sript a few more times. + +$ swift -tc.file tc p1.swift; cat _concurrent/* + +$ swift -tc.file tc p1.swift; cat _concurrent/* + +$ swift -tc.file tc p1.swift; cat _concurrent/* Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,8 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +file f = mysim(); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,33 @@ + +TOPIC: specifying the output filenames + +Study the Swift program: + +$ cat p2.swift + +Examine the tool catalog file: + +$ cat tc + +Run the program: + +$ swift -tc.file tc p2.swift + +Look at the output: + +$ cat sim.out + +Then test the sript a few more times. + +$ swift -tc.file tc p1.swift; cat sim.out + +$ swift -tc.file tc p1.swift; cat sim.out + +$ swift -tc.file tc p1.swift; cat sim.out + +Things to try: + +- change the output filename + +- add a dir component to the output filename + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,9 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +file f<"sim.out">; +f = mysim(); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,9 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +file f<"output/sim.out">; +f = mysim(); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,20 @@ + +TOPIC: run many instances of a "simulation" program in a foreach() loop + + +Run the program: + +$ swift -tc.file tc p3.swift + +Look at the output: + +$ cd _concurrent +$ ls -l +$ cat * + +Look at the order in which the files were written: + +$ ls -lt + +We'll come back to this... + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,11 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +foreach i in [0:9] { + file f = mysim(); +} + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,42 @@ + +TOPIC: run a program in a foreach() loop with explicitly named output files. + + +Study the program: + +- @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins) + +- Note that @strcat() coerces numeric args to strings + +- <"filename"> was a shorthand for but the latter is more flexible. + +Run the program: + +$ swift -tc.file tc p4.swift + +Look at the output: + +$ cd output +$ ls -l +$ cat * + + +Try: + +- Adjust the script to take the number of simulations to do from the command line + + @arg("argname") returns arguments after the .swift script on the swift command line: + + swift -tc.file tc p4.swift -myarg1=value1 ... + + @arg("argname","default") returns "default" if the argname is not given on the command line + + @toInt() converts strings to integers: + + @toInt(@arg("myArg1")) + + +- trace(expr1,...) traces expressions on stdout. + + Try inserting a few traces. But remember: Swift is *very* concurrent! + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,12 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +foreach i in [0:9] { + file f ; + f = mysim(); +} + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1 @@ +localhost random random.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,51 @@ + + +TOPIC: Add a program that "analyzes" the output the parallel simulations + + +Study the program: + +We added a new app to "analyze" all the simulation outputs: + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +Nots that it expects an array of files as its input, and that +it uses @filenames() to place the names of all the files on +the command line to the "average" program. + +Average does: +-------------------- +#! /bin/sh + +awk ' + +{ sum += $1} + +END { print sum/NR } +' $* +------------------- + + +At the end of the script we insert: + +file stats<"output/average.out">; +stats = analyze(sims); + +...which runs the analysis *after* all the simulations complete. + + +Run the program: + +$ swift -tc.file tc p5.swift + +Look at the output: + +$ cd output +$ ls -l +$ cat sim*.out +$ cat average.out + + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,24 @@ +type file; + +app (file o) mysim () +{ + random stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; + +int nsim = @toInt(@arg("nsim","10")); + +foreach i in [0:nsim-1] { + file simout ; + simout = mysim(); + sims[i] = simout; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,2 @@ +localhost random random.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,28 @@ + +TOPIC: add arguments to the "simulation" program +(to control number of steps, range of output, and number of output lines) + + +Test new versions of the "simulation" program: + + random.sh # original + random2.sh [runtime] # runtime in seconds; defaults to 1 sec + random3.sh [runtime] [range] # requests random numbers in {0:range-1} + random4.sh [runtime] [range] [count] # requests "count" random numbers in {0:range} + +p6.swift changes to random2 for the simulation program and adds an argument. + +Run the program: + +$ swift -tc.file tc p6.swift -steps=3 # each simulation takes 3 seconds + +Next we need to use the parallel cluster for our simulations! + +Try: + +- change to random3.sh and add the extra argument "range" + +- change to random4.sh and add yet another argument "count" + + + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,25 @@ +type file; + +app (file o) mysim2 (int timesteps) +{ + random2 timesteps stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; +int nsim = @toInt(@arg("nsim","10")); + +int steps = @toInt(@arg("steps","1")); + +foreach i in [0:nsim-1] { + file simout ; + simout = mysim2(steps); + sims[i] = simout; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,2 @@ +localhost random2 random2.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,81 @@ + +TOPIC: Run the "simulations" on the parallel cluster + + +Til now we've been running our "simulations" on the local login host. + +Now we'll run them on the parallel cluster. + +The script will be the same as previous, but we change the tool catalog to +indicate that our "simulation app" (random4.sh) should be run on the +"westmere" partition of the Midway cluster using the "slurm" scheduler: + +We changed file "tc" from: + +localhost random4 random4.sh +localhost average avg.sh + +to: + +westmere random4 random4.sh +localhost average avg.sh + +And we added the "sites.xml" file which specifies two "pools" of resources, +the "local host" pool (which we've been using till now) and the "westmere" pool. + +To run, we now add the sites.xml file to the swift command line: + +$ swift -tc.file tc -sites.file sites.xml p7.swift -steps=10 -range=1000 -count=6 -nsim=100 + +Note that we're now asking for 100 simulations to be run, each of which +is to run for 10 steps (ie 10 seconds). + +The sites file looks like this: + + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + westmere + 12 + + + + 1 + 1 + 1 + 12 + .11 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + + +Try: + +- running more app() calls at once: change jobsPerNode and jobThrottle + +- requesting more than 1 slurm job at once: change slots + +- requesting nodes in units greater than 1: change maxnodes and nodeGranularity Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,27 @@ +type file; + +app (file o) mysim4 (int timesteps, int range, int count) +{ + random4 timesteps range count stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; +int nsim = @toInt(@arg("nsim", "10")); + +int steps = @toInt(@arg("steps", "1")); +int range = @toInt(@arg("range", "100")); +int count = @toInt(@arg("count", "10")); + +foreach i in [0:nsim-1] { + file simout ; + simout = mysim4(steps,range,count); + sims[i] = simout; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,39 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + westmere + 12 + + + + 1 + 1 + 1 + 12 + .11 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,2 @@ +westmere random4 random4.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/avg.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/avg.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,9 @@ +#! /bin/sh + +awk ' + +{ sum += $1} + +END { print sum/NR } +' $* + Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/cleanup =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/cleanup (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/cleanup 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,17 @@ +#! /bin/sh + +echo Removing: +echo +ls -ltd *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log 2>/dev/null +echo +echo Enter y to proceed: +read ok +if [ _$ok = _y -o _$ok = _Y -o _$ok = _yes ]; then + echo + set -x + rm -rf *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log +else + echo + echo No files removed. +fi + Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/cleanup ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/highest.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/highest.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,2 @@ +#! /bin/sh +sort -nr | head -$1 Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,5 @@ +#! /bin/sh + +# Print the lowest N numbers from standard input (deafult: lowest 3) + +sort -n | head -${1:-3} Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/makeinput =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/makeinput (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/makeinput 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,22 @@ +#! /bin/sh + +nfiles=${1:-10} + +rm -rf input +mkdir input +cp ../data/sat/t? input/ +( cd input + n=0 + for h in $(seq -w 00 99); do + for v in $(seq -w 00 99); do + n=$((n+1)) + if [ $n -gt $nfiles ]; then + break; + else + f=t$(($RANDOM%10)) + ln $f h${h}v${v}.rgb + fi + done + done + rm t? +) Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/makeinput ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/myapp =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/myapp (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/myapp 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,6 @@ +#! /bin/sh + +hostname -f +date +sleep 3 +ps -u $USER -H -f Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/myapp ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/random.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/random.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,2 @@ +#! /bin/sh +echo $RANDOM Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random2.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/random2.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,7 @@ +#! /bin/sh + +runtime=${1:-0} + +sleep $runtime + +echo $(($RANDOM)) Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random3.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/random3.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,10 @@ +#! /bin/sh + +runtime=${1:-0} +range=${2:-30000} + +sleep $runtime + +echo $(($RANDOM%range)) + + Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,12 @@ +#! /bin/sh + +runtime=${1:-0} +range=${2:-30000} +n=${3:-10} + +sleep $runtime + +for ((i=0;i; + my @data = split(/ +/,$_); + my $rmsd=$data[2]*1.0; + + # Find Minimum + if ($rmsd<$rmsdmin) { + $rmsdmin=$rmsd; + $b1rmsdmin=$b1; + $b2rmsdmin=$b2; + } + + printf "%0.3f %0.3f %0.9f\n", $b1, $b2, $rmsd; + close(INPUT); +} + +printf "\nMinimum Values: RMSD=%0.9f eps_$b1name=%0.3f eps_$b2name=%0.3f\n", $rmsdmin, $b1rmsdmin, $b2rmsdmin; Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,7 @@ +wrapperlog.always.transfer=true +sitedir.keep=true +execution.retries=0 +lazy.errors=false +status.mode=provider +use.provider.staging=false +provider.staging.pin.swiftfiles=false Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,470 @@ +REMARK original generated coordinate pdb file +ATOM 1 HB0 CLA X 1 92.981 164.025 331.473 1.00 0.00 A0 +ATOM 2 PX1 CLA X 1 136.274 211.422 275.579 1.00 0.00 A0 +ATOM 3 DT1 CLA X 1 200.662 208.148 159.192 1.00 0.00 A0 +ATOM 4 AK1 CLA X 1 243.304 111.359 96.656 1.00 0.00 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SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,90 @@ +# NAMD Config file - autogenerated by NAMDgui plugin +# Author: Jan Saam, saam at charite.de + +#set DIR /lustre/beagle/fxv/CLATH/CG_MODEL/OPT/CAGE/PSWEEP + +set id FILEID +# input +coordinates ../cg_clath_cage.pdb +structure ../cg_clath_cage.psf +parameters ../PAR/${id}.inp +paratypecharmm on + +# output +#set output cg_clath_cage.BLAB1_BLAB2 +outputname ../OUT/$id +dcdfile ../OUT/${id}.dcd +xstFile ../OUT/${id}.xst +dcdfreq 1000 +xstFreq 1000 + +binaryoutput yes +binaryrestart yes +outputEnergies 1000 +restartfreq 1000 + +fixedAtoms off + +# Basic dynamics +exclude scaled1-4 +1-4scaling 1 +COMmotion no +dielectric 1.0 + + +# Simulation space partitioning +cutoff 630 +switching on +switchdist 629 +pairlistdist 640 + +# Multiple timestepping +firsttimestep 0 +timestep 1 +stepspercycle 20 +nonbondedFreq 1 +fullElectFrequency 1 +rigidBonds all + +# Temperature control + +set temperature 310 +set tempini 0 +temperature $temperature; # initial temperature + +# Langevin Dynamics +langevin on; # do langevin dynamics +langevinDamping 0.5 # damping coefficient (gamma) of 1/ps +langevinTemp $temperature; # bath temperature +langevinHydrogen no; # don't couple langevin bath to hydrogens + + + +# Scripting + +# Simulated Annealing +#reassignFreq 10000 +#reassignTemp 0 +#minimize 10000 +#for { set TEMP 0 } { $TEMP <= 310 } { incr TEMP 5 } { +# run 10000 +# reassignTemp $TEMP +# langevinTemp $TEMP +#} + +#run 2500000 +# +#for { set TEMP 650 } { $TEMP >= 0 } { incr TEMP -5 } { +# reassignTemp $TEMP +# langevinTemp $TEMP +# run 10000 +#} + +#reassignTemp $temperature +#langevinTemp $temperature + + +minimize 10000 +#reinitvels $temperature +#run 1000000 desired, 200000 min to get non-zero RMSDs +run 20000 Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,3 @@ +#!/bin/bash + +rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/* Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,79 @@ +* Charmm Parameter file +* For 13 bead CG clathrin model +* Handmade by FXV - 7-21-11 +* Initial guess (very rough) + +BONDS +! + +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! + +HB PX 0.5 85.5 +PX DT 0.018 135.2 +DT AK 0.045 124.2 +AK LT 0.08 94.1 + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +! +!atom types Ktheta Theta0 +! +PX HB PX 70.0 120.00 +DT PX HB 50.0 144.3 +AK DT PX 35.0 132.6 +LT AK DT 150.0 141.5 + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +X X X X 0.0 1 0.0 ! No dihedrals + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +!atom types Kpsi psi0 +! +PX PX HB PX 200.00 0 161.17 +PX HB PX DT 10.0 0 -30.4 +HB PX DT AK 9.5 0 -16.1 +PX DT AK LT 45.0 0 26.1 + +NONBONDED +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 +! +HB 0.000000 HBEPS 43.075000 +PX 0.000000 PXEPS 18.425000 +DT 0.000000 DTEPS 10.455000 +AK 0.000000 AKEPS 25.975000 +LT 0.000000 LTEPS 36.905000 + + +END Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,74 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +# This code will run many short simulations in order to +# sweep the nonbonded parameter space + +# File names +open (OFILE, ">", "rmsd_pd.dat"); + +# Bead names +my $b1name = "PX"; +my $b2name = "DT"; + +# Bead ranges +my $b1min=0.0; +my $b1max=10.0; + +my $b2min=0.0; +my $b2max=10.0; + +my $del=0.50; + +# Set large number to find RMSD min +my $rmsdmin = 123456789.0; +my $b1rmsdmin=0.0; +my $b2rmsdmin=0.0; + + +my $b1=$b1min; + +while ($b1<=$b1max) +{ + my $b2=$b2min; + + while ($b2<=$b2max) + { + + + + if (-s "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat") + { + open(INPUT, "<", "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat"); + my $_ = ; + + my @data = split(/ +/,$_); + my $rmsd=$data[2]*1.0; + + # Find Minimum + if ($rmsd<$rmsdmin) + { + $rmsdmin=$rmsd; + $b1rmsdmin=$b1; + $b2rmsdmin=$b2; + } + + print OFILE "$b1 $b2 $rmsd\n"; + close(INPUT); + } + + $b2 = $b2+$del; + + } + + print OFILE " \n"; + $b1 = $b1+$del; + +} + +close(OFILE); + +print "Minimum Values\n"; +print "RMSD = $rmsdmin, eps_$b1name = $b1rmsdmin, eps_$b2name = $b2rmsdmin\n" ; Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,11 @@ +#! /bin/sh + +id=$1 + +module load namd +module load vmd + + mpiexec namd2 CONF/$id.conf > OUT/$id.log 2>&1 +# mpiexec -n 8 namd2 CONF/$id.conf > OUT/$id.log 2>&1 + +vmd -dispdev text -e VMD/$id.tcl >> OUT/$id.log 2>&1 Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,44 @@ +type file; + +global string cwd = @arg("cwd","."); + +app (file blist) genConfigs (string max, string delta) +{ + gensweep cwd max delta stdout=@blist; +} + +app (file rmsdout, file rmsd) rmsd (file i[], string id) +{ + rmsd id; +} + +app (file plot_data) analyze (file[] rmsdfiles) +{ + analyze @filenames(rmsdfiles) stdout=@plot_data; +} + +file pdb <"cg_clath_cage.pdb">; +file psf <"cg_clath_cage.psf">; + +file rmsds[]; + +string sweepMax=@arg("max","0.6"), sweepDelta=@arg("delta","0.5"); + +string beadids[] = readData(genConfigs(sweepMax, sweepDelta)); + +trace("Processing these bead IDs:", beadids); + +foreach beadid, i in beadids { + file conf ; + file inp ; + file vmdtcl ; + + file log ; + file dat ; + + (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid); + rmsds[i] = dat; +} + +file plot_out <"OUT/plot_pd.txt">; +plot_out = analyze(rmsds); Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,56 @@ +#==================================== +# THis script will measure the +# the average angles, bond lengths +# and dihedral angles. +# +# -FXV Oct, 2011 +#=================================== + +mol delete all + +# set atom selection +set seltext "type HB AK" + +# Set the initial frame +set inifrm 200 + +set psf cg_clath_cage.psf +set pdb cg_clath_cage.pdb +set dcd OUT/FILEID.dcd + +# Load input files +mol load psf $psf +# Load trajectory +mol addfile $pdb type pdb +mol addfile $dcd type dcd first $inifrm last -1 waitfor all + +# Get molecule information +set mol [molinfo top] + +# Get the number of frames +set nmfrm [molinfo $mol get numframes] +puts "number of frames $nmfrm" + +# open rmsd file +set frmsd [open RMSD/FILEID.dat w] + +# Select atoms +set ref [atomselect top $seltext frame 0] + +# Loop over the number of frames +for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} { + + set sel [atomselect top $seltext frame $ifrm] + + set irmsd [measure rmsd $ref $sel] + + lappend rmsdlist $irmsd + + +} + +# Analysis +puts $frmsd "B1 B2 [vecmean $rmsdlist]" + +exit + Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,7 @@ +PATH=$PATH:$PWD + +# export SBATCH_RESERVATION=swift_test + +mkdir -p CONF PAR VMD RMSD OUT + +swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5} Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,10 @@ +#!/bin/bash + +mkdir -p saved/run000 +rundir=saved/run$(cd saved; /bin/ls -1 | tail -1 | sed -e 's/run//' | awk '{printf("%03d",$1+1)}') +mkdir $rundir +rmdir saved/run000 + +echo Saving run in $rundir + +mv *.log *.rlog *.d *.kml _concurrent *.swiftx CONF PAR VMD RMSD OUT $rundir 2>/dev/null Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,104 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + westmere + 12 + pi-gavoth + + + 1 + 2 + 2 + .03 + + + 00:15:00 + 1800 + + + true + single + 1 + 100 + 100 + 10000 + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + sandyb + 12 + pi-gavoth + + + 1 + 1 + 1 + .03 + + + 00:15:00 + 1800 + + + false + single + 1 + 100 + 100 + 10000 + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + bigmem + 16 + pi-gavoth + + + 1 + 1 + 1 + .03 + + + 00:05:00 + 1800 + + + false + single + 1 + 100 + 100 + 10000 + + + + + /scratch/midway/{env.USER}/swiftwork + + + Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,45 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +# Create NAMD input file for short simulations +# to sweep the nonbonded parameter space +# +# ARGS: dir max delta # FIXME: add bead names and epsilon + +chdir($ARGV[0]); + +# Bead names + +my $b1name = "PX"; +my $b2name = "DT"; + +# Bead ranges + +my $b1min=0.0; +my $b2min=0.0; + +my $b1max = $ARGV[1]; +my $b2max = $ARGV[1]; +my $del = $ARGV[2]; +my $eps = "-0.01"; + +my $b1=$b1min; +while ($b1<=$b1max) { + my $b2=$b2min; + while ($b2<=$b2max) { + + my $s1=sprintf("%05.2f",$b1); + my $s2=sprintf("%05.2f",$b2); + my $fileid="${b1name}_${s1}_${b2name}_${s2}"; + + print("$fileid\n"); + system("sed -e s/FILEID/${fileid}/g cg_clath_cage.temp.conf > CONF/$fileid.conf"); + system("sed -e s/FILEID/${fileid}/g -e s/B1/$s1/ -e s/B2/$s2/ rmsd.temp.tcl > VMD/$fileid.tcl"); + system("sed -e s/HBEPS/$eps/ -e s/PXEPS/-$s1/ -e s/DTEPS/-$s2/ -e s/AKEPS/$eps/ -e s/LTEPS/$eps/ par_cg_clath.temp.inp > PAR/$fileid.inp"); + + $b2 = $b2+$del; + } + $b1 = $b1+$del; +} Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl ___________________________________________________________________ Added: svn:executable + * Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,8 @@ + +local gensweep sweep_pd.pl null null null +local analyze analyze_pd.pl null null null + +#bigmem rmsd rmsd.sh null null null +#sandyb rmsd rmsd.sh null null null +#trestles rmsd rmsd.sh null null null +westmere rmsd rmsd.sh null null null Added: SwiftTutorials/CMTS_2013-06-17/setup.csh =================================================================== --- SwiftTutorials/CMTS_2013-06-17/setup.csh (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/setup.csh 2013-06-16 13:30:27 UTC (rev 6559) @@ -0,0 +1,35 @@ + +module load swift + +setenv SBATCH_RESERVATION swift + +set DIR=`dirname ${0}` +cd $DIR +set DIR=`pwd` + +echo Adding $DIR/bin to PATH: +setenv PATH $DIR/bin:$PATH + +mkdir -p $HOME/.swift + +if ( -f $HOME/.swift/swift.properties ) then + echo Adding properties to end of $HOME/.swift/swift.properties +else + echo creating $HOME/.swift/swift.properties +endif + +cat >>$HOME/.swift/swift.properties <>$HOME/.swift/swift.properties < Author: yadunandb Date: 2013-06-17 14:35:25 -0500 (Mon, 17 Jun 2013) New Revision: 6577 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README Log: Commiting part09 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 19:21:41 UTC (rev 6576) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README 2013-06-17 19:35:25 UTC (rev 6577) @@ -1,14 +1,12 @@ -TOPIC: Example pipeline +TOPIC: Example pipeline with readData -This example shows combining two app calls in a pipeline. There are two apps -defined in this script: mysim4, and mysim4_filename. +This example shows combining two app calls in a pipeline. The mysim4 app from the +previous example part08 is called twice here. -mysim4 takes integer to determine the number of random numbers to generate. -mysim4_filename reads a file to determine the number of random numbers to generate +mysim4 takes an integer to determine the number of random numbers to generate. +The random number generated by mysim4 is read from its output file and redirected +as an argument to itself to generate a random number of random numbers. -In this example, we use mysim4 to generate a random number. The output of mysim4 -get passed as input to mysim4_filename. - To run $ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift 2013-06-17 19:35:25 UTC (rev 6577) @@ -0,0 +1,32 @@ +type file; + +app (file o) mysim4 (int timesteps, int range_value, int count_value) +{ + random4 timesteps range_value count_value stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; +int nsim = @toInt(@arg("nsim", "10")); +int steps = @toInt(@arg("steps", "1")); +int range = @toInt(@arg("range", "100")); +int count = @toInt(@arg("count", "10")); + +foreach i in [0:nsim-1] { + + file simout ; + simout = mysim4(steps, range, 1); + int rand = readData(simout); + + file simout2 ; + simout2 = mysim4(steps, range, rand); + + sims[i] = simout2; +} + +file stats<"output/average.out">; +stats = analyze(sims); From yadunandb at ci.uchicago.edu Mon Jun 17 14:37:12 2013 From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu) Date: Mon, 17 Jun 2013 19:37:12 -0000 Subject: [Swift-commit] r6578 - in SwiftTutorials/CMTS_2013-06-17/basic_swift: . part09 Message-ID: <20130617193711.5D53D9CC43@svn.ci.uchicago.edu> Author: yadunandb Date: 2013-06-17 14:37:11 -0500 (Mon, 17 Jun 2013) New Revision: 6578 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml Log: Committing Part09 example Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README 2013-06-17 19:37:11 UTC (rev 6578) @@ -0,0 +1,12 @@ + +TOPIC: Example pipeline with readData + +This example shows combining two app calls in a pipeline. The mysim4 app from the +previous example part08 is called twice here. + +mysim4 takes an integer to determine the number of random numbers to generate. +The random number generated by mysim4 is read from its output file and redirected +as an argument to itself to generate a random number of random numbers. + +To run +$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1 Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps 2013-06-17 19:37:11 UTC (rev 6578) @@ -0,0 +1,2 @@ +cmtsworkshop random4 random4.sh +localhost average avg.sh Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift 2013-06-17 19:37:11 UTC (rev 6578) @@ -0,0 +1,32 @@ +type file; + +app (file o) mysim4 (int timesteps, int range_value, int count_value) +{ + random4 timesteps range_value count_value stdout=@filename(o); +} + +app (file o) analyze (file s[]) +{ + average @filenames(s) stdout=@filename(o); +} + +file sims[]; +int nsim = @toInt(@arg("nsim", "10")); +int steps = @toInt(@arg("steps", "1")); +int range = @toInt(@arg("range", "100")); +int count = @toInt(@arg("count", "10")); + +foreach i in [0:nsim-1] { + + file simout ; + simout = mysim4(steps, range, 1); + int rand = readData(simout); + + file simout2 ; + simout2 = mysim4(steps, range, rand); + + sims[i] = simout2; +} + +file stats<"output/average.out">; +stats = analyze(sims); Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml (rev 0) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml 2013-06-17 19:37:11 UTC (rev 6578) @@ -0,0 +1,39 @@ + + + + + + /scratch/midway/{env.USER}/swiftwork + + + + + + + cmtsworkshop + 8 + cmtsworkshop + + + 4 + 1 + 1 + 8 + .31 + + + 00:15:00 + 1800 + + + + /scratch/midway/{env.USER}/swiftwork + + + false + 100 + 100 + 10000 + + + From yadunandb at ci.uchicago.edu Mon Jun 17 14:40:35 2013 From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu) Date: Mon, 17 Jun 2013 19:40:35 -0000 Subject: [Swift-commit] r6580 - SwiftTutorials/CMTS_2013-06-17/basic_swift/part09 Message-ID: <20130617194034.DADA59CC43@svn.ci.uchicago.edu> Author: yadunandb Date: 2013-06-17 14:40:34 -0500 (Mon, 17 Jun 2013) New Revision: 6580 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README Log: Updated README for part09 Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README 2013-06-17 19:37:38 UTC (rev 6579) +++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README 2013-06-17 19:40:34 UTC (rev 6580) @@ -5,8 +5,9 @@ previous example part08 is called twice here. mysim4 takes an integer to determine the number of random numbers to generate. -The random number generated by mysim4 is read from its output file and redirected -as an argument to itself to generate a random number of random numbers. +Firt mysim4 is called with 1 to generate 1 random number. Then the random number +generated by mysim4 is read from its output file by the readData function and +redirected as an argument to mysim4 to generate a random number of random numbers. To run -$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1 +$ swift p9.swift -steps=10 -range=100 -count=6 -nsim=1 From yadunandb at ci.uchicago.edu Mon Jun 17 15:01:52 2013 From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu) Date: Mon, 17 Jun 2013 20:01:52 -0000 Subject: [Swift-commit] r6583 - SwiftTutorials/CMTS_2013-06-17/namd_sweep Message-ID: <20130617200151.B9F8B9CC43@svn.ci.uchicago.edu> Author: yadunandb Date: 2013-06-17 15:01:51 -0500 (Mon, 17 Jun 2013) New Revision: 6583 Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README Log: Updated README Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README =================================================================== --- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-17 19:55:12 UTC (rev 6582) +++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-17 20:01:51 UTC (rev 6583) @@ -25,4 +25,5 @@ swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5 # 9 param sets (3 x 3) - +Output: + The output should be generated in the OUT/plot_pd.txt file. \ No newline at end of file From yadunandb at ci.uchicago.edu Tue Jun 18 10:58:12 2013 From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu) Date: Tue, 18 Jun 2013 15:58:12 -0000 Subject: [Swift-commit] r6586 - branches/release-0.94/tests/stress/internals Message-ID: <20130618155812.44C989CC43@svn.ci.uchicago.edu> Author: yadunandb Date: 2013-06-18 10:58:12 -0500 (Tue, 18 Jun 2013) New Revision: 6586 Added: branches/release-0.94/tests/stress/internals/swift.properties branches/release-0.94/tests/stress/internals/tc.template.data Modified: branches/release-0.94/tests/stress/internals/x_recursion.timeout Log: Updated test scripts. Added: branches/release-0.94/tests/stress/internals/swift.properties =================================================================== --- branches/release-0.94/tests/stress/internals/swift.properties (rev 0) +++ branches/release-0.94/tests/stress/internals/swift.properties 2013-06-18 15:58:12 UTC (rev 6586) @@ -0,0 +1,7 @@ +wrapperlog.always.transfer=true +sitedir.keep=true +execution.retries=0 +lazy.errors=false +status.mode=provider +use.provider.staging=false +provider.staging.pin.swiftfiles=false Added: branches/release-0.94/tests/stress/internals/tc.template.data =================================================================== --- branches/release-0.94/tests/stress/internals/tc.template.data (rev 0) +++ branches/release-0.94/tests/stress/internals/tc.template.data 2013-06-18 15:58:12 UTC (rev 6586) @@ -0,0 +1,2 @@ +local bash /bin/bash null null null + Modified: branches/release-0.94/tests/stress/internals/x_recursion.timeout =================================================================== --- branches/release-0.94/tests/stress/internals/x_recursion.timeout 2013-06-17 20:23:15 UTC (rev 6585) +++ branches/release-0.94/tests/stress/internals/x_recursion.timeout 2013-06-18 15:58:12 UTC (rev 6586) @@ -1 +1 @@ -99999 \ No newline at end of file +300 \ No newline at end of file From yadunandb at ci.uchicago.edu Tue Jun 18 13:35:40 2013 From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu) Date: Tue, 18 Jun 2013 18:35:40 -0000 Subject: [Swift-commit] r6587 - branches/release-0.94/tests/language-behaviour/IO Message-ID: <20130618183539.6619B9CC9A@svn.ci.uchicago.edu> Author: yadunandb Date: 2013-06-18 13:35:39 -0500 (Tue, 18 Jun 2013) New Revision: 6587 Added: branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected branches/release-0.94/tests/language-behaviour/IO/readData3.swift branches/release-0.94/tests/language-behaviour/IO/title.txt Log: Adding test to confirm Bug: 1028 Added: branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected =================================================================== --- branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected (rev 0) +++ branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected 2013-06-18 18:35:39 UTC (rev 6587) @@ -0,0 +1 @@ +9 \ No newline at end of file Added: branches/release-0.94/tests/language-behaviour/IO/readData3.swift =================================================================== --- branches/release-0.94/tests/language-behaviour/IO/readData3.swift (rev 0) +++ branches/release-0.94/tests/language-behaviour/IO/readData3.swift 2013-06-18 18:35:39 UTC (rev 6587) @@ -0,0 +1,23 @@ +type file; + +/* + Test case added to confirm Bug 1028 - readData in a foreach loop fails to compile. + https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1028 + + This test is expected to fail to compile till bug is resolved. +*/ + +app (file o) mysim (int i) +{ + echo i stdout=@filename(o); +} + +int nums[]; +foreach i in [0:9] { + file f ; + f = mysim(i); + nums[i] = readData(f); +} + +file result <"readData3.out">; +result = mysim(nums[i]); \ No newline at end of file Added: branches/release-0.94/tests/language-behaviour/IO/title.txt =================================================================== --- branches/release-0.94/tests/language-behaviour/IO/title.txt (rev 0) +++ branches/release-0.94/tests/language-behaviour/IO/title.txt 2013-06-18 18:35:39 UTC (rev 6587) @@ -0,0 +1 @@ +Language Behavior tests : Subgroup local IO