<div dir="ltr">here is the output:<br><br>alfredo.jaramillo@sdumont11 tutorials]$ make ex19<br>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/<a href="http://3.1.2.006/lib/intel64">3.1.2.006/lib/intel64</a> -L/opt/intel/parallel_studio_xe_2016_update2/clck/<a href="http://3.1.2.006/lib/intel64">3.1.2.006/lib/intel64</a> -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<br>[alfredo.jaramillo@sdumont11 tutorials]$ make ex5f<br><div>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/<a href="http://3.1.2.006/lib/intel64">3.1.2.006/lib/intel64</a> -L/opt/intel/parallel_studio_xe_2016_update2/clck/<a href="http://3.1.2.006/lib/intel64">3.1.2.006/lib/intel64</a> -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</div><div><br></div><div>[alfredo.jaramillo@sdumont11 tutorials]$ ./ex5f <br>Number of SNES iterations =     4</div><div><br></div><div>[alfredo.jaramillo@sdumont11 tutorials]$ ./ex19<br>lid velocity = 0.0625, prandtl # = 1., grashof # = 1.<br>Number of SNES iterations = 2<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, May 21, 2020 at 6:53 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Please copy/paste complete [compile] commands from:<br>
<br>
src/snes/tutorials/<br>
make clean<br>
make ex19<br>
make ex5f<br>
<br>
Likely the link command used in your code is different than what is used here - triggering errors.<br>
<br>
Satish<br>
<br>
On Thu, 21 May 2020, Alfredo Jaramillo wrote:<br>
<br>
> hello Satish, no the tests seem to be ok altough some error related to mpd.<br>
> <br>
> ==============THE TESTS===================<br>
> <br>
> Running check examples to verify correct installation<br>
> Using PETSC_DIR=/scratch/simulreserv/softwares/petsc-3.13.0 and<br>
> PETSC_ARCH=x64-O3-3.13-intel2016-64<br>
> Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<br>
> See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
> mpiexec_sdumont11: cannot connect to local mpd<br>
> (/tmp/mpd2.console_alfredo.jaramillo); possible causes:<br>
>   1. no mpd is running on this host<br>
>   2. an mpd is running but was started without a "console" (-n option)<br>
> Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<br>
> See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
> mpiexec_sdumont11: cannot connect to local mpd<br>
> (/tmp/mpd2.console_alfredo.jaramillo); possible causes:<br>
>   1. no mpd is running on this host<br>
>   2. an mpd is running but was started without a "console" (-n option)<br>
> 1,5c1,3<br>
> < lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<br>
> <   0 SNES Function norm 0.0406612<br>
> <   1 SNES Function norm 4.12227e-06<br>
> <   2 SNES Function norm 6.098e-11<br>
> < Number of SNES iterations = 2<br>
> ---<br>
> > mpiexec_sdumont11: cannot connect to local mpd<br>
> (/tmp/mpd2.console_alfredo.jaramillo); possible causes:<br>
> >   1. no mpd is running on this host<br>
> >   2. an mpd is running but was started without a "console" (-n option)<br>
> /scratch/simulreserv/softwares/petsc-3.13.0/src/snes/tutorials<br>
> Possible problem with ex19 running with hypre, diffs above<br>
> =========================================<br>
> 1,9c1,3<br>
> < lid velocity = 0.0625, prandtl # = 1., grashof # = 1.<br>
> <   0 SNES Function norm 0.239155<br>
> <     0 KSP Residual norm 0.239155<br>
> <     1 KSP Residual norm < 1.e-11<br>
> <   1 SNES Function norm 6.81968e-05<br>
> <     0 KSP Residual norm 6.81968e-05<br>
> <     1 KSP Residual norm < 1.e-11<br>
> <   2 SNES Function norm < 1.e-11<br>
> < Number of SNES iterations = 2<br>
> ---<br>
> > mpiexec_sdumont11: cannot connect to local mpd<br>
> (/tmp/mpd2.console_alfredo.jaramillo); possible causes:<br>
> >   1. no mpd is running on this host<br>
> >   2. an mpd is running but was started without a "console" (-n option)<br>
> /scratch/simulreserv/softwares/petsc-3.13.0/src/snes/tutorials<br>
> Possible problem with ex19 running with mumps, diffs above<br>
> =========================================<br>
> Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI<br>
> process<br>
> See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html</a><br>
> mpiexec_sdumont11: cannot connect to local mpd<br>
> (/tmp/mpd2.console_alfredo.jaramillo); possible causes:<br>
>   1. no mpd is running on this host<br>
>   2. an mpd is running but was started without a "console" (-n option)<br>
> Completed test examples<br>
> <br>
> ===============================<br>
> <br>
> I entered in src/snes/tutorials/ and executed "make ex5f". The binary exf5<br>
> was created<br>
> <br>
> <br>
> <br>
> On Thu, May 21, 2020 at 6:37 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>> wrote:<br>
> <br>
> > Do you get this error when building PETSc examples [C and/or fortran] -<br>
> > when you build them with the corresponding petsc makefile?<br>
> ><br>
> > Can you send the log of the example compiles?<br>
> ><br>
> > Satish<br>
> ><br>
> > ---<br>
> ><br>
> > [the attachment got deleted - don't know by who..]<br>
> ><br>
> > DENIAL OF SERVICE ALERT<br>
> ><br>
> > A denial of service protection limit was exceeded. The file has been<br>
> > removed.<br>
> > Context: 'configure.log.7z'<br>
> > Reason: The data size limit was exceeded<br>
> > Limit: 10 MB<br>
> > Ticket Number : 0c9c-5ec6-f30f-0001<br>
> ><br>
> ><br>
> > For further information, contact your system administrator.<br>
> > Copyright 1999-2014 McAfee, Inc.<br>
> > All Rights Reserved.<br>
> > <a href="http://www.mcafee.com" rel="noreferrer" target="_blank">http://www.mcafee.com</a><br>
> ><br>
> ><br>
> ><br>
> > On Thu, 21 May 2020, Alfredo Jaramillo wrote:<br>
> ><br>
> > > dear PETSc team,<br>
> > ><br>
> > > I have compiled PETSc with a 2016 version of the intel compilers. The<br>
> > > installation went well, but when I tried to compile my code the following<br>
> > > error appears in the final step of compilation (linking with ld)<br>
> > ><br>
> > > ../build/linux_icc/obj_linux_icc_opt/main.o: In function `main':<br>
> > > main.c:(.text+0x0): multiple definition of `main'<br>
> > ><br>
> > /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):<br>
> > > first defined here<br>
> > ><br>
> > /opt/intel/parallel_studio_xe_2016_update2/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/libifcore_pic.a(for_main.o):<br>
> > > In function `main':<br>
> > > for_main.c:(.text+0x3e): undefined reference to `MAIN__'<br>
> > ><br>
> > > I searched for this and I found that the option "-nofor_main" should be<br>
> > > added when compiling with ifort, but our code is written only in C an<br>
> > C++.<br>
> > > The FORTRAN compiler is used when PETSc compiles MUMPS. So I dont know if<br>
> > > this would work for this case.<br>
> > ><br>
> > > The configure.log file and the log of the compilation giving the error<br>
> > are<br>
> > > attached to this message. These logs were obtained in a cluster, I'm<br>
> > > getting the same error on my personal computer with a 2020 version of the<br>
> > > Intel Parallel Studio.<br>
> > ><br>
> > > thank you for any help on this<br>
> > > Alfredo<br>
> > ><br>
> ><br>
> ><br>
> <br>
<br>
</blockquote></div>