ENH: parallel runTimeModifiable - master only

doc/changes/inotify.txt

@@ -24,21 +24,63 @@ be quite a gain on large numbers of processors.
 
 
 - all file monitoring is done by an instance of 'fileMonitor' in the Time
-class. The fileMonitor class can be found in OSspecific. Default is
-to use the (linux-specific) 'inotify' system calls.
-If compiled with -DFOAM_USE_STAT it will revert to the current 'stat' system
-calls.
+class. The fileMonitor class can be found in OSspecific. It uses either
+timestamps as before or the (linux-specific) 'inotify' system framework
+(available only if compiled with -DFOAM_USE_INOTIFY).
 
 
-- inotify does not need timestamps. There is no need for fileModificationSkew
-to allow for time differences. (there can still temporarily be a difference
-in modified status between different processors due to nfs lagging)
+- the monitoring can be done in one of four modes as set by
+    OptimisationSwitches::fileModificationChecking
+
+    - timeStamp : old behaviour : all nodes check the timestamp
+    - inotify   : using inotify instead of timestamps
+    - timeStampMaster,inotifyMaster : only the master node checks the file
+                and only the master node reads it and distribute it to the
+                slaves. This makes runTimeModifiable possible on distributed
+                running (see below).
+
+- distributed running:
+    - set fileModificationChecking to e.g. timeStampMaster
+    - decompose a case, e.g. cavity
+    - copy system and constant to processor0/
+    - put the all the processor* directories on the wanted nodes inside
+      the case directory. E.g.
+        - on master have /tmp/cavity/processor0
+        - on slaveN have /tmp/cavity/processorN
+    - so to reiterate:
+        - there is no need for cavity/constant or cavity/system, all the
+          dictionaries are only in processor0/constant or processor0/system
+        - the slave processor directories have no system directory and the
+          constant directory only contains the mesh.
+    - start the job in distributed mode by specifying the slave roots
+      (so one less than the number of processors) with
+      the -roots command line option:
+
+        mpirun -np 2 icoFoam -roots '("/tmp")' -parallel
+
+    - the alternative to the -roots option is to have a
+      cavity/system/decomposeParDict on the master with
+            distributed     yes;
+            roots           ("/tmp");
 
 
+Details:
+- timeStampMaster, inotifyMaster : this works only for IOdictionaries that
+are READ_IF_MODIFIED. It means that slaves read exactly the same dictionary
+as the master so cannot be used for dictionaries that contain e.g. mesh
+specific information.
+
+- inotify is a monitoring framework used to monitor changes in
+lots of files (e.g. used in desktop searched like beagle). You specify
+files to monitor and then get warned for any changes to these files.
+It does not need timestamps. There is no need for fileModificationSkew
+to allow for time differences. (there can still temporarily be a difference
+in modified status between different processors due to nfs lagging). The big
+problem is that it does not work over nfs3 (not sure about nfs4).
+
 - fileMonitor stores two hashtables per file so there is a small overhead
 adding and removing files from monitoring.
 
-
 - if runTimeModifiable is false at start of run no files will get monitored,
 however if runTimeModified gets set to false during the run the files
 will still get monitored (though never reloaded). This is only a hypothetical
@@ -46,7 +88,6 @@ problem in that the kernel still stores events for the monitored files. However
 inotify is very efficient - e.g. it gets used to track changes on file systems
 for desktop search engines.
 
-
 - in the old system one could call modified() on any object and get
 and uptodate state. In the new system it will return the state from
 the last runTime++ (which if it triggered any re-reads will have reset the

etc/controlDict

@@ -872,6 +872,14 @@ InfoSwitches
 OptimisationSwitches
 {
     fileModificationSkew 10;
+
+    //- Modification checking:
+    //  - timeStamp         : use modification time on file
+    //  - inotify           : use inotify framework
+    //  - timeStampMaster   : do time stamp (and file reading) only on master. 
+    //  - inotifyMaster     : do inotify (and file reading) only on master. 
+    fileModificationChecking timeStampMaster;//inotify;timeStamp;inotifyMaster;
+
     commsType       nonBlocking; //scheduled; //blocking;
     floatTransfer   0;
     nProcsSimpleSum 0;

src/OSspecific/POSIX/Allwmake

@@ -12,9 +12,9 @@ unset COMP_FLAGS LINK_FLAGS
 if [ -f /usr/include/sys/inotify.h -a "${1%USE_STAT}" = "$1" ]
 then
     echo "Found <sys/inotify.h>  --  using inotify for file monitoring."
-    unset COMP_FLAGS
+    export COMP_FLAGS="-DFOAM_USE_INOTIFY"
 else
-    export COMP_FLAGS="-DFOAM_USE_STAT"
+    unset COMP_FLAGS
 fi
 
 

src/OSspecific/POSIX/fileMonitor.H

@@ -28,10 +28,11 @@ Description
     Checking for changes to files.
 
 Note
-    The default is to use inotify (Linux specific, since 2.6.13)
+    The default is to use stat to get the timestamp.
 
-    Compiling with FOAM_USE_STAT (or if /usr/include/sys/inotify.h
-    does not exist) uses the stat function call.
+    Compile with FOAM_USE_INOTIFY to use the inotify
+    (Linux specific, since 2.6.13) framework. The problem is that inotify does
+    not work on nfs3 mounted directories!!
 
 SourceFiles
     fileMonitor.C
@@ -78,6 +79,9 @@ public:
 private:
     // Private data
 
+        //- Whether to use inotify (requires -DFOAM_USE_INOTIFY, see above)
+        const bool useInotify_;
+
         //- State for all watchFds
         mutable DynamicList<fileState> state_;
 
@@ -111,7 +115,7 @@ public:
     // Constructors
 
         //- Construct null
-        fileMonitor();
+        fileMonitor(const bool useInotify);
 
 
     //- Destructor
@@ -133,7 +137,11 @@ public:
         fileState getState(const label watchFd) const;
 
         //- Check state of all files. Updates state_.
-        void updateStates(const bool syncPar) const;
+        void updateStates
+        (
+            const bool masterOnly,
+            const bool syncPar
+        ) const;
 
         //- Reset state (e.g. after having read it) using handle
         void setUnmodified(const label watchFd);

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionary.C

@@ -31,12 +31,61 @@ Description
 
 #include "IOdictionary.H"
 #include "objectRegistry.H"
+#include "Pstream.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 defineTypeNameAndDebug(Foam::IOdictionary, 0);
 
 
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+// Parallel aware reading, using non-virtual type information (typeName instead
+// of type()) because of use in constructor.
+void Foam::IOdictionary::readFile(const bool masterOnly)
+{
+    if (Pstream::master() || !masterOnly)
+    {
+        if (debug)
+        {
+            Pout<< "IOdictionary : Reading " << objectPath()
+                << " from file " << endl;
+        }
+        readStream(typeName) >> *this;
+        close();
+    }
+
+    if (masterOnly)
+    {
+        // Scatter master data
+        if (Pstream::master())
+        {
+            for
+            (
+                int slave=Pstream::firstSlave();
+                slave<=Pstream::lastSlave();
+                slave++
+            )
+            {
+
+                OPstream toSlave(Pstream::scheduled, slave);
+                IOdictionary::writeData(toSlave);
+            }
+        }
+        else
+        {
+            if (debug)
+            {
+                Pout<< "IOdictionary : Reading " << objectPath()
+                    << " from master processor " << Pstream::masterNo() << endl;
+            }
+            IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
+            IOdictionary::readData(fromMaster);
+        }
+    }
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::IOdictionary::IOdictionary(const IOobject& io)
@@ -56,17 +105,41 @@ Foam::IOdictionary::IOdictionary(const IOobject& io)
             //<< abort(FatalError);
     }
 
+    // Everyone check or just master
+    bool masterOnly = 
+        regIOobject::fileModificationChecking == timeStampMaster
+     || regIOobject::fileModificationChecking == inotifyMaster;
+
+
+    // Check if header is ok for READ_IF_PRESENT
+    bool isHeaderOk = false;
+    if (io.readOpt() == IOobject::READ_IF_PRESENT)
+    {
+        if (masterOnly)
+        {
+            if (Pstream::master())
+            {
+                isHeaderOk = headerOk();
+            }
+            Pstream::scatter(isHeaderOk);
+        }
+        else
+        {
+            isHeaderOk = headerOk();
+        }
+    }
+
+
     if
     (
         (
             io.readOpt() == IOobject::MUST_READ
          || io.readOpt() == IOobject::MUST_READ_IF_MODIFIED
         )
-     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
+     || isHeaderOk
     )
     {
-        readStream(typeName) >> *this;
-        close();
+        readFile(masterOnly);
     }
 
     dictionary::name() = IOobject::objectPath();
@@ -90,17 +163,41 @@ Foam::IOdictionary::IOdictionary(const IOobject& io, const dictionary& dict)
             << endl;
     }
 
+    // Everyone check or just master
+    bool masterOnly = 
+        regIOobject::fileModificationChecking == timeStampMaster
+     || regIOobject::fileModificationChecking == inotifyMaster;
+
+
+    // Check if header is ok for READ_IF_PRESENT
+    bool isHeaderOk = false;
+    if (io.readOpt() == IOobject::READ_IF_PRESENT)
+    {
+        if (masterOnly)
+        {
+            if (Pstream::master())
+            {
+                isHeaderOk = headerOk();
+            }
+            Pstream::scatter(isHeaderOk);
+        }
+        else
+        {
+            isHeaderOk = headerOk();
+        }
+    }
+
+
     if
     (
         (
             io.readOpt() == IOobject::MUST_READ
          || io.readOpt() == IOobject::MUST_READ_IF_MODIFIED
         )
-     || (io.readOpt() == IOobject::READ_IF_PRESENT && headerOk())
+     || isHeaderOk
     )
     {
-        readStream(typeName) >> *this;
-        close();
+        readFile(masterOnly);
     }
     else
     {

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionary.H

@@ -57,6 +57,11 @@ class IOdictionary
     public dictionary
 {
 
+    // Private Member Functions
+
+        //- read dictionary from file
+        void readFile(const bool);
+
 public:
 
     TypeName("dictionary");

src/OpenFOAM/db/Time/Time.C

@@ -250,8 +250,27 @@ Foam::Time::Time
     // Time objects not registered so do like objectRegistry::checkIn ourselves.
     if (runTimeModifiable_)
     {
-        monitorPtr_.reset(new fileMonitor());
-        controlDict_.watchIndex() = addWatch(controlDict_.filePath());
+        monitorPtr_.reset
+        (
+            new fileMonitor
+            (
+                regIOobject::fileModificationChecking == inotify
+             || regIOobject::fileModificationChecking == inotifyMaster
+            )
+        );
+
+        // File might not exist yet.
+        fileName f(controlDict_.filePath());
+
+        if (!f.size())
+        {
+            // We don't have this file but would like to re-read it.
+            // Possibly if in master-only reading mode. Use a non-existing
+            // file to keep fileMonitor synced.
+            f = controlDict_.objectPath();
+        }
+
+        controlDict_.watchIndex() = addWatch(f);
     }
 }
 
@@ -308,19 +327,36 @@ Foam::Time::Time
     readLibs_(controlDict_, "libs"),
     functionObjects_(*this)
 {
+    // Since could not construct regIOobject with setting:
+    controlDict_.readOpt() = IOobject::MUST_READ_IF_MODIFIED;
+
+
     setControls();
 
     // Time objects not registered so do like objectRegistry::checkIn ourselves.
     if (runTimeModifiable_)
     {
-        monitorPtr_.reset(new fileMonitor());
+        monitorPtr_.reset
+        (
+            new fileMonitor
+            (
+                regIOobject::fileModificationChecking == inotify
+             || regIOobject::fileModificationChecking == inotifyMaster
+            )
+        );
 
         // File might not exist yet.
         fileName f(controlDict_.filePath());
-        if (f != fileName::null)
+
+        if (!f.size())
         {
-            controlDict_.watchIndex() = addWatch(f);
+            // We don't have this file but would like to re-read it.
+            // Possibly if in master-only reading mode. Use a non-existing
+            // file to keep fileMonitor synced.
+            f = controlDict_.objectPath();
         }
+
+        controlDict_.watchIndex() = addWatch(f);
     }
 }
 

src/OpenFOAM/db/Time/TimeIO.C

@@ -211,7 +211,14 @@ void Foam::Time::readModifiedObjects()
         // valid filePath).
         // Note: requires same ordering in objectRegistries on different
         // processors!
-        monitorPtr_().updateStates(Pstream::parRun());
+        monitorPtr_().updateStates
+        (
+            (
+                regIOobject::fileModificationChecking == inotifyMaster
+             || regIOobject::fileModificationChecking == timeStampMaster
+            ),
+            Pstream::parRun()
+        );
 
         // Time handling is special since controlDict_ is the one dictionary
         // that is not registered to any database.

src/OpenFOAM/db/regIOobject/regIOobject.C

@@ -36,6 +36,35 @@ int Foam::regIOobject::fileModificationSkew
     Foam::debug::optimisationSwitch("fileModificationSkew", 30)
 );
 
+namespace Foam
+{
+    template<>
+    const char* Foam::NamedEnum<Foam::regIOobject::fileCheckTypes, 4>::names[] =
+    {
+        "timeStamp",
+        "timeStampMaster",
+        "inotify",
+        "inotifyMaster"
+    };
+}
+
+
+const Foam::NamedEnum<Foam::regIOobject::fileCheckTypes, 4>
+    Foam::regIOobject::fileCheckTypesNames;
+
+// Default fileCheck type
+Foam::regIOobject::fileCheckTypes Foam::regIOobject::fileModificationChecking
+(
+    fileCheckTypesNames.read
+    (
+        debug::optimisationSwitches().lookup
+        (
+            "fileModificationChecking"
+            //Foam::regIOobject::timeStamp
+        )
+    )
+);
+
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -149,10 +178,13 @@ bool Foam::regIOobject::checkIn()
             }
 
             fileName f = filePath();
-            if (f != fileName::null)
+            if (!f.size())
             {
-                watchIndex_ = time().addWatch(f);
+                // We don't have this file but would like to re-read it.
+                // Possibly if master-only reading mode.
+                f = objectPath();
             }
+            watchIndex_ = time().addWatch(f);
         }
 
         // check-in on defaultRegion is allowed to fail, since subsetted meshes

src/OpenFOAM/db/regIOobject/regIOobject.H

@@ -41,6 +41,7 @@ SourceFiles
 #include "IOobject.H"
 #include "typeInfo.H"
 #include "OSspecific.H"
+#include "NamedEnum.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -57,6 +58,20 @@ class regIOobject
     public IOobject
 {
 
+public:
+
+    //- Types of communications
+    enum fileCheckTypes
+    {
+        timeStamp,
+        timeStampMaster,
+        inotify,
+        inotifyMaster
+    };
+
+    static const NamedEnum<fileCheckTypes, 4> fileCheckTypesNames;
+
+
 private:
 
     // Private data
@@ -95,6 +110,8 @@ public:
 
         static int fileModificationSkew;
 
+        static fileCheckTypes fileModificationChecking;
+
 
     // Constructors
 

src/OpenFOAM/db/regIOobject/regIOobjectRead.C

@@ -26,7 +26,7 @@ License
 #include "regIOobject.H"
 #include "IFstream.H"
 #include "Time.H"
-//#include "PstreamReduceOps.H"
+#include "Pstream.H"
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
@@ -170,8 +170,50 @@ bool Foam::regIOobject::readData(Istream&)
 
 bool Foam::regIOobject::read()
 {
-    bool ok = readData(readStream(type()));
-    close();
+    // Note: cannot do anything in readStream itself since this is used by
+    // e.g. GeometricField.
+
+    bool masterOnly = 
+        regIOobject::fileModificationChecking == timeStampMaster
+     || regIOobject::fileModificationChecking == inotifyMaster;
+
+    bool ok;
+    if (Pstream::master() || !masterOnly)
+    {
+        ok = readData(readStream(type()));
+        close();
+    }
+
+    if (masterOnly)
+    {
+        // Scatter master data
+        if (Pstream::master())
+        {
+            for
+            (
+                int slave=Pstream::firstSlave();
+                slave<=Pstream::lastSlave();
+                slave++
+            )
+            {
+
+                OPstream toSlave(Pstream::scheduled, slave);
+                writeData(toSlave);
+            }
+        }
+        else
+        {
+            if (IFstream::debug)
+            {
+                Pout<< "regIOobject::read() : "
+                    << "reading object " << name()
+                    << " from master processor " << Pstream::masterNo()
+                    << endl;
+            }
+            IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
+            ok = readData(fromMaster);
+        }
+    }
     return ok;
 }
 

src/OpenFOAM/global/argList/argList.C

@@ -55,6 +55,12 @@ Foam::argList::initValidTables::initValidTables()
     );
     argList::addBoolOption("parallel", "run in parallel");
     validParOptions.set("parallel", "");
+    argList::addOption
+    (
+        "roots", "(dir1 .. dirn)",
+        "slave root directories for distributed running"
+    );
+    validParOptions.set("roots", "(dir1 .. dirn)");
 
     Pstream::addValidParOptions(validParOptions);
 }
@@ -511,6 +517,10 @@ Foam::argList::argList
     // Case is a single processor run unless it is running parallel
     int nProcs = 1;
 
+    // Roots if running distributed
+    fileNameList roots;
+
+
     // If this actually is a parallel run
     if (parRunControl_.parRun())
     {
@@ -520,28 +530,42 @@ Foam::argList::argList
             // establish rootPath_/globalCase_/case_ for master
             getRootCase();
 
-            IFstream decompDictStream
-            (
-                rootPath_/globalCase_/"system/decomposeParDict"
-            );
+            // See if running distributed (different roots for different procs)
+            label dictNProcs = -1;
+            fileName source;
 
-            if (!decompDictStream.good())
+            if (options_.found("roots"))
             {
-                FatalError
-                    << "Cannot read "
-                    << decompDictStream.name()
-                    << exit(FatalError);
+                IStringStream str(options_["roots"]);
+                str >> roots;
+                dictNProcs = roots.size()+1;
+                source = "roots-command-line";
             }
+            else
+            {
+                source = rootPath_/globalCase_/"system/decomposeParDict";
+                IFstream decompDictStream(source);
 
-            dictionary decompDict(decompDictStream);
+                if (!decompDictStream.good())
+                {
+                    FatalError
+                        << "Cannot read "
+                        << decompDictStream.name()
+                        << exit(FatalError);
+                }
 
-            label dictNProcs
-            (
-                readLabel
+                dictionary decompDict(decompDictStream);