[petsc-dev] testing on Titan

Fri Jun 29 08:15:06 CDT 2018

Try copying files to scratch file system.
Home is not available when executive batch job. Probably interactive she'll
too.

On Fri, Jun 29, 2018 at 7:47 AM Mark Adams <mfadams at lbl.gov> wrote:

> I can not even run a job here. This is from an interactive shell:
>
> 64-pgi ex19-batch1:~/petsc/src/snes/examples/tutorials> make
> PETSC_DIR=/autofs/nccs-svm1_home1/adams/petsc PETSC_ARCH=arch-titan-dbg6
> cc -o ex19.o -c -fast -mp   -I/autofs/nccs-svm1_home1/adams/petsc/include
> -I/autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/include
> -I/ccs/proj/env003/petscv3.9-dbg64-pgi/include    `pwd`/ex19.c
> cc -fast -mp  -o ex19  ex19.o
> -L/autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib
> -Wl,-rpath,/ccs/proj/env003/petscv3.9-dbg64-pgi/lib
> -L/ccs/proj/env003/petscv3.9-dbg64-pgi/lib -lpetsc -lHYPRE -lflapack
> -lfblas -lparmetis -lmetis -lstdc++ -ldl
> /autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib/libpetsc.a(dlimpl.o):
> In function `PetscDLOpen':
> /autofs/nccs-svm1_home1/adams/petsc/src/sys/dll/dlimpl.c:54: warning:
> Using 'dlopen' in statically linked applications requires at runtime the
> shared libraries from the glibc version used for linking
> /autofs/nccs-svm1_home1/adams/petsc/arch-titan-dbg64-pgi/lib/libpetsc.a(send.o):
> In function `PetscOpenSocket':
> /autofs/nccs-svm1_home1/adams/petsc/src/sys/classes/viewer/impls/socket/send.c:106:
> warning: Using 'gethostbyname' in statically linked applications requires
> at runtime the shared libraries from the glibc version used for linking
> adams at titan-batch1:~/petsc/src/snes/examples/tutorials> aprun -n 1 ./ex19
> [NID 02258] 2018-06-29 07:45:09 Exec ./ex19 failed: chdir
> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such
> file or directory
> adams at titan-batch1:~/petsc/src/snes/examples/tutorials>
>
> Seung-Hoe runs here, maybe he can give me advice on what is wrong here.
>
>
> On Thu, Jun 28, 2018 at 7:53 PM Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
>
>>
>>   1) We need to get this PGI compiler into our regular testing. It
>> doesn't like some Fortran code the other compilers are ok with
>>
>>    2) Mark,  likely you just need to submit the examples manually to run
>> them. cd src/snes/examples/tutorials; make ex19  then use the batch system
>> to submit the example
>>
>>    Barry
>>
>>
>> > On Jun 28, 2018, at 5:35 PM, Mark Adams <mfadams at lbl.gov> wrote:
>> >
>> > I am trying to run on Titan and I am having problems running the tests.
>> I get this output. It says it can not find a directory, but I do an ls in
>> after the error and you can see that it is there.
>> >
>> > I've attached the logs.
>> >
>> > Any ideas?
>> > Thanks,
>> > Mark
>> >
>> > adams at titan-login6:~/petsc> make
>> PETSC_DIR=/ccs/proj/env003/petscv3.9-opt64-pgi PETSC_ARCH="" test
>> > Running test examples to verify correct installation
>> > Using PETSC_DIR=/ccs/proj/env003/petscv3.9-opt64-pgi and PETSC_ARCH=
>> > *******************Error detected during compile or
>> link!*******************
>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> > /ccs/home/adams/petsc/src/snes/examples/tutorials ex19
>> >
>> *********************************************************************************
>> > cc -o ex19.o -c -fast -mp
>>  -I/ccs/proj/env003/petscv3.9-opt64-pgi/include
>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include
>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include    `pwd`/ex19.c
>> > cc -fast -mp  -o ex19  ex19.o
>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib
>> -Wl,-rpath,/ccs/proj/env003/petscv3.9-opt64-pgi/lib
>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib -lpetsc -lHYPRE -lflapack
>> -lfblas -lparmetis -lmetis -lstdc++ -ldl
>> > /ccs/proj/env003/petscv3.9-opt64-pgi/lib/libpetsc.a(dlimpl.o): In
>> function `PetscDLOpen':
>> > /autofs/nccs-svm1_home1/adams/petsc/src/sys/dll/dlimpl.c:53: warning:
>> Using 'dlopen' in statically linked applications requires at runtime the
>> shared libraries from the glibc version used for linking
>> > /ccs/proj/env003/petscv3.9-opt64-pgi/lib/libpetsc.a(send.o): In
>> function `PetscOpenSocket':
>> >
>> /autofs/nccs-svm1_home1/adams/petsc/src/sys/classes/viewer/impls/socket/send.c:101:
>> warning: Using 'gethostbyname' in statically linked applications requires
>> at runtime the shared libraries from the glibc version used for linking
>> > /bin/rm -f ex19.o
>> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1
>> MPI process
>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> > [NID 18525] 2018-06-28 18:25:39 Exec ./ex19 failed: chdir
>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such
>> file or directory
>> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2
>> MPI processes
>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> > [NID 18525] 2018-06-28 18:25:46 Exec ./ex19 failed: chdir
>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such
>> file or directory
>> > 1,5c1
>> > < 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
>> > ---
>> > > [NID 18525] 2018-06-28 18:25:55 Exec ./ex19 failed: chdir
>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials No such
>> file or directory
>> > /ccs/home/adams/petsc/src/snes/examples/tutorials
>> > Possible problem with ex19_hypre, diffs above
>> > =========================================
>> > *******************Error detected during compile or
>> link!*******************
>> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> > /ccs/home/adams/petsc/src/snes/examples/tutorials ex5f
>> > *********************************************************
>> > ftn -c -fast  -mp   -I/ccs/proj/env003/petscv3.9-opt64-pgi/include
>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include
>> -I/ccs/proj/env003/petscv3.9-opt64-pgi/include    -o ex5f.o ex5f.F90
>> > PGF90-S-0155-Could not resolve generic procedure dmdacreate2d
>> (ex5f.F90: 120)
>> > PGF90-S-0450-Argument number 2 to snesgetiterationnumber: kind mismatch
>> (ex5f.F90: 180)
>> >   0 inform,   0 warnings,   2 severes, 0 fatal for main
>> > PGF90-S-0155-Could not resolve generic procedure matsetvalueslocal
>> (ex5f.F90: 464)
>> > PGF90-S-0155-Could not resolve generic procedure matsetvalueslocal
>> (ex5f.F90: 477)
>> >   0 inform,   0 warnings,   2 severes, 0 fatal for formjacobianlocal
>> > gmake[3]: [ex5f.o] Error 2 (ignored)
>> > ftn -fast  -mp  -o ex5f ex5f.o
>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib
>> -Wl,-rpath,/ccs/proj/env003/petscv3.9-opt64-pgi/lib
>> -L/ccs/proj/env003/petscv3.9-opt64-pgi/lib -lpetsc -lHYPRE -lflapack
>> -lfblas -lparmetis -lmetis -lstdc++ -ldl
>> > /usr/bin/ld: cannot find ex5f.o: No such file or directory
>> > /usr/bin/sha1sum: ex5f: No such file or directory
>> > gmake[3]: [ex5f] Error 2 (ignored)
>> > /bin/rm -f ex5f.o
>> > Completed test examples
>> > adams at titan-login6:~/petsc> ll
>> /autofs/nccs-svm1_home1/adams/petsc/src/snes/examples/tutorials
>> > total 1864
>> > -rw-rw-r-- 1 adams adams  11134 May  3 14:26 ex1.c
>> > drwxr-xr-x 3 adams adams   4096 May  3 14:26 ex10d
>> > -rw-rw-r-- 1 adams adams  92615 May  3 14:26 ex12.c
>> > -rw-r--r-- 1 adams adams  19324 Jun 21 17:59 ex13.c
>> > -rw-rw-r-- 1 adams adams  20550 May  3 14:26 ex14.c
>> >
>> > <make.log><configure.log>
>>
>> --
Sent from Iphone
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