improve req

cmt/requirements-lite

 package CAMEL
 
-#THE FOLLWING LINKS TO YOUR CLASS LIBRARY- YOU CAN TEST WHICH ONE IN YOUR
-#SHELL WITH THE FOLLWING COMMAND :  cmt show uses
-# you may put an explicit version instead of * (as v2.4.4 or v2.*...)
 use class *
 
 #CLASS optional FastPk access
 #macro_append cppflags " -DFASTPK "
 
 
-#COMPILER - TO EASE PAIN USE THE SAME THAN FOR CLASS/CLIK COMPILATION
-# DEFAULT IS gcc SO DO NOT UNCOMMENT IF YOUR ARE HAPPY WITH THIS (EXAMPLE FOR CHANGING TO ICPC)
-#macro cpp "icpc"
+#compiler options
+#default is gcc here are the C++ compiler options
+macro cppflags " -O3  -pipe -ansi -fPIC -Wall "
 
-#COMPILER FLAGS for default=gcc
-#C++ flags
-macro cppflags " -O2 -pipe -ansi -Woverloaded-virtual -Wpedantic -Wunused -Wmaybe-uninitialized -Wno-deprecated -Wno-div-by-zero -Wno-variadic-macros"
-# C flags
-macro_append cpplinkflags  " -fopenmp "
-
-# or for icpc (if you changed previously the compiler otherwise don't touch)
-#macro cppflags " -O2  -ip -ansi_alias -align -Wbrief "
+#do we need optimzations here?
+#macro_append cppflags "-ffast-math -m64 "
 
-#
-# CFITSIO IS REQUIRED. 
-# include_dirs indicates the path to fitsio.h/ and CAMEL_linkopts teh
-# link to the propoer library. In the following we use the one that was
-# compiled when building CLIK but it can be also found
-# in your /usr area. If the  library is shared you may need to update your
-# LD_LIBRARY_PATH or uncomment the next line before sourcing camel_setup.sh
-#path_append LD_LIBRARY_PATH "$(CLIKDIR)/lib"
+# although it may be strange we do not compile CAMEL with OMP because CLASS is not thread safe
+# no worries: CLASS is compiled with OMP
+#macro_append cppflags "-fopenmp "
+macro_append cpplinkflags  " -fopenmp "
 
-include_dirs "$(CLIKDIR)/include"
-macro_append  CAMEL_linkopts " -L$(CLIKDIR)/lib -lcfitsio"
 
+#CAMEL includes
+include_dirs " $(CAMELROOT)/src"
+include_dirs " $(CAMELROOT)/src/camel"
+include_dirs " $(CAMELROOT)/src/Minuit2-5.28.00/src"
+include_dirs " $(CAMELROOT)/src/Minuit2-5.28.00/inc"
+include_dirs  "$(CAMELROOT)/src/cxxsupport"
+include_dirs  "$(CAMELROOT)/src/AbsRand"
+include_dirs  "$(CAMELROOT)/src/camel/JLA"
+include_dirs  "$(CAMELROOT)/src/camel/JLA/jla_likelihood_v3/src"
+
+
+#cfitsio
+include_dirs "/usr/include/cfitsio"
+macro_append  CAMEL_linkopts " -lcfitsio"
+
+#JLA :requires cblas/lapack
+#macro_append cppflags ' -DJLA '
+#include_dirs  "/usr/include/atlas"
+#macro_append  CAMEL_linkopts " -L/usr/lib64/atlas -ltatlas -llapack -ljla "
+#application test_jla -group=test -s=$(CAMELROOT)/src/camel test/test_jla.cc
+#library jla  -no_share $(CAMELROOT)/src/camel/JLA/jla_likelihood_v3/src/ini.c $(CAMELROOT)/src/camel/JLA/jla_likelihood_v3/src/jla.cc
 
-# PLANCK CLIK support [optional]
-# NB: you always have access to PLanck/Hillipop (high-ell) likelihood since
-# it is native in CAMEL.
-# CLIKCFLAGS and CLIKLIBS were defined when you ran: camel_setup.sh
+#PLANCK
 #macro_append cppflags " -DCLIK  $(CLIKCFLAGS)"
 #macro_append cflags " -DCLIK  $(CLIKCFLAGS)"
 #macro_append  CAMEL_linkopts " $(CLIKLIBS) "
+#include_dirs "$(CLIKDIR)/include"
+#include_dirs  "$(CLIKDIR)/src"
+#macro_append cppflags " -DCLIK "
+#macro_append cflags " -DCLIK "
 #macro_append  CAMEL_linkopts "-L$(CLIKDIR)/lib -lclik "
-#application dump_clik -group=test -s=../src/camel test/test_clik.cc
-#application dump_lensing -group=test -s=../src/camel test/test_lensing.cc
-
-
-#JLA [optional] :requires cblas/lapack
-# in most linux distributions packaged with the atlas library.
-# if you installed CLIK you may also look for them in teh MKLROOT you used.
-# macro_append cppflags ' -DJLA '
-#include_dirs  "/usr/include/atlas"
-#macro_append  CAMEL_linkopts " -L/usr/lib64/atlas -lcblas -llapack -ljla "
-#application test_jla -group=test -s=../src/camel test/test_jla.cc
+#path_append LD_LIBRARY_PATH "$(CLIKDIR)/lib"
+#application dump_clik -group=test -s=$(CAMELROOT)/src/camel test/test_clik.cc
+#application dump_lensing -group=test -s=$(CAMELROOT)/src/camel test/test_lensing.cc
 
 
-# PICO  [optional]
+# PICO 
 #macro_append cppflags " -DPICO $(PICOINC) "
 #macro_append CAMEL_linkopts " -L$(PICO_CODE) -lpico -lpython2.7 "
-# if the previous link fails try using the PICOLIBS defined in camel_setup.sh
+# the previous line should be sufficient otherwise try the PICOLIBS 
+# (set in camel_setup.sh)
+#macro_append CAMEL_linkopts " $(PICOLIBS)"
 #macro_append cppflags ' -DPICODATA=\"$(PICO_DATA)\" '
-#application testPico -group=test -s=../src/camel/pico/exec testPico.cc
+#application testPico -group=test -s=$(CAMELROOT)/src/camel/pico/exec testPico.cc
 
-#macro_append cppflags " -DPICO "
-#include_dirs "/usr/include/python2.7"
-#include_dirs "/usr/lib64/python2.7/site-packages/numpy/core/include"
-#include_dirs "$(PICO_CODE)/pypico"
-#macro_append CAMEL_linkopts " -L$(PICO_CODE)/build/temp.linux-x86_64-2.7 -lpico -L/usr/lib64/python2.7/config -lpython2.7 "
-#macro_append cppflags ' -DPICODATA=\"$(PICO_DATA)\" '
-#application testPico -group=test -s=../src/camel/pico/exec testPico.cc
-#application FitClassFromPico -group=exec -s=../src/camel exec/FitClassFromPico.cc
-###########################################################################################
-###FROM THERE YOU SHOUL NOT NEED TO TOUCH ANYTHING
-###########################################################################################
-#CAMEL includes
-include_dirs " ../src"
-include_dirs "../src/camel"
-include_dirs "../src/Minuit2-5.28.00/src"
-include_dirs "../src/Minuit2-5.28.00/inc"
-include_dirs  "../src/cxxsupport"
-include_dirs  "../src/AbsRand"
-include_dirs  "../src/camel/JLA"
-include_dirs  "../src/camel/JLA/jla_likelihood_v3/src"
 
+
+###FROM THERE YOU DONT NEED TO TOUCH
+###########################################################################################
 #CAMEL LIBRARIES
-library Minuit -no_share ../src/Minuit2-5.28.00/src/*.cxx
-library Util -no_share -x=ddl.cc ../src/cxxsupport/*.cc
-library AbsRand -no_share ../src/AbsRand/*.cc
-library CLHEP -no_share ../src/CLHEP/src/*.cc
-library jla  -no_share ../src/camel/JLA/jla_likelihood_v3/src/ini.c ../src/camel/JLA/jla_likelihood_v3/src/jla.cc
+library Minuit -no_share $(CAMELROOT)/src/Minuit2-5.28.00/src/*.cxx
+library Util -no_share -x=ddl.cc $(CAMELROOT)/src/cxxsupport/*.cc
+library AbsRand -no_share $(CAMELROOT)/src/AbsRand/*.cc
+library CLHEP -no_share $(CAMELROOT)/src/CLHEP/src/*.cc
 
-macro camelsrc "*.cc CMB/*.cc BAO/*.cc Lensing/*.cc pico/*.cc JLA/*.cc Class/*.cc Constraints/*.cc"
-library MinuitFit  -no_share -s=../src/camel $(camelsrc)
-library MCMC  -no_share  -s=../src/camel/MCMC *.cc
+macro camelsrc "*.cc CMB/*.cc BAO/*.cc Lensing/*.cc pico/*.cc JLA/*.cc Class/*.cc Constraints/*.cc Pk/*.cc"
+library MinuitFit  -no_share -s=$(CAMELROOT)/src/camel $(camelsrc)
+library MCMC  -no_share  -s=$(CAMELROOT)/src/camel/MCMC *.cc
 
-macro CAMEL_linkopts "-L$(CAMEL_root)/${CMTCONFIG} -lMinuitFit -lMinuit -lMCMC -lCLHEP -lAbsRand -lUtil "
+macro CAMEL_linkopts "-L$(CAMELROOT)/${CMTCONFIG} -lMinuitFit -lMinuit -lMCMC -lCLHEP -lAbsRand -lUtil "
 macro_append cppflags ' -DRELPATH=\"$(CAMELROOT)/lik\" '
 
 
 #CAMEL applications
 # pour relinker si changement: toutes les application du package
-macro CAMEL_stamps $(PACKAGE_ROOT)/$(CMTCONFIG)/MinuitFit.stamp
+macro CAMEL_stamps " $(CAMELROOT)/$(CMTCONFIG)/MinuitFit.stamp $(CAMELROOT)/$(CMTCONFIG)/MCMC.stamp "
 macro application_suffix ""
 
-#groupe exec: to build run: make exec
-application writeChi2 -group=exec -s=../src/camel exec/writeChi2.cc
-application writeSpectra -group=exec -s=../src/camel exec/writeSpectra.cc
-application Minimize -group=exec -s=../src/camel exec/Minimize.cc
-application ScanParam -group=exec -s=../src/camel exec/ScanParam.cc
-application mcmc -group=exec -s=../src/camel/MCMC exec/mainMCMC.cc
+#groupe exec
+application writeChi2 -group=exec -s=$(CAMELROOT)/src/camel exec/writeChi2.cc
+application writeSpectra -group=exec -s=$(CAMELROOT)/src/camel exec/writeSpectra.cc
+application writeSpectraPk -group=exec -s=$(CAMELROOT)/src/camel exec/writeSpectraPk.cc
+application Minimize -group=exec -s=$(CAMELROOT)/src/camel exec/Minimize.cc
+application Profile -group=exec -s=$(CAMELROOT)/src/camel exec/Profile.cc
+application ScanParam -group=exec -s=$(CAMELROOT)/src/camel exec/ScanParam.cc
+application mcmc -group=exec -s=$(CAMELROOT)/src/camel/MCMC exec/mainMCMC.cc
 
 #tests
-application testKlass -group=test -s=../src/camel test/testKlass.cc
-application testCLHEP -group=test -s=../src/camel/test testCLHEP.cc
-application testBAO -group=test -s=../src/camel/test testBAO.cc
-application testHiLLiPOP -group=test -s=../src/camel/test testHiLLiPOP.cc
+application testKlass -group=test -s=$(CAMELROOT)/src/camel test/testKlass.cc
+application testCLHEP -group=test -s=$(CAMELROOT)/src/camel/test testCLHEP.cc
+application testBAO -group=test -s=$(CAMELROOT)/src/camel/test testBAO.cc
+application testHiLLiPOP -group=test -s=$(CAMELROOT)/src/camel/test testHiLLiPOP.cc
 
 #lIST OF ALL DEPENDENCIES
 macro_append Minimize_dependencies " MinuitFit "
+macro_append Profile_dependencies " MinuitFit "
 macro_append ScanParam_dependencies " MinuitFit "
 macro_append writeChi2_dependencies " MinuitFit "
 macro_append writeSpectra_dependencies " MinuitFit "
-macro_append mcmc_dependencies " MinuitFit MCMC"
+macro_append writeSpectraPkependencies " MinuitFit "
+macro_append mcmc_dependencies " MinuitFit "
+macro_append mcmc_dependencies " MCMC "
 macro_append testKlass_dependencies " MinuitFit"
 macro_append clik_example_CC_dependencies " MinuitFit "
 macro_append test_clik_dependencies " MinuitFit "
@@ -131,5 +119,4 @@ macro_append testCLHEP_dependencies " CLHEP "
 macro_append testBAO_dependencies " MinuitFit "
 macro_append testHiLLiPOP_dependencies " MinuitFit "
 macro_append test_jla_dependencies " MinuitFit "
-macro_append testPico_dependencies " MinuitFit "
 

src/camel/exec/writeSpectraPk.cc

@@ -232,11 +232,11 @@ int main(int argc,char** argv){
   Timer timer;
   cout <<"Pk timer test..." << endl;
   vector<double> pkvec(kval.size());
-  for (size_t i=0;i<1000;i++)
+  for (size_t i=0;i<100;i++)
     e->get_Pkvec(kval,z0,pkvec);
   cout << "fast=" << timer.partial() <<endl;
 
-  for (size_t i=0;i<1000;i++){
+  for (size_t i=0;i<100;i++){
     for (int k =0; k<kval.size() ; k++){
       double pk=e->get_Pklin(kval[k], 0);
     }