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

[Erin Hodgess]

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

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