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 <[email protected]> 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@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@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. <[email protected]> > 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 <[email protected]> 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@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@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
