[Rd] Error in simulation. NAN
Hi all,
im triyng to implement a bayesian model with R and c++.
I have a strange problem. I can't reproduce the error with a small
script and then i post the original one.
The problem is after the line
for(MCMC_iter2=0;MCMC_iter2For the first 34 iterations all work fine, after, all the simulations
of mu_acc_P return an "nan". If i delete the line
alpha_acc_P[0] = rnorm(app1_3,sqrt(app1_4) );
the simulations of mu_acc_P work fine. For me it is really strange,
Thanks!.
#include
#include
using namespace std;
#include
#include
#include
#include
#include
#include "funzioni.h"
#define _USE_MATH_DEFINES
extern "C" {
SEXP Model1_imp11Cpp(
SEXP ad_start_r, SEXP ad_end_r, SEXP ad_esp_r,
SEXP burnin_r, SEXP thin_r,SEXP iter_1_r,SEXP iter_2_r,
SEXP n_j_r,SEXP J_r,
SEXP prior_alpha_r,SEXP prior_rho_r,SEXP prior_sigma2_r,SEXP
prior_phi_r,SEXP prior_zeta2_r,
SEXP sdprop_rho_r,SEXP sdprop_sigma2_r,
SEXP start_alpha_r,SEXP start_mu_r,SEXP start_rho_r,SEXP
start_sigma2_r,SEXP start_k_r,SEXP start_phi_r, SEXP start_zeta2_r,
SEXP x_r,SEXP H_r, SEXP acceptratio_r
// SEXP Sigma_adapt_sp_r, SEXP mean_adapt_sp_r, SEXP sim_acc_sp_r,
SEXP ep_sp_r, SEXP acc_index_sp_r,
// SEXP Sigma_adapt_k_r, SEXP mean_adapt_k_r, SEXP sim_acc_k_r, SEXP
ep_k_r, SEXP acc_index_k_r
//
){
/*
Varie ed eventuali
*/
// indici
int i,j,k,l,h,t,f,info,MCMC_iter,MCMC_iter2;
int nProtect= 0;
int indice_adapt=0;
double duepi = (2*M_PI);
// costanti
char const *lower = "L";
char const *upper = "U";
char const *ntran = "N";
char const *ytran = "T";
char const *rside = "R";
char const *lside = "L";
const double one = 1.0;
const double negOne = -1.0;
const double zero = 0.0;
const int incOne = 1;
/*
Set-up
*/
double *x_P = REAL(x_r);
int n_j = INTEGER(n_j_r)[0];
int J= INTEGER(J_r)[0];
int N = n_j*J;
int iter_1 = INTEGER(iter_1_r)[0];
int iter_2 = INTEGER(iter_2_r)[0];
int burnin = INTEGER(burnin_r)[0];
int thin = INTEGER(thin_r)[0];
int ad_start = INTEGER(ad_start_r)[0];
int ad_end = INTEGER(ad_end_r)[0];
double *ad_esp_P = REAL(ad_esp_r);
double *acceptratio_P = REAL(acceptratio_r);
double *H_P = REAL(H_r);
// int nSamples_save = INTEGER(nSamples_save_r)[0];
// PRIOR
double *prior_alpha = REAL(prior_alpha_r);
double M_alpha = prior_alpha[0]; double sigma2_alpha =
prior_alpha[1];
double *prior_rho = REAL(prior_rho_r);
double a_rho = prior_rho[0];double b_rho = prior_rho[1];
double *prior_sigma2 = REAL(prior_sigma2_r);
double a_sigma2 = prior_sigma2[0]; double b_sigma2 = prior_sigma2[1];
double *prior_zeta2 = REAL(prior_zeta2_r);
double a_zeta2 = prior_zeta2[0]; double b_zeta2 = prior_zeta2[1];
double *prior_phi = REAL(prior_phi_r);
double M_phi= prior_phi[0]; double sigma2_phi = prior_phi[1];
double lim_down= prior_phi[2]; double lim_up = prior_phi[3];
// PROPOSAL
double *sdprop_rho = REAL(sdprop_rho_r);
double sd_rho = sdprop_rho[0];
double *sdprop_sigma2 = REAL(sdprop_sigma2_r);
double sd_sigma2 = sdprop_sigma2[0];
// STARTING
double *start_alpha_P = REAL(start_alpha_r);
double start_alpha = start_alpha_P[0];
double *start_mu_P = REAL(start_mu_r);
// for(j=0;jF77_NAME(dcopy)(&incOne, start_sigma2_P, &incOne, sigma2_acc_P,
&incOne);
// rho
double *rho_acc_P = (double *) R_alloc(1, sizeof(double));
F77_NAME(dcopy)(&incOne, start_rho_P, &incOne, rho_acc_P, &incOne);
// k
double *k_acc_P = (double *) R_alloc(n_j*J, sizeof(double));
F77_NAME(dcopy)(&incN, start_k_P, &incOne, k_acc_P, &incOne);
// variabili di appoggio per i parametri
double *mu_app_P = (double *) R_alloc(J, sizeof(double));
F77_NAME(dcopy)(&incJ, start_mu_P, &incOne, mu_app_P, &incOne);
/*
// OUTPUT di R
*/
SEXP mu_out_r,alpha_out_r;
PROTECT(mu_out_r = allocMatrix(REALSXP, J, nSamples_save));
nProtect++;
double *mu_out_P = REAL(mu_out_r);
PROTECT(alpha_out_r = allocMatrix(REALSXP, 1, nSamples_save));
nProtect++;
double *alpha_out_P = REAL(alpha_out_r);
//
// PROTECT(accept_r = allocMatrix(REALSXP, 1, 1)); nProtect++;
/*
Varie ed eventuali III
*/
// MATRICI COVARIANZA E AFFINI
double *C_P = (double *) R_alloc(nn_j, sizeof(double));
double *C_cand_P = (double *) R_alloc(nn_j, sizeof(double));
double Sum_Sig
Re: [Rd] libR.so: cannot open shared object file
Can you add some details? Suppose i have the package Model.tar.gz and my writable are is in user/area, what i have to do next to install the package? Il 04/09/13 00:04, Geoff Jentry ha scritto: One problem is that i have not the privileges to install a package. If you have a writable area you can install to there with the --library=LIB argument and then load the package using the lib.loc command. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] libR.so: cannot open shared object file
Hi all I have a R code that incorporates a C++ programm. I compiled the C++ code with the following: R CMD SHLIB Model.cpp -Wall funzioni.cpp it seems to work fine but when i run the R code i get this error message Error in dyn.load(paste(dir_func, "Model.so", sep = "")) : unable to load shared object '/lustre/work/uuu/RCpp/Model.so': libR.so: cannot open shared object file: No such file or directory I don't know how to fix it. The code is running on a cluster. Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] libR.so: cannot open shared object file
One problem is that i have not the privileges to install a package. Il 03/09/13 23:14, Dirk Eddelbuettel ha scritto: On 3 September 2013 at 22:48, gianluca.mastranto...@yahoo.it wrote: | Hi all | | I have a R code that incorporates a C++ programm. I compiled the C++ | code with the following: | | R CMD SHLIB Model.cpp -Wall funzioni.cpp | | it seems to work fine but when i run the R code i get this error message | | Error in dyn.load(paste(dir_func, "Model.so", sep = "")) : |unable to load shared object '/lustre/work/uuu/RCpp/Model.so': |libR.so: cannot open shared object file: No such file or directory | | I don't know how to fix it. | The code is running on a cluster. Qualified guess: you ran R CMD SHLIB on the _central / master_ node, but not the _compute_ nodes. They never got the object file. One more rigorous approach would be to wrap your function up in a package, and have each compute node load the package. Hope this helps, Dirk __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] libR.so: cannot open shared object file
First of all, thanks for your help.
I did all the things you told me. I was able to load the library, but then
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so':
libR.so: cannot open shared object file: No such file or directory
In addition: Warning message:
package 'BayesWrap' was built under R version 2.15.2
Error: package/namespace load failed for 'BayesWrap'
Execution halted
what does it means?
G.M.
Il 04/09/13 22:42, Prof Brian Ripley ha scritto:
On 04/09/2013 19:58, Geoff Jentry wrote:
Can you add some details?
Suppose i have the package Model.tar.gz and my writable are is in
user/area, what i have to do next to install the package?
What I was picturing was something like this (forgive me if syntax isn't
100%):
mkdir user/area/myRLib
R CMD INSTALL --library=user/area/myRLib Model.tar.gz
and then in R:
library(Model, lib.loc="user/area/myRLib")
Note though Brian Ripley's response to me where he indicates that this
is handled automatically.
Yes, install.packages("Model.tar.gz") should suffice.
-J
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Re: [Rd] libR.so: cannot open shared object file
just for completion
i need to use
library(Model, lib.loc="user/area/myRLib")
because if i use
library(Model)
i get this message
Error in library("BayesWrap") : there is no package called 'BayesWrap'
Il 05/09/13 11:59, gianluca.mastranto...@yahoo.it ha scritto:
First of all, thanks for your help.
I did all the things you told me. I was able to load the library, but
then
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so':
libR.so: cannot open shared object file: No such file or directory
In addition: Warning message:
package 'BayesWrap' was built under R version 2.15.2
Error: package/namespace load failed for 'BayesWrap'
Execution halted
what does it means?
G.M.
Il 04/09/13 22:42, Prof Brian Ripley ha scritto:
On 04/09/2013 19:58, Geoff Jentry wrote:
Can you add some details?
Suppose i have the package Model.tar.gz and my writable are is in
user/area, what i have to do next to install the package?
What I was picturing was something like this (forgive me if syntax
isn't
100%):
mkdir user/area/myRLib
R CMD INSTALL --library=user/area/myRLib Model.tar.gz
and then in R:
library(Model, lib.loc="user/area/myRLib")
Note though Brian Ripley's response to me where he indicates that this
is handled automatically.
Yes, install.packages("Model.tar.gz") should suffice.
-J
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__
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Re: [Rd] libR.so: cannot open shared object file
Thank you,
now all works well.
G.M.
Il 06/09/13 15:28, brian avants ha scritto:
> Hello Everyone
>
> I have been following this thread because I have similar issues with
> an outside-of-R package. The problem is related to dylib loading
> i.e. of the form
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/ANTsR/libs/libRantsRegistration.so':
> dlopen(/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/ANTsR/libs/libRantsRegistration.so,
>
> 6): Library not loaded: libitkdouble-conversion-4.5.1.dylib
> Referenced from:
> /Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/libl_antsRegistration.dylib
> Reason: image not found
>
> A solution that seems to work on both osx and linux is:
>
> export
> R_LD_LIBRARY_PATH=/Users/stnava/code/gitANTs/ANTsR/src/ANTS/ANTS-build/lib/
>
> but I would really like to avoid this, if possible.I tried using
> .libPaths ( suspecting it would not work ) and I got the same error as
> above ...
>
> as an aside, there seems very little documentation for
> R_LD_LIBRARY_PATH & I don't recall how I came across it ... i have
> some other notes here:
>
> https://github.com/stnava/ANTsR/blob/master/configure
>
> any thoughts appreciated , at your leisure ...
>
> & thanks, as usual,
>
>
>
> brian
>
>
>
>
> On Thu, Sep 5, 2013 at 4:38 PM, Prof Brian Ripley
> mailto:rip...@stats.ox.ac.uk>> wrote:
>
> On 05/09/2013 21:28, gianluca.mastranto...@yahoo.it
> <mailto:gianluca.mastranto...@yahoo.it> wrote:
>
> just for completion
>
> i need to use
> library(Model, lib.loc="user/area/myRLib")
> because if i use
> library(Model)
> i get this message
> Error in library("BayesWrap") : there is no package called
> 'BayesWrap'
>
>
> For the record: not if you follow my suggestion.
>
> See ?.libPaths for why.
>
>
>
>
>
> Il 05/09/13 11:59, gianluca.mastranto...@yahoo.it
> <mailto:gianluca.mastranto...@yahoo.it> ha scritto:
>
> First of all, thanks for your help.
>
> I did all the things you told me. I was able to load the
> library, but
> then
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared object
> '/lustre/work/gjona2/Wrap/BayesWrap/libs/BayesWrap.so':
> libR.so: cannot open shared object file: No such file or
> directory
> In addition: Warning message:
> package 'BayesWrap' was built under R version 2.15.2
> Error: package/namespace load failed for 'BayesWrap'
> Execution halted
>
> what does it means?
>
> G.M.
>
> Il 04/09/13 22:42, Prof Brian Ripley ha scritto:
>
> On 04/09/2013 19:58, Geoff Jentry wrote:
>
> Can you add some details?
> Suppose i have the package Model.tar.gz and my
> writable are is in
> user/area, what i have to do next to install
> the package?
>
>
> What I was picturing was something like this
> (forgive me if syntax
> isn't
> 100%):
>
> mkdir user/area/myRLib
> R CMD INSTALL --library=user/area/myRLib Model.tar.gz
>
> and then in R:
> library(Model, lib.loc="user/area/myRLib")
>
> Note though Brian Ripley's response to me where he
> indicates that this
> is handled automatically.
>
>
> Yes, install.packages("Model.tar.gz") should suffice.
>
>
> -J
>
> __
> R-devel@r-project.org
> <mailto:R-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
>
>
>
>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk <mailto:rip...@stats.ox.ac.uk>
> Professor of Applied Statistics,
> http://www.stats.ox.ac.uk/~ripley/
> <http://www.stats.ox.ac.uk/%7Eripley/>
> University of Oxford, Tel: +44 1865 272861
> (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
>
> __
> R-devel@r-project.org <mailto:R-devel@r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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