[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 06:55:31 CEST 2017
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
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