[Swift-commit] r3674 - in SwiftApps/SwiftR: . Swift/man

Fri Oct 8 14:35:09 CDT 2010

Author: wilde
Date: 2010-10-08 14:35:09 -0500 (Fri, 08 Oct 2010)
New Revision: 3674

Removed:
   SwiftApps/SwiftR/UserGuide
Modified:
   SwiftApps/SwiftR/Swift/man/Swift-package.Rd
   SwiftApps/SwiftR/TODO
Log:
Move prelim User Gude text to Swift R package doc file Swift/man/Swift-package.Rd. Some updates to TODO list.

Modified: SwiftApps/SwiftR/Swift/man/Swift-package.Rd
===================================================================

--- SwiftApps/SwiftR/Swift/man/Swift-package.Rd	2010-10-08 19:15:02 UTC (rev 3673)
+++ SwiftApps/SwiftR/Swift/man/Swift-package.Rd	2010-10-08 19:35:09 UTC (rev 3674)
@@ -29,11 +29,111 @@
 
 options(swift.site=sitename) # sitename = "local" to run on the current host and "pbs" to submit to a local PBS cluster.
  
+PREREQS
+
+Sun Java (pref 1.6 - will it work below?)
+How to get Java if needed
+
+R v2.11 or higher in your PATH (on client and server machines)
+
+Ability to ssh to server machines (without password: agents, master control channel, etc)
+? Needed?  Passwords or ssh key passphrases OK for some scenarios.
+
+ssh from Mac
+ssh -A when jumping to a new host (to forward the ssh agent)
+
+or set up ssh agents manually
+
+(document ssh tricks here for pw-less access)
+
+
+CAVEATS
+
+# fixed: Only one Swift server running per user; can only be used by one R client workspace at a time.
+
+when fifos get hung, need to use kill or Quit to break out of R; will fix.
+
+no auto-restart yet if swift dies in server loop.
+
+only lapply is implemented (also SwiftApply) - need to see if we can cut down arg passing overhead for many of the apply() cases
+
+log records build up fast; these will be reduced as we get more confidence withthe code and shake out bugs
+
+initVar only affects first calls on a server - if you change these you need to start a new server (FIXME)!
+
+
+
+INSTALL
+
+cd ???
+wget http://www.ci.uchicago.edu/~wilde/Swift_0.1.tar.gz
+R CMS INSTALL Swift_0.1.tar.gz
+
+SVN
+
+svn checkout https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/SwiftR
+
+CONFIGURE SERVERS
+
+edit configure-site-NAME in exec/
+
+can put local cores into an ssh pool
+
+
+START SERVERS
+
+# do this outside of R
+
+SWIFT=<your package install dir>/Swift/
+$SWIFT/exec/start-swift-workers hostname
+$SWIFT/exec/start-swift-server 
+
+local and ssh servers can be started and left running, across R runs
+found via:
+
+HELLO WORLD TEST
+
+RUN FULL TEST
+
+source("Swift/tests/TestSwift.R")
+
+  or R CMD TEST etc?
+
+USAGE
+
+Swift returns Error object when remote side fails.
+
+options:
+  swift.server: matched server name on start-swift
+  swift.callsperbatch
+  initialize: 
+
+less likely to touch:
+  remove temp reqs (sp???) FIXME
+  mode (service, manual, ???)
+
+OPENMX EXAMPLES
+
+DEBUGGING
+
+* manual mode
+
+* logs to look at
+
+* reporting bugs: what to send  (FIXME: need swiftsnapshot script)
+
+* setting Swift worker logging with $HOME/.globus/coasters/loglevel file. This file should contain a single text integer: 0=most detailed, 4=least detaild, 5=off.  This is an interim log control mechanism and may be deprecated in the future.
+
 }
+
 \author{
-Michael Wilde
 
+Swift R package developed by Michael Wilde
+
+Swift was developed by: Mihael Hategan, Ben Clifford, Justin Wozniak, Yong Zhao, Ian Foster, and Michael Wilde with contributions from Sarah Kenny, Ioan Raicu, Luiz Gadelha, Allan Espinosa, Zhao Zhang, David Kelly, Jon Monette, Glen Hocky, Tom Uram, Wenjun Wu, and other users.
+
 Maintainer: Michael Wilde <wilde at mcs.anl.gov>
+
 }
 \references{
 http://www.ci/uchicago.edu/swift

Modified: SwiftApps/SwiftR/TODO
===================================================================
--- SwiftApps/SwiftR/TODO	2010-10-08 19:15:02 UTC (rev 3673)
+++ SwiftApps/SwiftR/TODO	2010-10-08 19:35:09 UTC (rev 3674)
@@ -1,5 +1,8 @@
 *** TO DO LIST:
 
+BUG: Passivate failing on swift pbs config on pads.
+^^^^^^^^^^^^^^^^^^
+
 MAIN
 
 - still seeing sleep 1 mutex?
@@ -16,6 +19,7 @@
 
 - make start-swift restartable within a single R swiftapply()
 
+- only lapply is implemented (also SwiftApply) - need to see if we can cut down arg passing overhead for many of the apply() cases
 
 x complete change for envvars like SWIFTR_TMP
 - add sourcing of $HOME/.SwiftR.init: pick up variables for the configure_ scripts from here; maybe one file in this dir for each site supported? maybe configure scripts go here?

Deleted: SwiftApps/SwiftR/UserGuide
===================================================================
--- SwiftApps/SwiftR/UserGuide	2010-10-08 19:15:02 UTC (rev 3673)
+++ SwiftApps/SwiftR/UserGuide	2010-10-08 19:35:09 UTC (rev 3674)
@@ -1,99 +0,0 @@
-Prelim Swift R User Guide
--------------------------
-
-
-PREREQS
-
-Sun Java (pref 1.6 - will it work below?)
-How to get Java if needed
-
-R v2.11 or higher in your PATH (on client and server machines)
-
-Ability to ssh to server machines (without password: agents, master control channel, etc)
-? Needed?  Passwords or ssh key passphrases OK for some scenarios.
-
-ssh from Mac
-ssh -A when jumping to a new host (to forward the ssh agent)
-
-or set up ssh agents manually
-
-(document ssh tricks here for pw-less access)
-
-
-CAVEATS
-
-# fixed: Only one Swift server running per user; can only be used by one R client workspace at a time.
-
-when fifos get hung, need to use kill or Quit to break out of R; will fix.
-
-no auto-restart yet if swift dies in server loop.
-
-
-only lapply is implemented (also SwiftApply) - need to see if we can cut down arg passing overhead for many of the apply() cases
-
-log records build up fast; these will be reduced as we get more confidence withthe code and shake out bugs
-
-initVar only affects first calls on a server - if you change these you need to start a new server (FIXME)!
-
-INSTALL
-
-cd ???
-wget http://www.ci.uchicago.edu/~wilde/Swift_0.1.tar.gz
-R CMS INSTALL Swift_0.1.tar.gz
-
-SVN
-
-svn checkout https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/SwiftR
-
-CONFIGURE SERVERS
-
-edit configure-site-NAME in exec/
-
-can put local cores into an ssh pool
-
-
-START SERVERS
-
-# do this outside of R
-
-SWIFT=<your package install dir>/Swift/
-$SWIFT/exec/start-swift-workers hostname
-$SWIFT/exec/start-swift-server 
-
-local and ssh servers can be started and left running, across R runs
-found via:
-
-HELLO WORLD TEST
-
-RUN FULL TEST
-
-source("Swift/tests/TestSwift.R")
-
-  or R CMD TEST etc?
-
-USAGE
-
-Swift returns Error object when remote side fails.
-
-options:
-  swift.server: matched server name on start-swift
-  swift.callsperbatch
-  initialize: 
-
-less likely to touch:
-  remove temp reqs (sp???) FIXME
-  mode (service, manual, ???)
-
-OPENMX EXAMPLES
-
-DEBUGGING
-
-* manual mode
-
-* logs to look at
-
-* reporting bugs: what to send
-  (FIXME: need swiftsnapshot script)
-
-
-


