From noreply at svn.ci.uchicago.edu Sun Jan 2 16:31:01 2011
From: noreply at svn.ci.uchicago.edu (noreply at svn.ci.uchicago.edu)
Date: Sun, 2 Jan 2011 16:31:01 -0600 (CST)
Subject: [Swift-commit] r3836 - in trunk/src/org/griphyn/vdl: karajan/lib
mapping
Message-ID: <20110102223101.7C9E9FC41@svn.ci.uchicago.edu>
Author: hategan
Date: 2011-01-02 16:31:00 -0600 (Sun, 02 Jan 2011)
New Revision: 3836
Modified:
trunk/src/org/griphyn/vdl/karajan/lib/CloseDataset.java
trunk/src/org/griphyn/vdl/karajan/lib/SetFieldValue.java
trunk/src/org/griphyn/vdl/karajan/lib/VDLFunction.java
trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java
trunk/src/org/griphyn/vdl/mapping/ArrayDataNode.java
trunk/src/org/griphyn/vdl/mapping/Path.java
Log:
merged changes from 1.0 branch
Modified: trunk/src/org/griphyn/vdl/karajan/lib/CloseDataset.java
===================================================================
--- trunk/src/org/griphyn/vdl/karajan/lib/CloseDataset.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/karajan/lib/CloseDataset.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -6,6 +6,7 @@
import org.apache.log4j.Logger;
import org.globus.cog.karajan.arguments.Arg;
import org.globus.cog.karajan.stack.VariableStack;
+import org.globus.cog.karajan.util.TypeUtil;
import org.globus.cog.karajan.workflow.ExecutionException;
import org.griphyn.vdl.mapping.DSHandle;
import org.griphyn.vdl.mapping.InvalidPathException;
@@ -13,12 +14,13 @@
public class CloseDataset extends VDLFunction {
public static final Logger logger = Logger.getLogger(CloseDataset.class);
+
+ public static final Arg OA_CHILDREN_ONLY = new Arg.Optional("childrenOnly", Boolean.FALSE);
static {
- setArguments(CloseDataset.class, new Arg[] { PA_VAR, OA_PATH });
+ setArguments(CloseDataset.class, new Arg[] { PA_VAR, OA_PATH, OA_CHILDREN_ONLY });
}
- // TODO path is not used!
public Object function(VariableStack stack) throws ExecutionException {
Path path = parsePath(OA_PATH.getValue(stack), stack);
DSHandle var = (DSHandle) PA_VAR.getValue(stack);
@@ -27,7 +29,13 @@
logger.debug("Closing " + var);
}
var = var.getField(path);
- closeChildren(stack, var);
+
+ if (TypeUtil.toBoolean(OA_CHILDREN_ONLY.getValue(stack))) {
+ closeChildren(stack, var);
+ }
+ else {
+ closeDeep(stack, var);
+ }
}
catch (InvalidPathException e) {
throw new ExecutionException(e);
Modified: trunk/src/org/griphyn/vdl/karajan/lib/SetFieldValue.java
===================================================================
--- trunk/src/org/griphyn/vdl/karajan/lib/SetFieldValue.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/karajan/lib/SetFieldValue.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -42,6 +42,9 @@
if (!value.isClosed()) {
throw new FutureNotYetAvailable(addFutureListener(stack, value));
}
+ if (var.getParent() != null && var.getParent().getType().isArray()) {
+ markAsAvailable(stack, leaf.getParent(), leaf.getPathFromRoot().getLast());
+ }
}
synchronized (var.getRoot()) {
deepCopy(leaf, value, stack);
Modified: trunk/src/org/griphyn/vdl/karajan/lib/VDLFunction.java
===================================================================
--- trunk/src/org/griphyn/vdl/karajan/lib/VDLFunction.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/karajan/lib/VDLFunction.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -297,9 +297,10 @@
return relativize(String.valueOf(var.getValue()));
}
else {
- PhysicalFormat f;
- Path pathFromRoot = var.getPathFromRoot();
- f = mapper.map(pathFromRoot);
+ if (var.getMapper() == null) {
+ throw new ExecutionException("Cannot invoke filename() on data without a mapper: " + var);
+ }
+ PhysicalFormat f = var.getMapper().map(var.getPathFromRoot());
if (f instanceof GeneralizedFileFormat) {
String filename = ((GeneralizedFileFormat) f).getURIAsString();
if (filename == null) {
@@ -451,8 +452,31 @@
markToRoot(stack, handle);
}
}
+
+ protected void closeDeep(VariableStack stack, DSHandle handle)
+ throws ExecutionException, InvalidPathException {
+ synchronized(handle.getRoot()) {
+ closeDeep(stack, handle, getFutureWrapperMap(stack));
+ }
+ }
- private void markToRoot(VariableStack stack, DSHandle handle) throws ExecutionException {
+ private void closeDeep(VariableStack stack, DSHandle handle,
+ WrapperMap hash) throws InvalidPathException, ExecutionException {
+ handle.closeShallow();
+ hash.close(handle);
+ try {
+ // Mark all leaves
+ Iterator it = handle.getFields(Path.CHILDREN).iterator();
+ while (it.hasNext()) {
+ closeDeep(stack, (DSHandle) it.next(), hash);
+ }
+ }
+ catch (HandleOpenException e) {
+ throw new ExecutionException("Handle open in closeChildren",e);
+ }
+ }
+
+ private void markToRoot(VariableStack stack, DSHandle handle) throws ExecutionException {
// Also mark all arrays from root
Path fullPath = handle.getPathFromRoot();
DSHandle root = handle.getRoot();
Modified: trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java
===================================================================
--- trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -550,6 +550,26 @@
}
return pathFromRoot;
}
+
+ /**
+ * Recursively closes arrays through a tree of arrays and complex types.
+ */
+ public void closeArraySizes() {
+ if (!this.closed && this.getType().isArray()) {
+ closeShallow();
+ }
+ synchronized (handles) {
+ Iterator i = handles.entrySet().iterator();
+ while (i.hasNext()) {
+ Map.Entry e = (Map.Entry) i.next();
+ AbstractDataNode child = (AbstractDataNode) e.getValue();
+ if (child.getType().isArray() ||
+ child.getType().getFields().size() > 0) {
+ child.closeArraySizes();
+ }
+ }
+ }
+ }
public Mapper getMapper() {
return ((AbstractDataNode) getRoot()).getMapper();
Modified: trunk/src/org/griphyn/vdl/mapping/ArrayDataNode.java
===================================================================
--- trunk/src/org/griphyn/vdl/mapping/ArrayDataNode.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/mapping/ArrayDataNode.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -42,6 +42,24 @@
}
}
}
+
+ /** Recursively closes arrays through a tree of arrays and complex
+ types. */
+ public void closeDeep() {
+ assert(this.getType().isArray());
+ if (!this.isClosed()) {
+ closeShallow();
+ }
+ Map handles = getHandles();
+ synchronized (handles) {
+ Iterator i = handles.entrySet().iterator();
+ while (i.hasNext()) {
+ Map.Entry e = (Map.Entry) i.next();
+ AbstractDataNode child = (AbstractDataNode) e.getValue();
+ child.closeDeep();
+ }
+ }
+ }
public boolean isArray() {
Modified: trunk/src/org/griphyn/vdl/mapping/Path.java
===================================================================
--- trunk/src/org/griphyn/vdl/mapping/Path.java 2010-12-31 23:39:12 UTC (rev 3835)
+++ trunk/src/org/griphyn/vdl/mapping/Path.java 2011-01-02 22:31:00 UTC (rev 3836)
@@ -179,7 +179,7 @@
}
public String getLast() {
- return ((Entry) elements.get(elements.size() - 1)).name;
+ return ((Entry) elements.get(elements.size() - 1)).name;
}
public boolean isEmpty() {
From noreply at svn.ci.uchicago.edu Mon Jan 3 23:18:08 2011
From: noreply at svn.ci.uchicago.edu (noreply at svn.ci.uchicago.edu)
Date: Mon, 3 Jan 2011 23:18:08 -0600 (CST)
Subject: [Swift-commit] r3837 - trunk/src/org/griphyn/vdl/mapping
Message-ID: <20110104051808.6D2B89CCC2@svn.ci.uchicago.edu>
Author: hategan
Date: 2011-01-03 23:18:08 -0600 (Mon, 03 Jan 2011)
New Revision: 3837
Modified:
trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java
Log:
removed duplicate method after merge
Modified: trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java
===================================================================
--- trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java 2011-01-02 22:31:00 UTC (rev 3836)
+++ trunk/src/org/griphyn/vdl/mapping/AbstractDataNode.java 2011-01-04 05:18:08 UTC (rev 3837)
@@ -550,26 +550,6 @@
}
return pathFromRoot;
}
-
- /**
- * Recursively closes arrays through a tree of arrays and complex types.
- */
- public void closeArraySizes() {
- if (!this.closed && this.getType().isArray()) {
- closeShallow();
- }
- synchronized (handles) {
- Iterator i = handles.entrySet().iterator();
- while (i.hasNext()) {
- Map.Entry e = (Map.Entry) i.next();
- AbstractDataNode child = (AbstractDataNode) e.getValue();
- if (child.getType().isArray() ||
- child.getType().getFields().size() > 0) {
- child.closeArraySizes();
- }
- }
- }
- }
public Mapper getMapper() {
return ((AbstractDataNode) getRoot()).getMapper();
From noreply at svn.ci.uchicago.edu Mon Jan 3 23:28:18 2011
From: noreply at svn.ci.uchicago.edu (noreply at svn.ci.uchicago.edu)
Date: Mon, 3 Jan 2011 23:28:18 -0600 (CST)
Subject: [Swift-commit] r3838 - branches
Message-ID: <20110104052818.985F19CCC2@svn.ci.uchicago.edu>
Author: skenny
Date: 2011-01-03 23:28:18 -0600 (Mon, 03 Jan 2011)
New Revision: 3838
Added:
branches/release-0.92/
Log:
branching to stabilize for release
Copied: branches/release-0.92 (from rev 3837, trunk)
From noreply at svn.ci.uchicago.edu Tue Jan 4 14:06:02 2011
From: noreply at svn.ci.uchicago.edu (noreply at svn.ci.uchicago.edu)
Date: Tue, 4 Jan 2011 14:06:02 -0600 (CST)
Subject: [Swift-commit] r3839 - trunk/tests/groups
Message-ID: <20110104200602.4B31F9CC94@svn.ci.uchicago.edu>
Author: wozniak
Date: 2011-01-04 14:06:02 -0600 (Tue, 04 Jan 2011)
New Revision: 3839
Added:
trunk/tests/groups/group-mpi.sh
Log:
Add group-mpi
Added: trunk/tests/groups/group-mpi.sh
===================================================================
--- trunk/tests/groups/group-mpi.sh (rev 0)
+++ trunk/tests/groups/group-mpi.sh 2011-01-04 20:06:02 UTC (rev 3839)
@@ -0,0 +1,6 @@
+
+# GROUPLIST definition to run local MPI test
+
+GROUPLIST=( $TESTDIR/mpi )
+
+checkvars WORK
From noreply at svn.ci.uchicago.edu Tue Jan 4 15:41:40 2011
From: noreply at svn.ci.uchicago.edu (noreply at svn.ci.uchicago.edu)
Date: Tue, 4 Jan 2011 15:41:40 -0600 (CST)
Subject: [Swift-commit] r3840 - in www: . downloads inc main
Message-ID: <20110104214140.EAD059CC94@svn.ci.uchicago.edu>
Author: hategan
Date: 2011-01-04 15:41:40 -0600 (Tue, 04 Jan 2011)
New Revision: 3840
Added:
www/index.html
www/main/
www/main/index.php
Removed:
www/index.php
Modified:
www/downloads/index.php
www/inc/downloads_sidebar.php
www/inc/footer.php
www/inc/header.php
www/inc/home_sidebar.php
www/inc/nav.php
www/inc/papers_sidebar.php
Log:
made internal links relative
Modified: www/downloads/index.php
===================================================================
--- www/downloads/index.php 2011-01-04 20:06:02 UTC (rev 3839)
+++ www/downloads/index.php 2011-01-04 21:41:40 UTC (rev 3840)
@@ -226,7 +226,7 @@
Swift 0.4 - 2008/03/18
Swift v0.4 is a development release intended to release functionality
and fixes that have gone in to trunk since v0.3. More details are contained
-in the release notes.
+in the release notes.
[vdsk-0.4.tar.gz]
[release-notes-0.4.txt]
Modified: www/inc/downloads_sidebar.php
===================================================================
--- www/inc/downloads_sidebar.php 2011-01-04 20:06:02 UTC (rev 3839)
+++ www/inc/downloads_sidebar.php 2011-01-04 21:41:40 UTC (rev 3840)
@@ -1,6 +1,6 @@
GETTING STARTED
-Swift Quickstart Guide [html]
+Swift Quickstart Guide [html]
Use the Quickstart Guide to help you install and configure swift and run a simple 'Hello World' example.
BUG REPORTS
Modified: www/inc/footer.php
===================================================================
--- www/inc/footer.php 2011-01-04 20:06:02 UTC (rev 3839)
+++ www/inc/footer.php 2011-01-04 21:41:40 UTC (rev 3840)
@@ -1,7 +1,7 @@
-HOME
- : DOWNLOADS
- : SUPPORT
- : DOCUMENTATION
- : PAPERS
+HOME
+ : DOWNLOADS
+ : SUPPORT
+ : DOCUMENTATION
+ : PAPERS
Modified: www/inc/header.php
===================================================================
--- www/inc/header.php 2011-01-04 20:06:02 UTC (rev 3839)
+++ www/inc/header.php 2011-01-04 21:41:40 UTC (rev 3840)
@@ -1,3 +1,3 @@
-
-