[Rcpp-devel] A tough RcppArmadillo Error; address(nil) cause 'unknown' in R
井澤 毅
a-izawa at mail.ecc.u-tokyo.ac.jp
Mon Jul 10 07:36:22 CEST 2017
Dear KK,
Thanks for your advice. I am afraid that the "initialize" function would
make the initial parameters for our machine learning using an improved
ABC method.
After this learning, we got a thousand of selected parameter sets which
would mimic the updated parameter distributions, those are described in
var.mat.all in this case. Then, this time we use this like
simulate_R(var.mat.all, fobs="observed data", interval=6).
Thus, I am afraid that we do not need the initialize function for
simulation when we use the updated parameter sets. In fact, I confirmed
the simulation using simulate_R() works in R but did not give me the
"out" list as a result.
In this term, I am thinking the "out" list was not generated, due to
"the initialization of the array". But I have no idea how to generate
"out" list.
Best,
Takeshi
On 2017/07/10 14:04, Qiang Kou wrote:
> 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-izawa at mail.ecc.u-tokyo.ac.jp
> <mailto:a-izawa at 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-izawa at mail.ecc.u-tokyo.ac.jp
>>> <mailto:a-izawa at 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-izawa at mail.ecc.u-tokyo.ac.jp
>>>> <mailto:a-izawa at 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
>>>>> <http://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
>>>>> <http://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-izawa at mail.ecc.u-tokyo.ac.jp
>>>>>> <mailto:a-izawa at mail.ecc.u-tokyo.ac.jp>> wrote:
>>>>>>
>>>>>> Dear rcpp-devel at lists.r-forge.r-project.org
>>>>>> <mailto:rcpp-devel at 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 at lists.r-forge.r-project.org
>>>>>> <mailto:Rcpp-devel at lists.r-forge.r-project.org>
>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>>>>>> <https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Qiang Kou
>>>>>> qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
>>>>>> School of Informatics and Computing, Indiana University
>>>>
>>>> --
>>>> Qiang Kou
>>>> qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
>>>> School of Informatics and Computing, Indiana University
>>>
>>> --
>>> Qiang Kou
>>> qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
>>> School of Informatics and Computing, Indiana University
>
> --
> Qiang Kou
> qkou at umail.iu.edu <mailto:qkou at umail.iu.edu>
> School of Informatics and Computing, Indiana University
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