[petsc-users] multiple definition of `main' with intel compilers
Alfredo Jaramillo
ajaramillopalma at gmail.com
Thu May 21 20:25:01 CDT 2020
I just read at the end of the section "compilers" here
https://www.mcs.anl.gov/petsc/documentation/installation.html that one can
indicate these libraries by doing
./configure --LIBS='-Bstatic -lifcore -Bdynamic'
thank you very much for your help, Satish
alfredo
On Thu, May 21, 2020 at 10:08 PM Satish Balay <balay at mcs.anl.gov> wrote:
> Configure attempts to automatically determine the language compatible
> libraries by running 'icc -v' and 'ifort -v' - and uses what it says. [this
> list can be different based on compiler options used]
>
> And PETSc examples work fine - so its not clear why fcoremt_pic is causing
> issues with your app build.
>
> There are some differences in your build vs examples - so that could be
> one reason. So its best to build PETSc and your app with the exact same
> compilers and options and see if that works.
>
> Alternative is to specify to PETSc configure the compatibility libraries
> so that it doesn't try to figure this out. [and add extra un-needed
> libraries]
>
> With Intel compilers - its likely the additional configure option is:
>
> LIBS="-Bstatic -lifcore -Bdynamic"
>
> If this works - configure won't run 'ifort -v' and grab fcoremt_pic etc..
>
> Satish
>
> On Thu, 21 May 2020, Alfredo Jaramillo wrote:
>
> > In fact, removing -lifcore_pic from
> PETSC_DIR/PETSC_ARCH/lib/petscvariables
> > solved the problem (this was the first I traied and it worked), it
> compiles
> > and the program runs fine.
> >
> > Also, -lpetsc was being listed some times when compiling .c to .o, I
> fixed
> > that in the scripts.
> >
> > Now, I'm a bit lost about when fcoremt_pic is being linked or if it is
> > necessary at all?
> >
> > thank you very much!
> > alfredo
> >
> > On Thu, May 21, 2020 at 7:21 PM Satish Balay <balay at mcs.anl.gov> wrote:
> >
> > > 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
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
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