[petsc-users] multiple definition of `main' with intel compilers

Thu May 21 17:21:49 CDT 2020

For one - PETSc is built without -qopenmp flag - but your makefile is using it. Intel compiler can link in with
different [incompatible] compiler libraries when some flags change this way [causing conflict].

However - the issue could be:

your makefile is listing PETSC_LIB [or however you are accessing petsc info from petsc makefiles] redundantly.

i.e

 - its listing -lpetsc  etc when compiling .c to .o files [this should not happen]
 - its listing -lpetsc  etc twice [-lifcore_pic is listed once though] - don't know if this is the reason for the problem.

You can try [manually] removing -lifcore_pic from PETSC_DIR/PETSC_ARCH/lib/petscvariables - and see if this problem goes away

Satish

On Thu, 21 May 2020, Alfredo Jaramillo wrote:

> here is the output:
> 
> alfredo.jaramillo at sdumont11 tutorials]$ make ex19
> mpiicc -fPIC -O3 -march=native -mtune=native  -fPIC -O3 -march=native
> -mtune=native  -I/scratch/simulreserv/softwares/petsc-3.13.0/include
> -I/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/include
> -I/scratch/simulreserv/softwares/valgrind-3.15.0/include
>  -I/scratch/app/zlib/1.2.11/include    ex19.c
>  -Wl,-rpath,/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -L/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -Wl,-rpath,/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -L/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib/release_mt
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib/release_mt
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/clck/
> 3.1.2.006/lib/intel64 -L/opt/intel/parallel_studio_xe_2016_update2/clck/
> 3.1.2.006/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.4
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.4
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib/release_mt
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib -lpetsc -lHYPRE -lcmumps
> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lopenblas
> -lstdc++ -ldl -lmpifort -lmpi -lmpigi -lrt -lpthread -lifport -lifcore_pic
> -limf -lsvml -lm -lipgo -lirc -lgcc_s -lirc_s -lquadmath -lstdc++ -ldl -o
> ex19
> [alfredo.jaramillo at sdumont11 tutorials]$ make ex5f
> mpiifort -fPIC -O3 -march=native -mtune=native
> -I/scratch/simulreserv/softwares/petsc-3.13.0/include
> -I/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/include
> -I/scratch/simulreserv/softwares/valgrind-3.15.0/include      ex5f.F90
>  -Wl,-rpath,/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -L/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -Wl,-rpath,/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -L/scratch/simulreserv/softwares/petsc-3.13.0/x64-O3-3.13-intel2016-64/lib
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib/release_mt
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib/release_mt
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mpi/intel64/lib
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/clck/
> 3.1.2.006/lib/intel64 -L/opt/intel/parallel_studio_xe_2016_update2/clck/
> 3.1.2.006/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/ipp/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.4
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64/gcc4.4
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/daal/lib/intel64_lin
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/tbb/lib/intel64_lin/gcc4.4
> -Wl,-rpath,/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin
> -L/opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64_lin
> -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
> -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib/release_mt
> -Wl,-rpath,/opt/intel/mpi-rt/5.1/intel64/lib -lpetsc -lHYPRE -lcmumps
> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lopenblas
> -lstdc++ -ldl -lmpifort -lmpi -lmpigi -lrt -lpthread -lifport -lifcore_pic
> -limf -lsvml -lm -lipgo -lirc -lgcc_s -lirc_s -lquadmath -lstdc++ -ldl -o
> ex5f
> 
> [alfredo.jaramillo at sdumont11 tutorials]$ ./ex5f
> Number of SNES iterations =     4
> 
> [alfredo.jaramillo at sdumont11 tutorials]$ ./ex19
> lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
> Number of SNES iterations = 2
> 
> On Thu, May 21, 2020 at 6:53 PM Satish Balay <balay at mcs.anl.gov> wrote:
> 
> > Please copy/paste complete [compile] commands from:
> >
> > src/snes/tutorials/
> > make clean
> > make ex19
> > make ex5f
> >
> > Likely the link command used in your code is different than what is used
> > here - triggering errors.
> >
> > Satish
> >
> > On Thu, 21 May 2020, Alfredo Jaramillo wrote:
> >
> > > hello Satish, no the tests seem to be ok altough some error related to
> > mpd.
> > >
> > > ==============THE TESTS===================
> > >
> > > Running check examples to verify correct installation
> > > Using PETSC_DIR=/scratch/simulreserv/softwares/petsc-3.13.0 and
> > > PETSC_ARCH=x64-O3-3.13-intel2016-64
> > > Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > mpiexec_sdumont11: cannot connect to local mpd
> > > (/tmp/mpd2.console_alfredo.jaramillo); possible causes:
> > >   1. no mpd is running on this host
> > >   2. an mpd is running but was started without a "console" (-n option)
> > > Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > mpiexec_sdumont11: cannot connect to local mpd
> > > (/tmp/mpd2.console_alfredo.jaramillo); possible causes:
> > >   1. no mpd is running on this host
> > >   2. an mpd is running but was started without a "console" (-n option)
> > > 1,5c1,3
> > > < lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> > > <   0 SNES Function norm 0.0406612
> > > <   1 SNES Function norm 4.12227e-06
> > > <   2 SNES Function norm 6.098e-11
> > > < Number of SNES iterations = 2
> > > ---
> > > > mpiexec_sdumont11: cannot connect to local mpd
> > > (/tmp/mpd2.console_alfredo.jaramillo); possible causes:
> > > >   1. no mpd is running on this host
> > > >   2. an mpd is running but was started without a "console" (-n option)
> > > /scratch/simulreserv/softwares/petsc-3.13.0/src/snes/tutorials
> > > Possible problem with ex19 running with hypre, diffs above
> > > =========================================
> > > 1,9c1,3
> > > < lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
> > > <   0 SNES Function norm 0.239155
> > > <     0 KSP Residual norm 0.239155
> > > <     1 KSP Residual norm < 1.e-11
> > > <   1 SNES Function norm 6.81968e-05
> > > <     0 KSP Residual norm 6.81968e-05
> > > <     1 KSP Residual norm < 1.e-11
> > > <   2 SNES Function norm < 1.e-11
> > > < Number of SNES iterations = 2
> > > ---
> > > > mpiexec_sdumont11: cannot connect to local mpd
> > > (/tmp/mpd2.console_alfredo.jaramillo); possible causes:
> > > >   1. no mpd is running on this host
> > > >   2. an mpd is running but was started without a "console" (-n option)
> > > /scratch/simulreserv/softwares/petsc-3.13.0/src/snes/tutorials
> > > Possible problem with ex19 running with mumps, diffs above
> > > =========================================
> > > Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI
> > > process
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > mpiexec_sdumont11: cannot connect to local mpd
> > > (/tmp/mpd2.console_alfredo.jaramillo); possible causes:
> > >   1. no mpd is running on this host
> > >   2. an mpd is running but was started without a "console" (-n option)
> > > Completed test examples
> > >
> > > ===============================
> > >
> > > I entered in src/snes/tutorials/ and executed "make ex5f". The binary
> > exf5
> > > was created
> > >
> > >
> > >
> > > On Thu, May 21, 2020 at 6:37 PM Satish Balay <balay at mcs.anl.gov> wrote:
> > >
> > > > Do you get this error when building PETSc examples [C and/or fortran] -
> > > > when you build them with the corresponding petsc makefile?
> > > >
> > > > Can you send the log of the example compiles?
> > > >
> > > > Satish
> > > >
> > > > ---
> > > >
> > > > [the attachment got deleted - don't know by who..]
> > > >
> > > > DENIAL OF SERVICE ALERT
> > > >
> > > > A denial of service protection limit was exceeded. The file has been
> > > > removed.
> > > > Context: 'configure.log.7z'
> > > > Reason: The data size limit was exceeded
> > > > Limit: 10 MB
> > > > Ticket Number : 0c9c-5ec6-f30f-0001
> > > >
> > > >
> > > > For further information, contact your system administrator.
> > > > Copyright 1999-2014 McAfee, Inc.
> > > > All Rights Reserved.
> > > > http://www.mcafee.com
> > > >
> > > >
> > > >
> > > > On Thu, 21 May 2020, Alfredo Jaramillo wrote:
> > > >
> > > > > dear PETSc team,
> > > > >
> > > > > I have compiled PETSc with a 2016 version of the intel compilers. The
> > > > > installation went well, but when I tried to compile my code the
> > following
> > > > > error appears in the final step of compilation (linking with ld)
> > > > >
> > > > > ../build/linux_icc/obj_linux_icc_opt/main.o: In function `main':
> > > > > main.c:(.text+0x0): multiple definition of `main'
> > > > >
> > > >
> > /opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/libifcore_pic.a(for_main.o):for_main.c:(.text+0x0):
> > > > > first defined here
> > > > >
> > > >
> > /opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/libifcore_pic.a(for_main.o):
> > > > > In function `main':
> > > > > for_main.c:(.text+0x3e): undefined reference to `MAIN__'
> > > > >
> > > > > I searched for this and I found that the option "-nofor_main" should
> > be
> > > > > added when compiling with ifort, but our code is written only in C an
> > > > C++.
> > > > > The FORTRAN compiler is used when PETSc compiles MUMPS. So I dont
> > know if
> > > > > this would work for this case.
> > > > >
> > > > > The configure.log file and the log of the compilation giving the
> > error
> > > > are
> > > > > attached to this message. These logs were obtained in a cluster, I'm
> > > > > getting the same error on my personal computer with a 2020 version
> > of the
> > > > > Intel Parallel Studio.
> > > > >
> > > > > thank you for any help on this
> > > > > Alfredo
> > > > >
> > > >
> > > >
> > >
> >
> >
> 