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

Alfredo Jaramillo ajaramillopalma at gmail.com
Thu May 21 16:57:02 CDT 2020 

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
> > > >
> > >
> > >
> >
>
>
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