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@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@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@sdumont11 tutorials]$ ./ex5f > Number of SNES iterations = 4 > > [alfredo.jaramillo@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 <[email protected]> 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 <[email protected]> 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 > > > > > > > > > > > > > > > > > > > > >
