[petsc-users] Using PETSC with an openMP program
Adrián Amor
aamor at pa.uc3m.es
Fri Mar 2 09:39:16 CST 2018
Thanks a lot for your early response! So, sorry if this is a very
straightforward question from your answer, and just to be sure, then can't
I use PETSC in a code where in some place OpenMP parallelization is used
while PETSC is called in a part of the program non-parallelized with OpenMP?
Thanks!
Adrian.
2018-03-02 16:32 GMT+01:00 Smith, Barry F. <bsmith at mcs.anl.gov>:
>
> PETSc is for writing parallel codes using MPI, it is not for writing
> parallel codes with OpenMP. http://www.mcs.anl.gov/petsc/
> miscellaneous/petscthreads.html
>
> Barry
>
>
> > On Mar 2, 2018, at 9:00 AM, Adrián Amor <aamor at pa.uc3m.es> wrote:
> >
> > Hi all,
> >
> > I have been working in the last months with PETSC in a FEM program
> written on FORTRAN, so far sequential. Now, I want to parallelize it with
> OpenMP and I have found some problems. Finally, I have built a mockup
> program trying to localize the error.
> >
> > 1. I have compiled PETSC with these options:
> > ./configure --with-cc=mpiicc --with-cxx=mpiicpc --with-fc=mpiifort
> --with-blas-lapack-dir=/opt/intel/mkl/lib/intel64/ --with-debugging=1
> --with-scalar-type=complex --with-threadcomm --with-pthreadclasses
> --with-openmp --with-openmp-include=/opt/intel/compilers_and_libraries_
> 2016.1.150/linux/compiler/lib/intel64_lin --with-openmp-lib=/opt/intel/
> compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin/libiomp5.a
> PETSC_ARCH=linux-intel-dbg PETSC-AVOID-MPIF-H=1
> >
> > (I have tried also removing --with-threadcomm --with-pthreadclasses
> and with libiomp5.so).
> >
> > 2. The program to be executed is composed of two files, one is
> hellocount.F90:
> > MODULE hello_count
> > use omp_lib
> > IMPLICIT none
> >
> > CONTAINS
> > subroutine hello_print ()
> > integer :: nthreads,mythread
> >
> > !pragma hello-who-omp-f
> > !$omp parallel
> > nthreads = omp_get_num_threads()
> > mythread = omp_get_thread_num()
> > write(*,'("Hello from",i3," out of",i3)') mythread,nthreads
> > !$omp end parallel
> > !pragma end
> > end subroutine hello_print
> > END MODULE hello_count
> >
> > and the other one is hellocount_main.F90:
> > Program Hello
> >
> > USE hello_count
> >
> > call hello_print
> >
> > STOP
> >
> > end Program Hello
> >
> > 3. To compile these two functions I use:
> > rm -rf _obj
> > mkdir _obj
> >
> > ifort -E -I/home/aamor/petsc/include -I/home/aamor/petsc/linux-intel-dbg/include
> -c hellocount.F90 >_obj/hellocount.f90
> > ifort -E -I/home/aamor/petsc/include -I/home/aamor/petsc/linux-intel-dbg/include
> -c hellocount_main.F90 >_obj/hellocount_main.f90
> >
> > mpiifort -CB -g -warn all -O0 -shared-intel -check:none -qopenmp -module
> _obj -I./_obj -I/home/aamor/MUMPS_5.1.2/include
> -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/include
> -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/include/intel64/lp64/
> -I/home/aamor/petsc/include -I/home/aamor/petsc/linux-intel-dbg/include
> -o _obj/hellocount.o -c _obj/hellocount.f90
> > mpiifort -CB -g -warn all -O0 -shared-intel -check:none -qopenmp -module
> _obj -I./_obj -I/home/aamor/MUMPS_5.1.2/include
> -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/include
> -I/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/include/intel64/lp64/
> -I/home/aamor/petsc/include -I/home/aamor/petsc/linux-intel-dbg/include
> -o _obj/hellocount_main.o -c _obj/hellocount_main.f90
> >
> > mpiifort -CB -g -warn all -O0 -shared-intel -check:none -qopenmp -module
> _obj -I./_obj -o exec/HELLO _obj/hellocount.o _obj/hellocount_main.o
> /home/aamor/lib_tmp/libarpack_LinuxIntel15.a /home/aamor/MUMPS_5.1.2/lib/libzmumps.a
> /home/aamor/MUMPS_5.1.2/lib/libmumps_common.a /home/aamor/MUMPS_5.1.2/lib/libpord.a
> /home/aamor/parmetis-4.0.3/lib/libparmetis.a /home/aamor/parmetis-4.0.3/lib/libmetis.a
> -L/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64
> -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lpetsc -lmkl_intel_lp64
> -lmkl_intel_thread -lmkl_core -lmkl_lapack95_lp64 -liomp5 -lpthread -lm
> -L/home/aamor/lib_tmp -lgidpost -lz /home/aamor/lua-5.3.3/src/liblua.a
> /home/aamor/ESEAS-master/libeseas.a -Wl,-rpath,/home/aamor/petsc/linux-intel-dbg/lib
> -L/home/aamor/petsc/linux-intel-dbg/lib -Wl,-rpath,/opt/intel/mkl/lib/intel64
> -L/opt/intel/mkl/lib/intel64 -Wl,-rpath,/opt/intel/impi/5.
> 1.2.150/intel64/lib/debug_mt -L/opt/intel/impi/5.1.2.150/
> intel64/lib/debug_mt -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib
> -L/opt/intel/impi/5.1.2.150/intel64/lib -Wl,-rpath,/opt/intel/
> compilers_and_libraries_2016/linux/mkl/lib/intel64
> -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/compilers_and_libraries_2016.
> 1.150/linux/compiler/lib/intel64_lin -L/opt/intel/compilers_and_
> libraries_2016.1.150/linux/compiler/lib/intel64_lin
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib/debug_mt
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib -lmkl_intel_lp64
> -lmkl_sequential -lmkl_core -lpthread -lX11 -lssl -lcrypto -lifport
> -lifcore_pic -lmpicxx -ldl -Wl,-rpath,/opt/intel/impi/5.
> 1.2.150/intel64/lib/debug_mt -L/opt/intel/impi/5.1.2.150/
> intel64/lib/debug_mt -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib
> -L/opt/intel/impi/5.1.2.150/intel64/lib -lmpifort -lmpi -lmpigi -lrt
> -lpthread -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib/debug_mt
> -L/opt/intel/impi/5.1.2.150/intel64/lib/debug_mt
> -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib -L/opt/intel/impi/
> 5.1.2.150/intel64/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/compilers_and_libraries_2016.
> 1.150/linux/compiler/lib/intel64_lin -L/opt/intel/compilers_and_
> libraries_2016.1.150/linux/compiler/lib/intel64_lin
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -Wl,-rpath,/opt/intel/
> compilers_and_libraries_2016/linux/mkl/lib/intel64
> -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib/debug_mt
> -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib/debug_mt
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib -limf -lsvml -lirng -lm
> -lipgo -ldecimal -lcilkrts -lstdc++ -lgcc_s -lirc -lirc_s
> -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib/debug_mt
> -L/opt/intel/impi/5.1.2.150/intel64/lib/debug_mt
> -Wl,-rpath,/opt/intel/impi/5.1.2.150/intel64/lib -L/opt/intel/impi/
> 5.1.2.150/intel64/lib -Wl,-rpath,/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/compilers_and_libraries_2016.
> 1.150/linux/compiler/lib/intel64_lin -L/opt/intel/compilers_and_
> libraries_2016.1.150/linux/compiler/lib/intel64_lin
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.4.7
> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -Wl,-rpath,/opt/intel/
> compilers_and_libraries_2016/linux/mkl/lib/intel64
> -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64 -ldl
> >
> > exec/HELLO
> >
> > 4. Then I have seen that:
> > 4.1. If I set OMP_NUM_THREADS=2 and I remove -lpetsc and -lifcore_pic
> from the last step, I got:
> > Hello from 0 out of 2
> > Hello from 1 out of 2
> > 4.2 But if add -lpetsc and -lifcore_pic (because I want to use PETSC) I
> get this error:
> > Hello from 0 out of 2
> > forrtl: severe (40): recursive I/O operation, unit -1, file unknown
> > Image PC Routine Line
> Source
> > HELLO 000000000041665C Unknown Unknown
> Unknown
> > HELLO 00000000004083C8 Unknown Unknown
> Unknown
> > libiomp5.so 00007F9C603566A3 Unknown Unknown
> Unknown
> > libiomp5.so 00007F9C60325007 Unknown Unknown
> Unknown
> > libiomp5.so 00007F9C603246F5 Unknown Unknown
> Unknown
> > libiomp5.so 00007F9C603569C3 Unknown Unknown
> Unknown
> > libpthread.so.0 0000003CE76079D1 Unknown Unknown
> Unknown
> > libc.so.6 0000003CE6AE88FD Unknown Unknown
> Unknown
> > If you set OMP_NUM_THREADS to 8, I get:
> > forrtl: severe (40): recursive I/O operation, unit -1, file unknown
> > forrtl: severe (40): recursive I/O operation, unit -1, file unknown
> > forrtl: severe (40): recursive I/O operation, unit -1, file unknown
> >
> > I am sorry if this is a trivial problem because I guess that lots of
> people use PETSC with OpenMP in FORTRAN, but I have really done my best to
> figure out where the error is. Can you help me?
> >
> > Thanks a lot!
> >
> > Adrian.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20180302/18f1f022/attachment.html>
More information about the petsc-users
mailing list