Author: eudoxos
Date: 2009-02-28 11:26:47 +0100 (Sat, 28 Feb 2009)
New Revision: 1699
Modified:
trunk/extra/clump/Shop.cpp
trunk/gui/py/timing.py
trunk/gui/py/utils.py
trunk/gui/py/yade-multi
trunk/pkg/common/Engine/StandAloneEngine/PersistentSAPCollider.cpp
Log:
1. Make Shop load 4/5/6 columns text files for spheres (and skip 5-cols)
2. Change evaluation of args in readParamsFromTable to be able to pass strings
better (single quotes) and consistently
3. Parameters passed as env. vars by yade-multi are prefixed with !
4. fix typo in timing for resetting timers.
Modified: trunk/extra/clump/Shop.cpp
===================================================================
--- trunk/extra/clump/Shop.cpp 2009-02-26 17:27:54 UTC (rev 1698)
+++ trunk/extra/clump/Shop.cpp 2009-02-28 10:26:47 UTC (rev 1699)
@@ -4,6 +4,7 @@
#include<limits>
#include<boost/filesystem/convenience.hpp>
+#include<boost/tokenizer.hpp>
#include<yade/core/MetaBody.hpp>
#include<yade/core/Body.hpp>
@@ -474,21 +475,29 @@
vector<pair<Vector3r,Real> > spheres;
ifstream sphereFile(fname.c_str());
if(!sphereFile.good()) throw std::runtime_error("File with spheres
`"+fname+"' couldn't be opened.");
- int tmp1,tmp2;
Vector3r C;
- Real r;
- while(!sphereFile.eof()){
- sphereFile>>C[0]; sphereFile>>C[1]; sphereFile>>C[2];
- sphereFile>>r;
- // TRVAR3(spheres.size(),C,r);
- sphereFile>>tmp1;
- if(r==1) continue; // arrrgh, boxes have 5 record/line, spheres
have 6; 4th number for box is 1 and we assume there is no sphere with radius 1;
Wenjie, I'm gonna tell you one day how smart this format is.
- if(sphereFile.eof()) continue; // prevents trailing newlines
from copying last sphere as well
- sphereFile>>tmp2; // read the 6th (unused) number for spheres
+ Real r=0;
+ string line;
+ size_t lineNo=0;
+ while(std::getline(sphereFile, line, '\n')){
+ lineNo++;
+ boost::tokenizer<boost::char_separator<char> >
toks(line,boost::char_separator<char>(" \t"));
+ int i=0;
+ FOREACH(const string& s, toks){
+ if(i<3) C[i]=lexical_cast<Real>(s);
+ if(i==4) r=lexical_cast<Real>(s);
+ i++;
+ }
+ if(i==0) continue; // empty line, skipped (can be the last one)
+ // Wenjie's format: 5 per line are boxes, which should be
skipped
+ if(i==5) continue;
+ if((i!=4) and (i!=6)) {
+ LOG_ERROR("Line "+lexical_cast<string>(lineNo)+" in the
spheres file "+fname+" has "+lexical_cast<string>(i)+" columns instead of 0,4,5
or 6.");
+ LOG_ERROR("The result may be garbage!");
+ }
for(int j=0; j<3; j++) {
minXYZ[j]=(spheres.size()>0?min(C[j]-r,minXYZ[j]):C[j]-r);
maxXYZ[j]=(spheres.size()>0?max(C[j]+r,maxXYZ[j]):C[j]+r);}
spheres.push_back(pair<Vector3r,Real>(C,r));
}
- //TRVAR2(minXYZ,maxXYZ);
return spheres;
}
Modified: trunk/gui/py/timing.py
===================================================================
--- trunk/gui/py/timing.py 2009-02-26 17:27:54 UTC (rev 1698)
+++ trunk/gui/py/timing.py 2009-02-28 10:26:47 UTC (rev 1699)
@@ -9,7 +9,7 @@
e.execTime,e.execCount=0,0
def reset():
- for e in O.engines(): _resetEngine(e)
+ for e in O.engines: _resetEngine(e)
_statCols={'label':40,'count':20,'time':20,'relTime':20}
_maxLev=3
Modified: trunk/gui/py/utils.py
===================================================================
--- trunk/gui/py/utils.py 2009-02-26 17:27:54 UTC (rev 1698)
+++ trunk/gui/py/utils.py 2009-02-28 10:26:47 UTC (rev 1699)
@@ -354,13 +354,13 @@
for i in range(len(names)):
if names[i]=='description':
o.tags['description']=values[i]
else:
- if names[i] not in kw.keys() and not unknownOk:
raise NameError("Parameter `%s' has no default value assigned"%names[i])
+ if names[i] not in kw.keys() and (not unknownOk
or names[i][0]=='!'): raise NameError("Parameter `%s' has no default value
assigned"%names[i])
if names[i] in kw.keys(): kw.pop(names[i])
- eq="%s=%s"%(names[i],values[i])
+ eq="%s=%s"%(names[i],repr(values[i]))
exec('__builtin__.%s=%s'%(names[i],values[i]));
tagsParams+=['%s=%s'%(names[i],values[i])]; dictParams[names[i]]=values[i]
defaults=[]
for k in kw.keys():
- exec("__builtin__.%s=%s"%(k,kw[k]))
+ exec("__builtin__.%s=%s"%(k,repr(kw[k])))
defaults+=["%s=%s"%(k,kw[k])]; dictDefaults[k]=kw[k]
o.tags['defaultParams']=",".join(defaults)
o.tags['params']=",".join(tagsParams)
Modified: trunk/gui/py/yade-multi
===================================================================
--- trunk/gui/py/yade-multi 2009-02-26 17:27:54 UTC (rev 1698)
+++ trunk/gui/py/yade-multi 2009-02-28 10:26:47 UTC (rev 1699)
@@ -125,7 +125,6 @@
ll=['']+open(table,'r').readlines()
availableLines=[i for i in range(len(ll)) if not
re.match(r'^\s*(#.*)?$',ll[i][:-1]) and i>1]
-print availableLines
# read actual data
values={}
@@ -171,7 +170,8 @@
else: logFile=logFile.replace('@',str(l))
envVars=[]
for col,head in enumerate(headings):
- if re.match('^[A-Z_]+[A-Z0-9_]+',head):
envVars+=['%s=%s'%(head,values[l][col])]
+ if head=='!EXEC': executable=values[l][col]
+ if head[0]=='!': envVars+=['%s=%s'%(head[1:],values[l][col])]
jobs.append(JobInfo(i,idStrings[l] if idStrings else
'#'+str(i),'PARAM_TABLE=%s:%d %s nice -n %d %s -N PythonUI -- -n -x %s > %s
2>&1'%(table,l,' '.join(envVars),nice,executable,simul,logFile),logFile))
print "Job summary:"
Modified: trunk/pkg/common/Engine/StandAloneEngine/PersistentSAPCollider.cpp
===================================================================
--- trunk/pkg/common/Engine/StandAloneEngine/PersistentSAPCollider.cpp
2009-02-26 17:27:54 UTC (rev 1698)
+++ trunk/pkg/common/Engine/StandAloneEngine/PersistentSAPCollider.cpp
2009-02-28 10:26:47 UTC (rev 1699)
@@ -26,6 +26,8 @@
zBounds.clear();
minima.clear();
maxima.clear();
+
+ //timingDeltas=shared_ptr<TimingDeltas>(new TimingDeltas);
}
PersistentSAPCollider::~PersistentSAPCollider()
@@ -38,6 +40,8 @@
rootBody=ncb;
shared_ptr<BodyContainer> bodies=ncb->bodies;
transientInteractions=ncb->transientInteractions;
+
+// timingDeltas->start();
if (2*bodies->size()!=xBounds.size()){
xBounds.resize(2*bodies->size());
@@ -47,6 +51,8 @@
maxima.resize(3*bodies->size());
}
+// timingDeltas->checkpoint("resizeArrays");
+
// Updates the minima and maxima arrays according to the new center and
radius of the spheres
int offset;
Vector3r min,max;
@@ -70,6 +76,9 @@
maxima[offset+0]=pos[0]; maxima[offset+1]=pos[1];
maxima[offset+2]=pos[2];
}
}
+
+// timingDeltas->checkpoint("minMaxUpdate");
+
typedef pair<body_id_t,body_id_t> bodyIdPair;
list<bodyIdPair> toBeDeleted;
FOREACH(const shared_ptr<Interaction>& I,*ncb->transientInteractions){
@@ -87,8 +96,13 @@
//if(!I->isReal){LOG_DEBUG("Interaction
#"<<I->getId1()<<"=#"<<I->getId2()<<" is not real.");}
}
FOREACH(const bodyIdPair& p, toBeDeleted){
transientInteractions->erase(p.first,p.second); }
+
+// timingDeltas->checkpoint("deleteInvalid");
updateIds(bodies->size());
+
+// timingDeltas->checkpoint("updateIds");
+
nbObjects=bodies->size();
// permutation sort of the AABBBounds along the 3 axis performed in a
independant manner
@@ -101,6 +115,8 @@
//#pragma omp section
sortBounds(zBounds, nbObjects);
}
+
+// timingDeltas->checkpoint("sortBounds");
}
bool PersistentSAPCollider::probeBoundingVolume(const BoundingVolume& bv)
@@ -132,6 +148,8 @@
int begin=0, end=nbElements;
if (nbElements>nbObjects) begin=nbObjects;
+ //timingDeltas->start();
+
// initialization if the xBounds, yBounds, zBounds
for(int i=begin;i<end;i++){
xBounds[2*i] = shared_ptr<AABBBound>(new
AABBBound(i,1));
@@ -142,6 +160,8 @@
zBounds[2*i+1] = shared_ptr<AABBBound>(new
AABBBound(i,0));
}
+ //timingDeltas->checkpoint("init");
+
// initialization if the field "value" of the xBounds, yBounds,
zBounds arrays
updateBounds(nbElements);
@@ -149,16 +169,22 @@
// The first time these arrays are not sorted so it is faster
to use such a sort instead
// of the permutation we are going to use next
std::sort(xBounds.begin(),xBounds.begin()+2*nbElements,AABBBoundComparator());
+ //timingDeltas->checkpoint("sortX");
std::sort(yBounds.begin(),yBounds.begin()+2*nbElements,AABBBoundComparator());
+ //timingDeltas->checkpoint("sortY");
std::sort(zBounds.begin(),zBounds.begin()+2*nbElements,AABBBoundComparator());
+ //timingDeltas->checkpoint("sortZ");
// initialize the overlappingBB collection
//for(unsigned int j=0;j<nbElements;j++)
// overlappingBB[j].clear(); //attention memoire
findOverlappingBB(xBounds, nbElements);
+ //timingDeltas->checkpoint("findX");
findOverlappingBB(yBounds, nbElements);
+ //timingDeltas->checkpoint("findY");
findOverlappingBB(zBounds, nbElements);
+ //timingDeltas->checkpoint("findZ");
}
else updateBounds(nbElements);
}
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