Re: [Repast-interest] Repast HPC: compilation on Linux (icc) isuues

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Dear All

The problem is weird. I started a step by step compilation, starting with
header files only. Following is the sequence of inclusions:

FollowingObserver.h

AgentPackage.h

patchExt.h or Patch.h

Each file compiled individually.

Then I compiled main.cpp. It compiles unless I enable the statement:
runner.run<FollowingObserver, patchExt>(props); which generates following
error:

k330174@service0:~/sim/src/following> icpc main.cpp -lboost_mpi
-lboost_filesystem -lrepast_hpc-1.0 -lrelogo-1.0 -lmpi -lnetcdf_c++

FollowingObserver.h(29): warning #1125: function
"repast::relogo::Observer::setup(repast::Properties &)" is hidden by
"FollowingObserver::setup" -- virtual function override intended?

        void setup(repast::Properties props); // Setting up simulation

             ^

/usr/lib64/sgi/intel9/libimf.so: warning: warning: feupdateenv is not
implemented and will always fail

ld: warning: libboost_filesystem.so.1.33.1, needed by
/apps/repasthpc-1.0b/lib/librepast_hpc-1.0.so, may conflict with
libboost_filesystem.so.1.45.0

/tmp/icpcM2fXnu.o: In function `void
repast::relogo::SimulationRunner::run<FollowingObserver,
patchExt>(repast::Properties&)':

main.cpp:(.gnu.linkonce.t._ZN6repast6relogo16SimulationRunner3runI17Followin
gObserver8patchExtEEvRNS_10PropertiesE[.gnu.linkonce.t._ZN6repast6relogo16Si
mulationRunner3runI17FollowingObserver8patchExtEEvRNS_10PropertiesE]+0x6f2):
undefined reference to `FollowingObserver::setup(repast::Properties)'

/tmp/icpcM2fXnu.o: In function `FollowingObserver*
repast::relogo::WorldCreator::createWorld<FollowingObserver, patchExt,
repast::relogo::DefaultAgentCreator<patchExt>
>(repast::relogo::WorldDefinition const&, std::vector<int,
std::allocator<int> > const&,
repast::relogo::DefaultAgentCreator<patchExt>&)':

main.cpp:(.gnu.linkonce.t._ZN6repast6relogo12WorldCreator11createWorldI17Fol
lowingObserver8patchExtNS0_19DefaultAgentCreatorIS4_EEEEPT_RKNS0_15WorldDefi
nitionERKSt6vectorIiSaIiEERT1_[.gnu.linkonce.t._ZN6repast6relogo12WorldCreat
or11createWorldI17FollowingObserver8patchExtNS0_19DefaultAgentCreatorIS4_EEE
EPT_RKNS0_15WorldDefinitionERKSt6vectorIiSaIiEERT1_]+0x74): undefined
reference to `vtable for FollowingObserver'

Following is listing of all these files.

FollowingObserver.h:

/*

Header file for Model Observer; creating agent, commnads at agentset level
etc.

Has to be inherited from Observer class

started on july 13, 2011

Author: Kashif 

*/

#include "relogo/Observer.h"

#include "repast_hpc/AgentRequest.h"

#include "repast_hpc/Properties.h"

//#include "relogo/AgentSet.h"

#include "AgentPackage.h"

using namespace std;

class FollowingObserver : public repast::relogo::Observer {

private:

       repast::Properties props; // properites for creating agents ; setting
simulation

       int AmIType, nonAmIType; // Agents breeds

       int _saveCount; // global variable at all-agents level

public:

       FollowingObserver() : _saveCount(0) {}

       virtual ~FollowingObserver() {}

       //higher level observer

       void setup(repast::Properties props); // Setting up simulation

       void go(); // what to do at each iteration       

       //sub-observers

       void setupPatches();

       void initializeAmIDir();

       void intializeLeaders();

       void proximityCalc();

       //PRINT

       void printnonAmI();  

       void printAmI();

       void printPatches();

       // create and provide for agents moving between processes

repast::relogo::RelogoAgent* createAgent(const AgentPackage& content);

void provideContent(const repast::AgentRequest& request,
std::vector<AgentPackage>& out);

       // create and provide for buffer sync

void createAgents(std::vector<AgentPackage>& content,
std::vector<repast::relogo::RelogoAgent*>& out);

void provideContent(repast::relogo::RelogoAgent* agent,
std::vector<AgentPackage>& out);

       //SETTING UP GLOBAL PARAMETER: SAVED

       void incrementsaveCount() {

              _saveCount++;               

       }

       int saveCount() const {

              return _saveCount;

       }

};

AgentPackage.h:

#pragma once

#include "repast_hpc/AgentId.h"

using namespace repast;

//using namespace relogo;

struct AgentPackage {

       template<class Archive>

       void serialize(Archive& ar, const unsigned int version) {

              ar & id;

              ar & proc;

              ar & type;

              ar & ort; // both agent types

              ar & targetPID; // AmI             

              //nonAmI

              ar & leaderID;

              ar & prox_dummy;

              ar & isTunnel;

       }

       int id, proc, type;

              float ort;

              AgentId targetPID;

              AgentId leaderID;

              double prox_dummy;

              int isTunnel;

       repast::AgentId getId() const {

              return repast::AgentId(id, proc, type);

       }

};

patchExt.h or Patch.h:

/*

Header file for Patch Extentions to include structure

Has to be inherited from Patch class

started on july 13, 2011

Author: Kashif 

*/

#include "relogo/Patch.h"

#include "AgentPackage.h"

class patchExt : public repast::relogo::Patch {

private: 

       int _isTunnel; // patch variables

public:       

       patchExt(repast::AgentId id, repast::relogo::Observer* obs):
repast::relogo::Patch(id, obs), _isTunnel(-1) {} // overriden Turtle
constructor

       patchExt(repast::AgentId id, repast::relogo::Observer* obs, const
AgentPackage& package): repast::relogo::Patch(id, obs),
_isTunnel(package.isTunnel) {}

       virtual ~patchExt() {}

       void resetPatch();

       void applyn();

       void printPatch();

       int isTunnel() const {  // get variable          

              return _isTunnel;

       }      

};

Main.cpp:

/*

Main program

*/

#include <boost/mpi.hpp>

#include "repast_hpc/RepastProcess.h"

#include "relogo/SimulationRunner.h"

#include "patchExt.h"

#include "FollowingObserver.h"

namespace mpi = boost::mpi;

using namespace repast;

using namespace relogo;

void usage() {

       std::cerr << "usage: X  string string" << std::endl;

       std::cerr << "  first string: string is the path to the Repast HPC
\n\tconfiguartion properties file"

                     << std::endl;

       std::cerr << "  second string: string is the path to the model
properties file" << std::endl;

}

void runFollowing(std::string propsFile) {

       Properties props(propsFile);

       SimulationRunner runner;

       //runner.run<FollowingObserver, patchExt>(props);

       runner.run<FollowingObserver, patchExt>(props);

       //std::cerr << "******** RUNNING PROPERLY*********" << std::endl;

}

int main(int argc, char **argv) {

       mpi::environment env(argc, argv);

       std::string config, props;

       mpi::communicator world;

       if (argc == 3) {

              // assume short args where first arg is the config, and second
is model properties

              config = argv[1];

              props = argv[2];

       } else {

              //std::cerr << "usage: X  CALLED FROM POINT 1, MEANS ARGS NOT
3" << std::endl;

              if (world.rank() == 0) usage();

              return 0;

       }

       if (config.size() > 0 && props.size() > 0) {

              RepastProcess::init(config);

              runFollowing(props);        

       } else {

              if (world.rank() == 0) usage();

              return 0;

       }

       RepastProcess::instance()->done();

       return 0;

}

Regards.

---

Kashif Zia

PhD Candidate

Institut für Pervasive Computing, Johannes Kepler Universität Linz,
Altenberger Straße 69, A-4040 Linz

Room: P105, Phone: +43-732-2468-9673, Fax: +43-732-2468-8426
E-Mail:  <mailto:ka...@pe...> ka...@pe...

From: Kashif Zia [mailto:ka...@pe...] 
Sent: Thursday, July 28, 2011 11:50 AM
To: 'Kashif Zia'; rep...@li...
Subject: RE: [Repast-interest] Repast HPC: compilation on Linux (icc) isuues

Also tried to compile rumor model, stuck in these errors:

k330174@service0:~/sim/src/rumor> icpc main.cpp -lboost_mpi
-lboost_filesystem -lrepast_hpc-1.0 -lrelogo-1.0 -lmpi -lnetcdf_c++

/usr/lib64/sgi/intel9/libimf.so: warning: warning: feupdateenv is not
implemented and will always fail

ld: warning: libboost_filesystem.so.1.33.1, needed by
/apps/repasthpc-1.0b/lib/librepast_hpc-1.0.so, may conflict with
libboost_filesystem.so.1.45.0

/tmp/icpcRJuE4r.o: In function `main':

main.cpp:(.text+0x265): undefined reference to
`RumorModel::RumorModel(std::string const&)'

main.cpp:(.text+0x275): undefined reference to `RumorModel::init()'

main.cpp:(.text+0x28c): undefined reference to
`RumorModel::initSchedule(repast::ScheduleRunner&)'

/tmp/icpcRJuE4r.o: In function `runRumorModel(std::string)':

main.cpp:(.text+0x1369): undefined reference to
`RumorModel::RumorModel(std::string const&)'

main.cpp:(.text+0x1379): undefined reference to `RumorModel::init()'

main.cpp:(.text+0x1390): undefined reference to
`RumorModel::initSchedule(repast::ScheduleRunner&)' 

---

Kashif Zia

PhD Candidate

Institut für Pervasive Computing, Johannes Kepler Universität Linz,
Altenberger Straße 69, A-4040 Linz

Room: P105, Phone: +43-732-2468-9673, Fax: +43-732-2468-8426
E-Mail:  <mailto:ka...@pe...> ka...@pe...

From: Kashif Zia [mailto:ka...@pe...] 
Sent: Thursday, July 28, 2011 10:00 AM
To: rep...@li...
Subject: [Repast-interest] Repast HPC: compilation on Linux (icc) isuues

Hello Everyone

Trying to compile zombie_model on Linux using Intel C. 

First I recognized that in icc, the virtual functions overriding is not
supported as I have understanding of it. For example: in ZombieObserver.h

The functions:

       void go();

       void setup(repast::Properties props);

should work as it is, but the following error was generated:

icpc main.cpp -lboost_mpi -lboost_filesystem -lrepast_hpc-1.0 -lrelogo-1.0
-lmpi -lnetcdf_c++

ZombieObserver.h(64): warning #1125: function
"repast::relogo::Observer::setup(repast::Properties &)" is hidden by
"ZombieObserver::setup" -- virtual function override intended?

        void setup(repast::Properties props);

             ^

/usr/lib64/sgi/intel9/libimf.so: warning: warning: feupdateenv is not
implemented and will always fail

ld: warning: libboost_filesystem.so.1.33.1, needed by
/apps/repasthpc-1.0b/lib/librepast_hpc-1.0.so, may conflict with
libboost_filesystem.so.1.45.0

/tmp/icpclI4dfT.o: In function `void
repast::relogo::SimulationRunner::run<ZombieObserver,
repast::relogo::Patch>(repast::Properties&)':

main.cpp:(.gnu.linkonce.t._ZN6repast6relogo16SimulationRunner3runI14ZombieOb
serverNS0_5PatchEEEvRNS_10PropertiesE[.gnu.linkonce.t._ZN6repast6relogo16Sim
ulationRunner3runI14ZombieObserverNS0_5PatchEEEvRNS_10PropertiesE]+0x6f2):
undefined reference to `ZombieObserver::setup(repast::Properties)'

/tmp/icpclI4dfT.o: In function `ZombieObserver*
repast::relogo::WorldCreator::createWorld<ZombieObserver,
repast::relogo::Patch,
repast::relogo::DefaultAgentCreator<repast::relogo::Patch>
>(repast::relogo::WorldDefinition const&, std::vector<int,
std::allocator<int> > const&,
repast::relogo::DefaultAgentCreator<repast::relogo::Patch>&)':

main.cpp:(.gnu.linkonce.t._ZN6repast6relogo12WorldCreator11createWorldI14Zom
bieObserverNS0_5PatchENS0_19DefaultAgentCreatorIS4_EEEEPT_RKNS0_15WorldDefin
itionERKSt6vectorIiSaIiEERT1_[.gnu.linkonce.t._ZN6repast6relogo12WorldCreato
r11createWorldI14ZombieObserverNS0_5PatchENS0_19DefaultAgentCreatorIS4_EEEEP
T_RKNS0_15WorldDefinitionERKSt6vectorIiSaIiEERT1_]+0x74): undefined
reference to `vtable for ZombieObserver'

make: *** [default] Error 1

After searching for two hours, I came to know that some intel compilers
model need explicit mention of virtual functions. So I added the following
line:

       using repast::relogo::Observer::setup;

       void go();

       void setup(repast::Properties props);

Still not successful and faced the following error:

k330174@service0:~/sim/src/zombie> make

icpc main.cpp -lboost_mpi -lboost_filesystem -lrepast_hpc-1.0 -lrelogo-1.0
-lmpi -lnetcdf_c++

/apps/repasthpc-1.0b/include/relogo/SimulationRunner.h(116): error: more
than one instance of overloaded function "ZombieObserver::setup" matches the
argument list:

            function "repast::relogo::Observer::setup(repast::Properties &)"

            function "ZombieObserver::setup(repast::Properties)"

            argument types are: (repast::Properties)

            object type is: ZombieObserver

        obs->setup(props);

             ^

          detected during instantiation of "void
repast::relogo::SimulationRunner::run<ObserverType,PatchType>(repast::Proper
ties &) [with ObserverType=ZombieObserver, PatchType=repast::relogo::Patch]"
at line 57 of "main.cpp"

compilation aborted for main.cpp (code 2)

make: *** [default] Error 2

It seemed that there is some problem with intel during its handling with
dynamic binding. Look at:
http://octave.1599824.n4.nabble.com/Compiling-Octave-3-2-3-with-icpc-10-1-fa
ils-more-than-one-instance-of-overloaded-function-quot-octav-td2327457.html

So I simply changed the function name entirely (from setup to setup1). Now
the above errors are removed, but still not able to compile. See recent
errors below:

k330174@service0:~/sim/src/zombie> make

icpc main.cpp -lboost_mpi -lboost_filesystem -lrepast_hpc-1.0 -lrelogo-1.0
-lmpi -lnetcdf_c++

/usr/lib64/sgi/intel9/libimf.so: warning: warning: feupdateenv is not
implemented and will always fail

ld: warning: libboost_filesystem.so.1.33.1, needed by
/apps/repasthpc-1.0b/lib/librepast_hpc-1.0.so, may conflict with
libboost_filesystem.so.1.45.0

/tmp/icpcefhQ0V.o: In function `ZombieObserver*
repast::relogo::WorldCreator::createWorld<ZombieObserver,
repast::relogo::Patch,
repast::relogo::DefaultAgentCreator<repast::relogo::Patch>
>(repast::relogo::WorldDefinition const&, std::vector<int,
std::allocator<int> > const&,
repast::relogo::DefaultAgentCreator<repast::relogo::Patch>&)':

main.cpp:(.gnu.linkonce.t._ZN6repast6relogo12WorldCreator11createWorldI14Zom
bieObserverNS0_5PatchENS0_19DefaultAgentCreatorIS4_EEEEPT_RKNS0_15WorldDefin
itionERKSt6vectorIiSaIiEERT1_[.gnu.linkonce.t._ZN6repast6relogo12WorldCreato
r11createWorldI14ZombieObserverNS0_5PatchENS0_19DefaultAgentCreatorIS4_EEEEP
T_RKNS0_15WorldDefinitionERKSt6vectorIiSaIiEERT1_]+0x74): undefined
reference to `vtable for ZombieObserver'

make: *** [default] Error 1

Changing the function name probably will work as it is the highest level
function. However it need to remove the remaining errors first.

Any ideas?

Thanks and Regards.

---

Kashif Zia

PhD Candidate

Institut für Pervasive Computing, Johannes Kepler Universität Linz,
Altenberger Straße 69, A-4040 Linz

Room: P105, Phone: +43-732-2468-9673, Fax: +43-732-2468-8426
E-Mail:  <mailto:ka...@pe...> ka...@pe...

Re: [Repast-interest] Repast HPC: compilation on Linux (icc) isuues

The Repast Suite is a family of free agent-based modeling libraries.

Re: [Repast-interest] Repast HPC: compilation on Linux (icc) isuues