I mean line 49 in ge-model.cpp. You have a function called "initialize"
there.
The "initialize" function will initialize the _rand array.
Best,
KK
On Sun, Jul 9, 2017 at 9:55 PM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp> wrote:
> Dear KK,
>
> Sorry for bothering you again, I still have some problems.
>
> According to your advice, in order to initialize the array in ge-r.cpp,
>
> I put
>
>
> Model.out_y=cube(Model.n_acc, Model._obs._n_group,
> Model._obs._n_out_date,fill::zeros);
> Model.out_res_1=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date,fill::zeros);
> Model.out_res_2=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date,fill::zeros);
> Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date,fill::zeros);
> Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date,fill::zeros);
> instead of the old ones,
>
> Model.out_y=cube(Model.n_acc, Model._obs._n_group,
> Model._obs._n_out_date);
> Model.out_res_1=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date);
> Model.out_res_2=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date);
> Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date);
> Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group,
> Model._obs._n_out_date);
>
> However, I got the same error in R.
>
> What should I do next ?
>
> I am afraid that I do not know how rand generated in ge-model.cpp (line
> 37) is linked to the array in ge-r.cpp (line 49) yet. Should I use fill::
> randu instead of fill:: zeros?
>
> Best,
>
> Takeshi
>
>
>
>
> On 2017/07/10 13:03, 井澤 毅 wrote:
>
> Dear KK,
>
> Thanks for this explanation. Now I got it.
>
> I did not think that ge-model.cpp is involved in this problem since it
> works well as a C++ script even in our current system.
>
> I still wonder why this ge-r.cpp works in the old system, but I will ask
> this to the maintainer of our system.
> I have learned a lot from your suggestion.
>
> Thanks again!
>
> Best,
>
> Takeshi
>
>
> On 2017/07/10 10:34, Qiang Kou wrote:
>
> In line 37 of ge-model.cpp, you try to free _rand. However, if you don't
> call initialize in line 49 first, the array won't be initialized.
>
> Best,
>
> KK
>
> On Sun, Jul 9, 2017 at 4:45 PM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp>
> wrote:
>
>> Dear KK,
>>
>> I owe you a lot! I will check it as soon as possible.
>>
>> Since I am not familiar with this much, I would be very happy to tell me
>> some urls describing "initialize".
>>
>> Best,
>>
>> Takeshi
>>
>> On 2017/07/10 7:38, Qiang Kou wrote:
>>
>> Hi, professor,
>>
>> I think the problem is in ge-r. cpp, you forgot to call *initialize*.
>>
>> The error has nothing to do with Rcpp.
>>
>> Best,
>>
>> KK
>>
>> On Tue, Jul 4, 2017 at 2:45 AM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp>
>> wrote:
>>
>>> Sorry, I forgot the attached file.
>>> On 2017/07/04 18:43, 井澤 毅 wrote:
>>>
>>> Dear KK,
>>>
>>> Thanks for your kind reply.
>>>
>>> I am afraid that one of the input file is very heavy, this time but I am
>>> sending a ZIP file including all.
>>>
>>> Please make v30 package using install.simulate_R_1.r and then
>>> install.simulate_R_2.r. Then, try ge-r_test.r, please.
>>>
>>> To make the v30 package, we need ge-r.cpp, ge-model.cpp, ge-model.h,
>>> ge-obs.cpp, ge-obs.h, ge-range.h.
>>>
>>> As the input file, we need var.mat.all matrix data in R and
>>> obs.Os01g0182600_g1.nc file in the directry.
>>>
>>> Then, you will see the error I have been suffering from for a month.
>>>
>>> The obs.Os01g0182600_g1.nc file is a file containing environmental
>>> fluctuation data.
>>>
>>> Best,
>>>
>>> Takeshi
>>>
>>> On 2017/07/04 5:40, Qiang Kou wrote:
>>>
>>> Hi, I am afraid the example you provided is not a reproducible example.
>>>
>>> First, we don't know the content of ge-model.h. Second, we don't know
>>> which input will trigger the fault.
>>>
>>> Please provide a reproducible example if you really want to get help.
>>>
>>> Best,
>>>
>>> KK
>>>
>>> On Sat, Jul 1, 2017 at 11:06 AM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp>
>>> wrote:
>>>
>>>> Dear rcpp-devel@lists.r-forge.r-project.org,
>>>>
>>>> Sorry for bothering you much, but do me a favor please. Please help me
>>>> some.
>>>>
>>>> I am just a molecular biologist working on plants. Thus, I am still a
>>>> newcomer in this field.
>>>>
>>>> Recently, I have been working with a script using RcppArmadillo, This
>>>> has helped me a lot. However, after updating the system in our institute,
>>>> the script gives me an error repeatedly. My former Postdoc wrote this
>>>> script. Thus, I did not know this inside much.
>>>>
>>>> I have tried to fix it for more than a month, but now I have no idea
>>>> how to fix it. I would appreciate it very much if you could help and give
>>>> me your advice.
>>>>
>>>> Please see an attached cpp file, termed ge-r.cpp. With this cpp file
>>>> and other ones, I have succeeded to install a skeleton R package into R
>>>> using your function Rcpp.package.skeleton.
>>>>
>>>> In this ge-r.cpp, there is one R function called simulate_R() written.
>>>> In this R fucntion, there are two C++ functions, load() and simulate(),
>>>> both are described in other cpp files, called from C++ into R. With cout
>>>> function described in simulate_R(), I confirmed these two function work in
>>>> R thanks to RcppArmadillo, however, it suddenly stops with an error,
>>>> address(nil) cause 'unknown' in R. It has seemed to stop when it return
>>>> (out) at the last in ge-r.cpp. I do not know why it happens. Note that the
>>>> C++ script works normally after the update of the system. Only this
>>>> RcppArmadillo conversion from C++ function into a R function is deformed.
>>>>
>>>> Please give me an advice, please. Of course, I can give you more
>>>> information on the C++ script in details if you need.
>>>>
>>>> Best regards,
>>>>
>>>> Takeshi
>>>>
>>>>
>>>>
>>>> ge-r.cpp
>>>>
>>>> #ifndef __R__
>>>>
>>>> #define __R__
>>>> #endif
>>>>
>>>> #ifndef USE_OMP
>>>> #define USE_OMP
>>>> #endif
>>>>
>>>>
>>>> #include <RcppArmadillo.h>
>>>>
>>>>
>>>> #include "ge-model.h"
>>>>
>>>> using namespace arma;
>>>>
>>>>
>>>>
>>>> // input:
>>>> // parameter matrix: row for particle, col for parameter
>>>> // filename of observation
>>>> // output:
>>>> // simulation for regular time points: row for particle, col for
>>>> time, slice for term
>>>> // existing observation to corresponding regular time points
>>>>
>>>> // [[Rcpp::depends(RcppArmadillo)]]
>>>> // [[Rcpp::export]]
>>>> Rcpp::List simulate_R(const arma::mat& param_r, const char* fobs, const
>>>> int interval) {
>>>>
>>>> try {
>>>> geModel Model;
>>>> Model.n_thread=omp_get_num_procs();
>>>> Model._param=param_r;
>>>> cout << "params set.\n";
>>>>
>>>> cout << "filename of obs: "<< fobs << ".\n";
>>>>
>>>> Model._obs.load(fobs);
>>>>
>>>> cout << "obs loaded.\n";
>>>>
>>>> Model.n_acc=Model._param.n_rows;
>>>> cout << "n_acc set to be " << Model.n_acc << ".\n";
>>>>
>>>> Model._obs._out_interval = interval;
>>>> Model._obs._n_out_date = (Model._obs._n_date /
>>>> Model._obs._out_interval) + 1;
>>>>
>>>> Model.out_y=cube(Model.n_acc, Model._obs._n_group,
>>>> Model._obs._n_out_date);
>>>> Model.out_res_1=cube(Model.n_acc,Model._obs._n_group,
>>>> Model._obs._n_out_date);
>>>> Model.out_res_2=cube(Model.n_acc,Model._obs._n_group,
>>>> Model._obs._n_out_date);
>>>> Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group,
>>>> Model._obs._n_out_date);
>>>> Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group,
>>>> Model._obs._n_out_date);
>>>>
>>>> cout << "output matrix initialized.\n";
>>>>
>>>> //necessary for simulate_obs
>>>> Model._distance=vec(Model.n_acc);
>>>>
>>>> Model.simulate(0,Model.n_acc-1,true);
>>>> cout << "simulation complete.\n";
>>>>
>>>> fflush(stdout);
>>>>
>>>> cout << size(Model.out_y)<<".\n"<<
>>>> Model.out_y[0]<<".\n"<<Model.out_y[1]<<".\n"<<Model.out_y[2]<<".\n";
>>>>
>>>> Rcpp::List out = Rcpp::List::create(
>>>> Rcpp::Named("out_y")=Model.out_y,
>>>> Rcpp::Named("out_res_1")=Model.out_res_1,
>>>> Rcpp::Named("out_res_2")=Model.out_res_2,
>>>>
>>>> Rcpp::Named("out_res_clock")=Model.out_res_clock,
>>>> Rcpp::Named("out_res_dev")=Model.out_res_dev
>>>> );
>>>>
>>>> cout << "List constructed.\n";
>>>>
>>>> fflush(stdout);
>>>>
>>>> return (out);
>>>> }
>>>>
>>>> catch(char* e) {
>>>> cout << e << "\n";
>>>> exit(EXIT_FAILURE);
>>>> }
>>>> catch(...) {
>>>> cout << "Error\n";
>>>> exit(EXIT_FAILURE);
>>>> }
>>>> }
>>>>
>>>> _______________________________________________ Rcpp-devel mailing
>>>> list Rcpp-devel@lists.r-forge.r-project.org
>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>
>>> --
>>> Qiang Kou
>>> q...@umail.iu.edu
>>> School of Informatics and Computing, Indiana University
>>>
>>> --
>> Qiang Kou
>> q...@umail.iu.edu
>> School of Informatics and Computing, Indiana University
>>
>> --
> Qiang Kou
> q...@umail.iu.edu
> School of Informatics and Computing, Indiana University
>
>
--
Qiang Kou
q...@umail.iu.edu
School of Informatics and Computing, Indiana University
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