optimise command generator a make error

[Yann-Edern L'Hour]

Hi, I recently started to try to use LibBi with a custom model. I installed it on Ubuntu.

I have times series data, a model and parameters which I want to estimate.
For this I have converted my csv files of time series into netCDF files via python (xarray module).

Error: make failed with return code 2, see .####model/build_openmp_sse/make.log for details

and these are the details.. :
make: *** No rule to make target `optimise_cpu'.  Stop.

Do you have any clue why it isn't running ?

Thanks in advance !
Best regards

Yann

[Yann-Edern L'Hour]

The title was meant to be "optimise command generates a make error."
Indeed when i run the following command I get the afored mentioned error and log :

libbi optimise @optimise.conf

 where optimise.conf contains

--nthreads 2
--enable-sse
--disable-assert
--disable-cuda
--model-file model.bi
--input-file data/input_site_1_month_2015-12.nc
--obs-file data/obs_site_1_month_2015-12.nc
--output-file results/optimise.nc

and model.bi contains :

model Xmodel {
  const T0 = 19.0
  const h = 600.0
  dim nr(size=4464)
  param C, R, B, sigma, e
  state T[nr]
  noise dW[nr]
  input Ta[nr], Qh[nr]
  obs Ti_obs[nr]
  sub parameter {
    // specify the parameter model
    C ~ gaussian(12000000.0, 400000.0)
    R ~ gaussian(5.0, 4.0)
    B ~ uniform(0.2 ,1.0)
    sigma ~ uniform(-50.0, 5.0)
    e ~ uniform(-50.0, 5.0)
  }

  sub initial {
    // specify the initial condition model
    T[nr] ~ gaussian(T0, 1)
  }

  sub transition(delta = h) {
    // specify the transition model
    dW[nr] ~ wiener()
    ode(alg = "RK5(4)", h=h){
      dT[nr]/dt = ((T[nr-1] - Ta[nr-1])/R + B*Qh[nr] + exp(sigma*dW[nr]/h))/C
    }  
  }
 
  sub observation {
    Ti_obs[nr] ~ gaussian(T[nr], exp(e))
  }
}

[Lawrence Murray]

Hi Yann,

I'll look into this one for you. I'm aware of some problems with the optimise command at present, although this is not the error that I'd expect you to be getting.

With that said, the optimise command in LibBi has always been a bit of a placeholder for future ideas. It doesn't do much sophisticated at the moment, just a Nelder-Mead simplex method with the likelihood estimate provided by a particle filter, which isn't too clever. For a linear model, you can use it with a Kalman filter to get sensible results.

Have you attempted just sampling from the model rather than optimising first?

Cheers,

Lawrence

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[Yann-Edern L'Hour]

Hi Lawrence,

Thanks for your answer. At first, I thought it would be indeed simpler to run the 'optimise' command (ie. Nelder-Mead) in order to quickly validate my model and input formats before running more complex (simulation) methods for getting a set of parameter estimates. I'm aware that Kalman filtering would be suitable in the case of this model.And I can try to run it.

In the mean time, I indeed ran some sampling from prior and then posterior densities. I'm rather a novice with bayesian computations (with not-so-fresh memories from grad' school) and don't know well which different options must be set in the configuration files (nparticules , nsamples, noutputs, end-time). I'm still reading the manual for such use.

The first batches I got resulted in a posterior nc output file with a loglikelihood equals to 0.0 all along the sample generated by LibBi, which is not strange. I think this might come from the observation block of my model (ie. likelihood function).

Cheers,

Yann

[Andreas]

Hi Lawrence / all,

Using LibBi 1.2.0, I got the same make.log as Yann when trying the optimise command.

Having updated to 1.3.0, I still get an error but the make.log contains another output (attached below).
It seems that the files bi/buffer/InputNetCDFBuffer.hpp and bi/buffer/OptimiserNetCDFBuffer.hpp are missing.

Have I done any mistake during installation? Is there any workaround to fix that?

Many thanks!

Andy

Error: make failed with return code 2, see .Stochastic_Volatility_Jumps_Param/build_assert_openmp/make.log for details

depbase=`echo src/optimise_cpu.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/optimise_cpu.o -MD -MP -MF $depbase.Tpo -c -o src/optimise_cpu.o src/optimise_cpu.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/bi/adapter/AdapterFactory.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/adapter/AdapterFactory.o -MD -MP -MF $depbase.Tpo -c -o src/bi/adapter/AdapterFactory.o src/bi/adapter/AdapterFactory.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/bi/adapter/GaussianAdapter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/adapter/GaussianAdapter.o -MD -MP -MF $depbase.Tpo -c -o src/bi/adapter/GaussianAdapter.o src/bi/adapter/GaussianAdapter.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/bi/netcdf/MCMCNetCDFBuffer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/netcdf/MCMCNetCDFBuffer.o -MD -MP -MF $depbase.Tpo -c -o src/bi/netcdf/MCMCNetCDFBuffer.o src/bi/netcdf/MCMCNetCDFBuffer.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
src/optimise_cpu.cpp:42:43: error: bi/buffer/InputNetCDFBuffer.hpp: No such file or directory
src/optimise_cpu.cpp:43:47: error: bi/buffer/OptimiserNetCDFBuffer.hpp: No such file or directory
depbase=`echo src/bi/netcdf/SMCNetCDFBuffer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/netcdf/SMCNetCDFBuffer.o -MD -MP -MF $depbase.Tpo -c -o src/bi/netcdf/SMCNetCDFBuffer.o src/bi/netcdf/SMCNetCDFBuffer.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/bi/netcdf/SimulatorNetCDFBuffer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/netcdf/SimulatorNetCDFBuffer.o -MD -MP -MF $depbase.Tpo -c -o src/bi/netcdf/SimulatorNetCDFBuffer.o src/bi/netcdf/SimulatorNetCDFBuffer.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
In file included from src/optimise_cpu.cpp:24:
src/bi/method/NelderMeadOptimiser.hpp:114: error: ISO C++ forbids declaration of ‘OptimiserMode’ with no type
src/bi/method/NelderMeadOptimiser.hpp:114: error: expected ‘,’ or ‘...’ before ‘mode’
src/bi/method/NelderMeadOptimiser.hpp:254: error: ‘OptimiserMode’ does not name a type
src/bi/method/NelderMeadOptimiser.hpp:113: error: default argument missing for parameter 4 of ‘bi::NelderMeadOptimiser<B, F, IO1>::NelderMeadOptimiser(B&, F*, IO1&, int)’
src/bi/method/NelderMeadOptimiser.hpp:294: error: ISO C++ forbids declaration of ‘OptimiserMode’ with no type
src/bi/method/NelderMeadOptimiser.hpp:294: error: expected ‘,’ or ‘...’ before ‘mode’
src/bi/method/NelderMeadOptimiser.hpp:293: error: default argument missing for parameter 4 of ‘static bi::NelderMeadOptimiser<B, F, IO1>* bi::NelderMeadOptimiserFactory<CL>::create(B&, F*, IO1&, int)’
src/bi/method/NelderMeadOptimiser.hpp: In static member function ‘static bi::NelderMeadOptimiser<B, F, IO1>* bi::NelderMeadOptimiserFactory<CL>::create(B&, F*, IO1&, int)’:
src/bi/method/NelderMeadOptimiser.hpp:295: error: ‘mode’ was not declared in this scope
In file included from src/optimise_cpu.cpp:24:
src/bi/method/NelderMeadOptimiser.hpp: At global scope:
src/bi/method/NelderMeadOptimiser.hpp:307: error: ISO C++ forbids declaration of ‘OptimiserMode’ with no type
src/bi/method/NelderMeadOptimiser.hpp:307: error: expected ‘,’ or ‘...’ before ‘mode’
src/bi/method/NelderMeadOptimiser.hpp: In constructor ‘bi::NelderMeadOptimiser<B, F, IO1>::NelderMeadOptimiser(B&, F*, IO1&, int)’:
src/bi/method/NelderMeadOptimiser.hpp:308: error: class ‘bi::NelderMeadOptimiser<B, F, IO1>’ does not have any field named ‘mode’
src/bi/method/NelderMeadOptimiser.hpp:308: error: ‘mode’ was not declared in this scope
depbase=`echo src/bi/netcdf/InputNetCDFBuffer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
    g++ -DPACKAGE_NAME=\"LibBi\" -DPACKAGE_TARNAME=\"libbi\" -DPACKAGE_VERSION=\"1.3.0\" -DPACKAGE_STRING=\"LibBi\ 1.3.0\" -DPACKAGE_BUGREPORT=\"bug-r...@libbi.org\" -DHAVE_OMP_H=1 -DTHRUST_DEVICE_SYSTEM=THRUST_DEVICE_SYSTEM_CPP -DTHRUST_HOST_SYSTEM=THRUST_HOST_SYSTEM_OMP -DHAVE_LIBM=1 -DHAVE_LIBGFORTRAN=1 -DHAVE_LIBQRUPDATE=1 -DHAVE_LIBGSL=1 -DHAVE_LIBNETCDF=1 -DNDEBUG=1 -DHAVE_NETCDF_H=1 -DHAVE_CBLAS_H=1 -DHAVE_GSL_GSL_CBLAS_H=1 -DHAVE_BOOST_MPL_IF_HPP=1 -DHAVE_BOOST_RANDOM_BERNOULLI_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_GAMMA_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_MERSENNE_TWISTER_HPP=1 -DHAVE_BOOST_RANDOM_NORMAL_DISTRIBUTION_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_INT_HPP=1 -DHAVE_BOOST_RANDOM_UNIFORM_REAL_HPP=1 -DHAVE_BOOST_RANDOM_VARIATE_GENERATOR_HPP=1 -DHAVE_BOOST_TYPEOF_TYPEOF_HPP=1 -DHAVE_THRUST_ADJACENT_DIFFERENCE_H=1 -DHAVE_THRUST_BINARY_SEARCH_H=1 -DHAVE_THRUST_COPY_H=1 -DHAVE_THRUST_DEVICE_PTR_H=1 -DHAVE_THRUST_DISTANCE_H=1 -DHAVE_THRUST_EXTREMA_H=1 -DHAVE_THRUST_FILL_H=1 -DHAVE_THRUST_FOR_EACH_H=1 -DHAVE_THRUST_FUNCTIONAL_H=1 -DHAVE_THRUST_GATHER_H=1 -DHAVE_THRUST_INNER_PRODUCT_H=1 -DHAVE_THRUST_ITERATOR_COUNTING_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DETAIL_NORMAL_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_DISCARD_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_PERMUTATION_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_TRANSFORM_ITERATOR_H=1 -DHAVE_THRUST_ITERATOR_ZIP_ITERATOR_H=1 -DHAVE_THRUST_LOGICAL_H=1 -DHAVE_THRUST_REDUCE_H=1 -DHAVE_THRUST_SCAN_H=1 -DHAVE_THRUST_SEQUENCE_H=1 -DHAVE_THRUST_SORT_H=1 -DHAVE_THRUST_TRANSFORM_H=1 -DHAVE_THRUST_TRANSFORM_REDUCE_H=1 -DHAVE_THRUST_TRANSFORM_SCAN_H=1 -DHAVE_THRUST_TUPLE_H=1 -DHAVE_GSL_GSL_MULTIMIN_H=1 -DENABLE_DIAGNOSTICS=no -DHAVE_STDBOOL_H=1 -I.  -Isrc  -I/usr/local/cuda/include      -DENABLE_OPENMP    -fopenmp -O3 -g3 -funroll-loops   -MT src/bi/netcdf/InputNetCDFBuffer.o -MD -MP -MF $depbase.Tpo -c -o src/bi/netcdf/InputNetCDFBuffer.o src/bi/netcdf/InputNetCDFBuffer.cpp &&\
    mv -f $depbase.Tpo $depbase.Po
src/bi/method/NelderMeadOptimiser.hpp: In member function ‘void bi::NelderMeadOptimiser<B, F, IO1>::init(bi::Random&, bi::ScheduleIterator, bi::ScheduleIterator, bi::State<B, L2>&, IO2&, real)’:
src/bi/method/NelderMeadOptimiser.hpp:376: error: ‘mode’ was not declared in this scope
src/bi/method/NelderMeadOptimiser.hpp:376: error: ‘MAXIMUM_A_POSTERIORI’ was not declared in this scope
In file included from src/bi/method/BootstrapPF.hpp:12,
                 from src/optimise_cpu.cpp:28:
src/bi/method/Simulator.hpp: In member function ‘void bi::Simulator<B, F, O>::init(bi::Random&, bi::ScheduleElement, bi::State<B, L2>&, IO2&)’:
src/bi/method/Simulator.hpp:247: error: ‘InputBuffer’ was not declared in this scope
src/bi/method/Simulator.hpp:247: error: template argument 2 is invalid
src/bi/method/Simulator.hpp:275: error: ‘InputBuffer’ was not declared in this scope
src/bi/method/Simulator.hpp:275: error: template argument 2 is invalid
In file included from src/optimise_cpu.cpp:28:
src/bi/method/BootstrapPF.hpp: In member function ‘bool bi::BootstrapPF<B, S, R>::resample(bi::Random&, bi::ScheduleElement, S1&)’:
src/bi/method/BootstrapPF.hpp:328: error: ‘Resampler’ has not been declared
In file included from src/optimise_cpu.cpp:32:
src/bi/resampler/MetropolisResampler.hpp: At global scope:
src/bi/resampler/MetropolisResampler.hpp:50: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:50: error: expected ‘,’ or ‘...’ before ‘<’ token
src/bi/resampler/MetropolisResampler.hpp:57: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:57: error: expected ‘,’ or ‘...’ before ‘<’ token
src/bi/resampler/MetropolisResampler.hpp:64: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:64: error: expected ‘,’ or ‘...’ before ‘<’ token
src/bi/resampler/MetropolisResampler.hpp:78: error: ISO C++ forbids declaration of ‘ResamplerPrecompute’ with no type
src/bi/resampler/MetropolisResampler.hpp:78: error: expected ‘;’ before ‘<’ token
In file included from src/optimise_cpu.cpp:32:
src/bi/resampler/MetropolisResampler.hpp:103: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:103: error: expected ‘,’ or ‘...’ before ‘<’ token
src/bi/resampler/MetropolisResampler.hpp:115: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:115: error: expected ‘,’ or ‘...’ before ‘<’ token
src/bi/resampler/MetropolisResampler.hpp:128: error: ‘ResamplerPrecompute’ has not been declared
src/bi/resampler/MetropolisResampler.hpp:128: error: expected ‘,’ or ‘...’ before ‘<’ token
In file included from src/optimise_cpu.cpp:34:
src/bi/resampler/KernelResampler.hpp:26: error: expected class-name before ‘{’ token
In file included from src/optimise_cpu.cpp:34:
src/bi/resampler/KernelResampler.hpp: In constructor ‘bi::KernelResampler<R>::KernelResampler(R*, real, bool, double, double)’:
src/bi/resampler/KernelResampler.hpp:103: error: class ‘bi::KernelResampler<R>’ does not have any field named ‘Resampler’
src/optimise_cpu.cpp: In function ‘int main(int, char**)’:
src/optimise_cpu.cpp:511: error: ‘OptimiserNetCDFBuffer’ was not declared in this scope
src/optimise_cpu.cpp:511: error: ‘bufOutput’ was not declared in this scope
src/optimise_cpu.cpp:512: error: ‘WITH_OUTPUT’ was not declared in this scope
src/optimise_cpu.cpp:513: error: expected type-specifier before ‘OptimiserNetCDFBuffer’
src/optimise_cpu.cpp:513: error: expected ‘;’ before ‘OptimiserNetCDFBuffer’
src/optimise_cpu.cpp:523: error: ‘BootstrapPFCacheFactory’ is not a member of ‘bi’
src/optimise_cpu.cpp:523: error: ‘::create’ has not been declared
src/optimise_cpu.cpp:523: error: invalid type in declaration before ‘=’ token
src/optimise_cpu.cpp:523: error: ‘BootstrapPFCacheFactory’ is not a member of ‘bi’
src/optimise_cpu.cpp:523: error: ‘::create’ has not been declared
src/optimise_cpu.cpp:527: error: ‘WITH_SORT’ was not declared in this scope
src/optimise_cpu.cpp:532: error: ‘BootstrapPFFactory’ was not declared in this scope
src/optimise_cpu.cpp:532: error: expected primary-expression before ‘typeof’
src/optimise_cpu.cpp:532: error: expected ‘;’ before ‘typeof’
src/optimise_cpu.cpp:537: error: ‘OptimiserMode’ was not declared in this scope
src/optimise_cpu.cpp:537: error: expected ‘;’ before ‘mode’
src/optimise_cpu.cpp:539: error: ‘mode’ was not declared in this scope
src/optimise_cpu.cpp:539: error: ‘MAXIMUM_A_POSTERIORI’ was not declared in this scope
src/optimise_cpu.cpp:541: error: ‘mode’ was not declared in this scope
src/optimise_cpu.cpp:541: error: ‘MAXIMUM_LIKELIHOOD’ was not declared in this scope
src/optimise_cpu.cpp:543: error: ‘filter’ was not declared in this scope
src/optimise_cpu.cpp:543: error: ‘mode’ was not declared in this scope
src/optimise_cpu.cpp:543: error: invalid type in declaration before ‘=’ token
src/optimise_cpu.cpp:550: error: base operand of ‘->’ is not a pointer
src/optimise_cpu.cpp:551: error: ‘out’ was not declared in this scope
src/optimise_cpu.cpp:557: error: type ‘int’ argument given to ‘delete’, expected pointer
src/optimise_cpu.cpp:559: error: type ‘<type error>’ argument given to ‘delete’, expected pointer
src/optimise_cpu.cpp:560: error: type ‘int’ argument given to ‘delete’, expected pointer
src/optimise_cpu.cpp:564: error: type ‘<type error>’ argument given to ‘delete’, expected pointer
In file included from src/bi/method/NelderMeadOptimiser.hpp:11,
                 from src/optimise_cpu.cpp:24:
src/bi/method/../state/Schedule.hpp: In constructor ‘bi::Schedule::Schedule(B&, real, real, int, int, IO1&, IO2&, bool) [with B = main(int, char**)::model_type, IO1 = bi::InputNetCDFBuffer*, IO2 = bi::InputNetCDFBuffer*]’:
src/optimise_cpu.cpp:508:   instantiated from here
src/bi/method/../state/Schedule.hpp:256: error: request for member ‘readTimes’ in ‘in’, which is of non-class type ‘bi::InputNetCDFBuffer*’
src/optimise_cpu.cpp:508:   instantiated from here
src/bi/method/../state/Schedule.hpp:271: error: request for member ‘readTimes’ in ‘obs’, which is of non-class type ‘bi::InputNetCDFBuffer*’
make: *** [src/optimise_cpu.o] Error 1
make: *** Waiting for unfinished jobs....