thr3ads.net - R help - [R] Using Fortran with MPI, RInside, and calling R functions [Feb 2016]

If this information is useful, please help other people find it:
Share via:

Erin Hodgess

2016-Feb-27 20:00 UTC

[R] Using Fortran with MPI, RInside, and calling R functions

Hello again.

This time, I would like to add MPI to my Fortran program.  Here are the
Fortran and C++ codes:

program buzzy
   use iso_c_binding
  implicit none
  include '/opt/openmpi/include/mpif.h'




  integer :: rank,size,ierror,tag,status(MPI_STATUS_SIZE), i,np
  integer :: argc = 1000000
  real :: x,tot1
  character(len=32) :: argv


      INTERFACE
         SUBROUTINE R_FUN(argc,argv) bind(C, name="buzzyC")
           use iso_c_binding
        character(kind=c_char), INTENT(INOUT) :: argv
        INTEGER(kind=c_int), INTENT(IN) :: argc

      END SUBROUTINE R_FUN
    END INTERFACE

      call MPI_INIT(ierror)
      call MPI_COMM_SIZE(MPI_COMM_WORLD,size,ierror)
      call MPI_COMM_RANK(MPI_COMM_WORLD,rank,ierror)




        print *, "Fortran Calling RInside",rank
    CALL R_FUN (argc,argv)
    print *,rank

    call MPI_FINALIZE(ierror)

  end program buzzy

and

#include <iostream>
#include <RInside.h>

void buzzyC_(int argc,char *argv[]);

extern "C" void buzzyC(int argc,char *argv[]) {

    // create an embedded R instance
  RInside R(argc,argv);

    // convert to string for RInside assignment


    // eval the string, give R notice
  R.parseEvalQ("cat(mean(rnorm(argc))");
}

Now my steps for compiling and linking are the following:

erin at erin-Bonobo-Extreme:~$ mpif90 -c buzzy.f90
erin at erin-Bonobo-Extreme:~$ mpic++ buzzyC.cpp -c
-I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/include
-I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include
-I/usr/share/R/include -libstdc++
erin at erin-Bonobo-Extreme:~$ mpifort -o fcra buzzy.o buzzyC.o
-L/usr/lib/R/lib -lR -L
/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib -lRInside
-L/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/
-Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib/
-lRInside
-Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/ -lstdc++
/usr/lib/x86_64-linux-gnu/libstdc++.so.6

So far so good
But when I run this, disaster strikes:

erin at erin-Bonobo-Extreme:~$ mpirun -np 4 ./fcra
 Fortran Calling RInside           0
 Fortran Calling RInside           1
 Fortran Calling RInside           3
 Fortran Calling RInside           2

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x7FC59706CE48
#1  0x7FC59706BFD0
#2  0x7FC596AA52EF
#3  0x7FC596AFB69A
#4  0x7FC597C5E8E8
#5  0x7FC5979671E8
#6  0x7FC5979677A1
#7  0x402A55 in buzzyC
#8  0x402891 in MAIN__ at buzzy.f90:?
#0  0x7F2482294E48
#1  0x7F2482293FD0
#2  0x7F2481CCD2EF
#3  0x7F2481D2369A
#4  0x7F2482E868E8
#5  0x7F2482B8F1E8
#6  0x7F2482B8F7A1
#7  0x402A55 in buzzyC
#8  0x402891 in MAIN__ at buzzy.f90:?
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 2188 on node
erin-Bonobo-Extreme exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
erin at erin-Bonobo-Extreme:~$

Maybe I should be asking:  is this even possible, please?

Thanks,
Erin


-- 
Erin Hodgess
Associate Professor
Department of Mathematical and Statistics
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com

	[[alternative HTML version deleted]]

Jeff Newmiller

2016-Feb-27 20:15 UTC

head link

[R] Using Fortran with MPI, RInside, and calling R functions

This is off topic here... wrong audience.  Read the Posting Guide. 
-- 
Sent from my phone. Please excuse my brevity.

On February 27, 2016 12:00:23 PM PST, Erin Hodgess <erinm.hodgess at
gmail.com> wrote:>Hello again.
>
>This time, I would like to add MPI to my Fortran program.  Here are the
>Fortran and C++ codes:
>
>program buzzy
>   use iso_c_binding
>  implicit none
>  include '/opt/openmpi/include/mpif.h'
>
>
>
>
>  integer :: rank,size,ierror,tag,status(MPI_STATUS_SIZE), i,np
>  integer :: argc = 1000000
>  real :: x,tot1
>  character(len=32) :: argv
>
>
>      INTERFACE
>         SUBROUTINE R_FUN(argc,argv) bind(C, name="buzzyC")
>           use iso_c_binding
>        character(kind=c_char), INTENT(INOUT) :: argv
>        INTEGER(kind=c_int), INTENT(IN) :: argc
>
>      END SUBROUTINE R_FUN
>    END INTERFACE
>
>      call MPI_INIT(ierror)
>      call MPI_COMM_SIZE(MPI_COMM_WORLD,size,ierror)
>      call MPI_COMM_RANK(MPI_COMM_WORLD,rank,ierror)
>
>
>
>
>        print *, "Fortran Calling RInside",rank
>    CALL R_FUN (argc,argv)
>    print *,rank
>
>    call MPI_FINALIZE(ierror)
>
>  end program buzzy
>
>and
>
>#include <iostream>
>#include <RInside.h>
>
>void buzzyC_(int argc,char *argv[]);
>
>extern "C" void buzzyC(int argc,char *argv[]) {
>
>    // create an embedded R instance
>  RInside R(argc,argv);
>
>    // convert to string for RInside assignment
>
>
>    // eval the string, give R notice
>  R.parseEvalQ("cat(mean(rnorm(argc))");
>}
>
>Now my steps for compiling and linking are the following:
>
>erin at erin-Bonobo-Extreme:~$ mpif90 -c buzzy.f90
>erin at erin-Bonobo-Extreme:~$ mpic++ buzzyC.cpp -c
>-I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/include
>-I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include
>-I/usr/share/R/include -libstdc++
>erin at erin-Bonobo-Extreme:~$ mpifort -o fcra buzzy.o buzzyC.o
>-L/usr/lib/R/lib -lR -L
>/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib -lRInside
>-L/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/
>-Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib/
>-lRInside
>-Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/
>-lstdc++
>/usr/lib/x86_64-linux-gnu/libstdc++.so.6
>
>So far so good
>But when I run this, disaster strikes:
>
>erin at erin-Bonobo-Extreme:~$ mpirun -np 4 ./fcra
> Fortran Calling RInside           0
> Fortran Calling RInside           1
> Fortran Calling RInside           3
> Fortran Calling RInside           2
>
>Program received signal SIGSEGV: Segmentation fault - invalid memory
>reference.
>
>Backtrace for this error:
>
>Program received signal SIGSEGV: Segmentation fault - invalid memory
>reference.
>
>Backtrace for this error:
>#0  0x7FC59706CE48
>#1  0x7FC59706BFD0
>#2  0x7FC596AA52EF
>#3  0x7FC596AFB69A
>#4  0x7FC597C5E8E8
>#5  0x7FC5979671E8
>#6  0x7FC5979677A1
>#7  0x402A55 in buzzyC
>#8  0x402891 in MAIN__ at buzzy.f90:?
>#0  0x7F2482294E48
>#1  0x7F2482293FD0
>#2  0x7F2481CCD2EF
>#3  0x7F2481D2369A
>#4  0x7F2482E868E8
>#5  0x7F2482B8F1E8
>#6  0x7F2482B8F7A1
>#7  0x402A55 in buzzyC
>#8  0x402891 in MAIN__ at buzzy.f90:?
>--------------------------------------------------------------------------
>mpirun noticed that process rank 1 with PID 2188 on node
>erin-Bonobo-Extreme exited on signal 11 (Segmentation fault).
>--------------------------------------------------------------------------
>erin at erin-Bonobo-Extreme:~$
>
>Maybe I should be asking:  is this even possible, please?
>
>Thanks,
>Erin
>
>
>-- 
>Erin Hodgess
>Associate Professor
>Department of Mathematical and Statistics
>University of Houston - Downtown
>mailto: erinm.hodgess at gmail.com
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
	[[alternative HTML version deleted]]

Erin Hodgess

2016-Feb-27 20:30 UTC

head link

[R] Using Fortran with MPI, RInside, and calling R functions

Sorry...thought it was ok since it uses RInside and Rcpp.


On Sat, Feb 27, 2016 at 2:15 PM, Jeff Newmiller <jdnewmil at
dcn.davis.ca.us>
wrote:
> This is off topic here... wrong audience. Read the Posting Guide.
> --
> Sent from my phone. Please excuse my brevity.
>
> On February 27, 2016 12:00:23 PM PST, Erin Hodgess <
> erinm.hodgess at gmail.com> wrote:
>
>> Hello again.
>>
>> This time, I would like to add MPI to my Fortran program.  Here are the
>> Fortran and C++ codes:
>>
>> program buzzy
>>    use iso_c_binding
>>   implicit none
>>   include '/opt/openmpi/include/mpif.h'
>>
>>
>>
>>
>>   integer :: rank,size,ierror,tag,status(MPI_STATUS_SIZE), i,np
>>   integer :: argc = 1000000
>>   real :: x,tot1
>>   character(len=32) :: argv
>>
>>
>>       INTERFACE
>>          SUBROUTINE R_FUN(argc,argv) bind(C, name="buzzyC")
>>            use iso_c_binding
>>         character(kind=c_char), INTENT(INOUT) :: argv
>>         INTEGER(kind=c_int), INTENT(IN) :: argc
>>
>>       END SUBROUTINE R_FUN
>>     END INTERFACE
>>
>>       call MPI_INIT(ierror)
>>       call MPI_COMM_SIZE(MPI_COMM_WORLD,size,ierror)
>>       call MPI_COMM_RANK(MPI_COMM_WORLD,rank,ierror)
>>
>>
>>
>>
>>         print *, "Fortran Calling RInside",rank
>>     CALL
>> R_FUN (argc,argv)
>>     print *,rank
>>
>>     call MPI_FINALIZE(ierror)
>>
>>   end program buzzy
>>
>> and
>>
>> #include <iostream>
>> #include <RInside.h>
>>
>> void buzzyC_(int argc,char *argv[]);
>>
>> extern "C" void buzzyC(int argc,char *argv[]) {
>>
>>     // create an embedded R instance
>>   RInside R(argc,argv);
>>
>>     // convert to string for RInside assignment
>>
>>
>>     // eval the string, give R notice
>>   R.parseEvalQ("cat(mean(rnorm(argc))");
>> }
>>
>> Now my steps for compiling and linking are the following:
>>
>> erin at erin-Bonobo-Extreme:~$ mpif90 -c buzzy.f90
>> erin at erin-Bonobo-Extreme:~$ mpic++ buzzyC.cpp -c
>> -I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/include
>> -I/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include
>> -I/usr/share/R/include -libstdc++
>> erin at erin-Bonobo-Extreme:~$ mpifort -o fcra buzzy.o buzzyC.o
>> -L/usr/lib/R/lib -lR
>> -L
>> /home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib -lRInside
>> -L/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/
>> -Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/RInside/lib/
>> -lRInside
>> -Wl,-rpath,/home/erin/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/libs/
-lstdc++
>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>>
>> So far so good
>> But when I run this, disaster strikes:
>>
>> erin at erin-Bonobo-Extreme:~$ mpirun -np 4 ./fcra
>>  Fortran Calling RInside           0
>>  Fortran Calling RInside           1
>>  Fortran Calling RInside           3
>>  Fortran Calling RInside           2
>>
>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>> reference.
>>
>> Backtrace for this error:
>>
>> Program received signal SIGSEGV: Segmentation fault - invalid memory
>> reference.
>>
>> Backtrace for this error:
>> #0  0x7FC59706CE48
>> #1  0x7FC59706BFD0
>> #2  0x7FC596AA52EF
>> #3
>> 0x7FC596AFB69A
>> #4  0x7FC597C5E8E8
>> #5  0x7FC5979671E8
>> #6  0x7FC5979677A1
>> #7  0x402A55 in buzzyC
>> #8  0x402891 in MAIN__ at buzzy.f90:?
>> #0  0x7F2482294E48
>> #1  0x7F2482293FD0
>> #2  0x7F2481CCD2EF
>> #3  0x7F2481D2369A
>> #4  0x7F2482E868E8
>> #5  0x7F2482B8F1E8
>> #6  0x7F2482B8F7A1
>> #7  0x402A55 in buzzyC
>> #8  0x402891 in MAIN__ at buzzy.f90:?
>> ------------------------------
>>
>> mpirun noticed that process rank 1 with PID 2188 on node
>> erin-Bonobo-Extreme exited on signal 11 (Segmentation fault).
>> ------------------------------
>>
>> erin at erin-Bonobo-Extreme:~$
>>
>> Maybe I should be asking:  is this even possible, please?
>>
>> Thanks,
>> Erin
>>
>>

-- 
Erin Hodgess
Associate Professor
Department of Mathematical and Statistics
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com

	[[alternative HTML version deleted]]

R help - Feb 2016 - Using Fortran with MPI, RInside, and calling R functions

[R] Using Fortran with MPI, RInside, and calling R functions

[R] Using Fortran with MPI, RInside, and calling R functions

[R] Using Fortran with MPI, RInside, and calling R functions