When using MKL - PETSc attempts to default to sequential MKL.
Perhaps this pulls in a *conflicting* dependency against -liomp5 - and
one has to use threaded MKL for this case. i.e not use
-lmkl_sequential
You appear to have multiple mkl libraires linked in - its not clear
what they are for - and if there are any conflicts there.
> -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
> -lmkl_intel_lp64 lmkl_sequential -lmkl_core -lpthread
To test this out - suggest rebuilding PETSc with
--download-fblaslapack [and no mkl or related pacakges] - and then run
this test case you have [with openmp]
And then add back one mkl package at a time..
Satish
On Fri, 2 Mar 2018, Adrián Amor 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.
>
