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author
Friedemann Zenke
committed
Merge branch 'develop' into release-v0.8.0
Conflicts: CMakeLists.txt examples/sim_epsp_binmon.cpp src/AurynVector.h src/Device.cpp src/LinearTrace.cpp tools/python/membrane_potential.py
2 parents ded8c58 + 33a573d commit 1982206

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‎.gitignore

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,9 @@
44
*.l[oa]
55
*/.libs
66

7+
*.pyc
8+
9+
710
# Ignore docs
811
docs/*
912

‎.travis.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ install:
88
- sudo apt-get install -y -qq libboost-all-dev openmpi-bin libopenmpi-dev
99
- sudo apt-get install -y -qq cmake
1010
script:
11-
- cd build/release && cmake ../../ -DCMAKE_BUILD_TYPE=Release && make && cd ../../tests && ./run_tests.sh
11+
- cd build/release && cmake ../../ -DCMAKE_BUILD_TYPE=Release && make && cd ../../test && ./run_tests.sh
1212

1313
notifications:
1414
email:

‎CMakeLists.txt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,4 +33,4 @@ ADD_SUBDIRECTORY(examples)
3333
ADD_SUBDIRECTORY(tools)
3434

3535
# Unit tests
36-
ADD_SUBDIRECTORY(tests/src)
36+
ADD_SUBDIRECTORY(test/src)

‎examples/sim_background.cpp

Lines changed: 29 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -475,27 +475,18 @@ int main(int ac, char* av[])
475475
double primetime = 3*tau_hom;
476476

477477

478-
// BEGIN Global stuff
479-
mpi::environment env(ac, av);
480-
mpi::communicator world;
481-
communicator = &world;
478+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s", dir.c_str(), file_prefix, eta, tau_hom, label.c_str());
479+
std::string logfile_prefix = strbuf;
482480

483-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.log", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
484-
std::string logfile = strbuf;
481+
auryn_init(ac, av, dir=".", "", logfile_prefix);
485482

486-
LogMessageType log_level_file = PROGRESS;
487-
if ( verbose ) log_level_file = EVERYTHING;
488-
logger = new Logger(logfile,world.rank(),PROGRESS,log_level_file);
483+
logger->set_logfile_loglevel( PROGRESS );
484+
if ( verbose ) logger->set_logfile_loglevel( EVERYTHING );
489485

490-
sys = new System(&world);
491-
// boost::filesystem::path p = av[0];
492-
// string binaryname = p.stem().string();
493-
// sys->set_simulation_name(binaryname);
494-
// END Global stuff
495486

496487
if (!infilename.empty()) {
497488
std::stringstream iss;
498-
iss << infilename << "." << world.rank();
489+
iss << infilename << "." << sys->mpi_rank();
499490
infilename = iss.str();
500491
}
501492

@@ -615,12 +606,12 @@ int main(int ac, char* av[])
615606
logger->msg(msg,PROGRESS,true);
616607

617608
if (wmatdump) {
618-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.weight", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
609+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.weight", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
619610
WeightMatrixMonitor * wmatmon = new WeightMatrixMonitor( con_ee, strbuf , wmat_interval );
620611
}
621612

622613
if ( !fast ) {
623-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.syn", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
614+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.syn", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
624615
WeightMonitor * wmon = new WeightMonitor( con_ee, strbuf, 10 );
625616
for ( int i = 0 ; i < 5 ; ++i ) {
626617
for ( int j = 0 ; j < 5 ; ++j ) {
@@ -630,28 +621,28 @@ int main(int ac, char* av[])
630621
}
631622
}
632623

633-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
624+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
634625
SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, strbuf , 2500);
635626

636-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'p');
627+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'p');
637628
// SpikeMonitor * smon_p = new SpikeMonitor( poisson, strbuf , 2500);
638629
}
639630

640-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
631+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
641632
PopulationRateMonitor * pmon_e = new PopulationRateMonitor( neurons_e, strbuf, 1.0 );
642633

643634
if ( wall ) {
644-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.rt", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
635+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.rt", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
645636
RealTimeMonitor * rtmon = new RealTimeMonitor( strbuf );
646637
}
647638

648-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'i');
639+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'i');
649640
// PopulationRateMonitor * pmon_i = new PopulationRateMonitor( neurons_i, strbuf, 1.0 );
650641

651-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.mem", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
642+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.mem", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
652643
// VoltageMonitor * vmon_e = new VoltageMonitor( neurons_e, 33, strbuf );
653644

654-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'i');
645+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'i');
655646
// SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, strbuf , 500);
656647

657648
RateChecker * chk = new RateChecker( neurons_e , 0.1 , 20.*kappa , tau_chk);
@@ -669,19 +660,19 @@ int main(int ac, char* av[])
669660
oss << "Changing cell input ... ";
670661
logger->msg(oss.str(),PROGRESS,true);
671662

672-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
663+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
673664
PatternMonitor * patmon = new PatternMonitor(neurons_e,strbuf,patfile.c_str(), 10, 1.);
674665
PatternStimulator * patstim = new PatternStimulator(neurons_e,currentfile.c_str(),patfile.c_str());
675666

676-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.scal", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
667+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.scal", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
677668
WeightMonitor * wmon_scal = new WeightMonitor( con_ee, 0, 0, strbuf, 1, ELEMENTLIST);
678669
wmon_scal->add_to_list( con_ee->get_pre_partners(0) );
679670
wmon_scal->add_to_list( con_ee->get_pre_partners(10) );
680671

681672
}
682673

683674
// if ( corr ) {
684-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
675+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
685676
// PatternMonitor * pmon_c = new PatternMonitor( neurons_e, strbuf,corr_pat_file.c_str() );
686677
// }
687678

@@ -719,7 +710,7 @@ int main(int ac, char* av[])
719710
SparseConnection * con_corr_i = new SparseConnection(corr_e,neurons_i,w*strength,sparseness*plen*psize/ni,GLUT);
720711

721712
// set up Weight monitor
722-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
713+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
723714
SpikeMonitor * smon_c = new SpikeMonitor( corr_e, strbuf , psize );
724715
}
725716

@@ -762,7 +753,7 @@ int main(int ac, char* av[])
762753
// SparseConnection * con_corr_i = new SparseConnection(corr_e,neurons_i,w*strength,sparseness*plen*psize/ni,GLUT);
763754

764755
// set up Weight monitor
765-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
756+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
766757
SpikeMonitor * smon_c = new SpikeMonitor( corr_e, strbuf , psize );
767758
}
768759

@@ -796,7 +787,7 @@ if ( prefile != "" ) {
796787
// adding patterns
797788
if ( patfile != "" ) {
798789
logger->msg("Preparing stimulus ...",PROGRESS,true);
799-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.stim", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
790+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.stim", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
800791
StimulusGroup * stimgroup = new StimulusGroup(ne,patfile,strbuf);
801792
stimgroup->set_mean_on_period(onperiod);
802793
stimgroup->set_mean_off_period(offperiod);
@@ -829,33 +820,33 @@ if ( patfile != "" ) {
829820

830821
if (!fast) {
831822
logger->msg("Saving neurons state ...",PROGRESS,true);
832-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.e.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
823+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.e.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
833824
neurons_e->write_to_file(strbuf);
834-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.i.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
825+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.i.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
835826
neurons_i->write_to_file(strbuf);
836827

837828
logger->msg("Saving weight matrix ...",PROGRESS,true);
838-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
829+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
839830
con_ee->write_to_file(strbuf);
840831

841-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.ei.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
832+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.ei.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
842833
con_ei->write_to_file(strbuf);
843834

844835
for ( int i = 0 ; i < corr_connections.size() ; ++i ) {
845-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), i, world.rank());
836+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), i, sys->mpi_rank());
846837
corr_connections[i]->write_to_file(strbuf);
847838
}
848839
}
849840

850841
// save lifetime
851-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.lifetime", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
842+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.lifetime", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
852843
std::ofstream killfile;
853844
killfile.open(strbuf);
854845
killfile << sys->get_time()-primetime << std::endl;
855846
killfile.close();
856847

857848

858-
if ( world.rank() == 0 ) {
849+
if ( sys->mpi_rank() == 0 ) {
859850
logger->msg("Saving elapsed time ..." ,PROGRESS,true);
860851
char filenamebuf [255];
861852
sprintf(filenamebuf, "%s/elapsed.dat", dir.c_str());
@@ -869,7 +860,7 @@ if ( patfile != "" ) {
869860
delete sys;
870861

871862
if (errcode) {
872-
env.abort(errcode);
863+
mpienv->abort(errcode);
873864
}
874865

875866
return errcode;

‎examples/sim_bg_lowpass.cpp

Lines changed: 26 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -479,26 +479,10 @@ int main(int ac, char* av[])
479479
double primetime = 3*tau_hom;
480480

481481

482-
// BEGIN Global stuff
483-
mpi::environment env(ac, av);
484-
mpi::communicator world;
485-
communicator = &world;
486-
487-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.log", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
488-
std::string logfile = strbuf;
489-
logger = new Logger(logfile,world.rank(),PROGRESS,EVERYTHING);
490-
491-
sys = new System(&world);
492-
// boost::filesystem::path p = av[0];
493-
// string binaryname = p.stem().string();
494-
// sys->set_simulation_name(binaryname);
495-
// END Global stuff
496-
497-
if (!infilename.empty()) {
498-
std::stringstream iss;
499-
iss << infilename << "." << world.rank();
500-
infilename = iss.str();
501-
}
482+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s", dir.c_str(), file_prefix, eta, tau_hom, label.c_str());
483+
std::string logfile_prefix = strbuf;
484+
485+
auryn_init(ac, av, dir=".", "", logfile_prefix);
502486

503487
logger->msg("Setting up neuron groups ...",PROGRESS,true);
504488

@@ -606,12 +590,12 @@ int main(int ac, char* av[])
606590
logger->msg(msg,PROGRESS,true);
607591

608592
if (wmatdump) {
609-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.weight", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
593+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.weight", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
610594
WeightMatrixMonitor * wmatmon = new WeightMatrixMonitor( con_ee, strbuf , wmat_interval );
611595
}
612596

613597
if ( !fast ) {
614-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.syn", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
598+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.syn", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
615599
WeightMonitor * wmon = new WeightMonitor( con_ee, strbuf, 10 );
616600
for ( int i = 0 ; i < 5 ; ++i ) {
617601
for ( int j = 0 ; j < 5 ; ++j ) {
@@ -620,28 +604,28 @@ int main(int ac, char* av[])
620604
}
621605
}
622606

623-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
607+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
624608
SpikeMonitor * smon_e = new SpikeMonitor( neurons_e, strbuf , 2500);
625609

626-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'p');
610+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'p');
627611
// SpikeMonitor * smon_p = new SpikeMonitor( poisson, strbuf , 2500);
628612
}
629613

630-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
614+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
631615
PopulationRateMonitor * pmon_e = new PopulationRateMonitor( neurons_e, strbuf, 1.0 );
632616

633617
if ( wall ) {
634-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.rt", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
618+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.rt", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
635619
RealTimeMonitor * rtmon = new RealTimeMonitor( strbuf );
636620
}
637621

638-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'i');
622+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.prate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'i');
639623
// PopulationRateMonitor * pmon_i = new PopulationRateMonitor( neurons_i, strbuf, 1.0 );
640624

641-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.mem", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'e');
625+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.mem", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'e');
642626
// VoltageMonitor * vmon_e = new VoltageMonitor( neurons_e, 33, strbuf );
643627

644-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'i');
628+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'i');
645629
// SpikeMonitor * smon_i = new SpikeMonitor( neurons_i, strbuf , 500);
646630

647631
RateChecker * chk = new RateChecker( neurons_e , 0.1 , 20.*kappa , tau_chk);
@@ -653,19 +637,19 @@ int main(int ac, char* av[])
653637
oss << "Changing cell input ... ";
654638
logger->msg(oss.str(),PROGRESS,true);
655639

656-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
640+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
657641
PatternMonitor * patmon = new PatternMonitor(neurons_e,strbuf,patfile.c_str(), 10, 1.);
658642
PatternStimulator * patstim = new PatternStimulator(neurons_e,currentfile.c_str(),patfile.c_str());
659643

660-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.scal", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
644+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.scal", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
661645
WeightMonitor * wmon_scal = new WeightMonitor( con_ee, 0, 0, strbuf, 1, ELEMENTLIST);
662646
wmon_scal->add_to_list( con_ee->get_pre_partners(0) );
663647
wmon_scal->add_to_list( con_ee->get_pre_partners(10) );
664648

665649
}
666650

667651
// if ( corr ) {
668-
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
652+
// sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.pat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
669653
// PatternMonitor * pmon_c = new PatternMonitor( neurons_e, strbuf,corr_pat_file.c_str() );
670654
// }
671655

@@ -703,7 +687,7 @@ int main(int ac, char* av[])
703687
SparseConnection * con_corr_i = new SparseConnection(corr_e,neurons_i,w*strength,sparseness*plen*psize/ni,GLUT);
704688

705689
// set up Weight monitor
706-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
690+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
707691
SpikeMonitor * smon_c = new SpikeMonitor( corr_e, strbuf , psize );
708692
}
709693

@@ -746,7 +730,7 @@ int main(int ac, char* av[])
746730
// SparseConnection * con_corr_i = new SparseConnection(corr_e,neurons_i,w*strength,sparseness*plen*psize/ni,GLUT);
747731

748732
// set up Weight monitor
749-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank(), 'c');
733+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%c.ras", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank(), 'c');
750734
SpikeMonitor * smon_c = new SpikeMonitor( corr_e, strbuf , psize );
751735
}
752736

@@ -780,7 +764,7 @@ if ( prefile != "" ) {
780764
// adding patterns
781765
if ( patfile != "" ) {
782766
logger->msg("Preparing stimulus ...",PROGRESS,true);
783-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.stim", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
767+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.stim", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
784768
StimulusGroup * stimgroup = new StimulusGroup(ne,patfile,strbuf);
785769
stimgroup->set_mean_on_period(onperiod);
786770
stimgroup->set_mean_off_period(offperiod);
@@ -813,27 +797,27 @@ if ( patfile != "" ) {
813797

814798
if (!fast) {
815799
logger->msg("Saving neurons state ...",PROGRESS,true);
816-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.e.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
800+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.e.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
817801
neurons_e->write_to_file(strbuf);
818-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.i.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
802+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.i.nstate", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
819803
neurons_i->write_to_file(strbuf);
820804

821805
logger->msg("Saving weight matrix ...",PROGRESS,true);
822-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
806+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
823807
con_ee->write_to_file(strbuf);
824808

825-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.ei.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
809+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.ei.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
826810
con_ei->write_to_file(strbuf);
827811

828812
for ( int i = 0 ; i < corr_connections.size() ; ++i ) {
829-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), i, world.rank());
813+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.%d.wmat", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), i, sys->mpi_rank());
830814
corr_connections[i]->write_to_file(strbuf);
831815
}
832816
}
833817

834818

835819
// save lifetime
836-
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.lifetime", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), world.rank());
820+
sprintf(strbuf, "%s/%s_e%.2et%.2f%s.%d.lifetime", dir.c_str(), file_prefix, eta, tau_hom, label.c_str(), sys->mpi_rank());
837821
std::ofstream killfile;
838822
killfile.open(strbuf);
839823
killfile << sys->get_time()-primetime << std::endl;
@@ -843,7 +827,7 @@ if ( patfile != "" ) {
843827
delete sys;
844828

845829
if (errcode) {
846-
env.abort(errcode);
830+
mpienv->abort(errcode);
847831
}
848832

849833
return errcode;

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