Hi Matt, I did go ahead and install the libraries but I’m getting some I/O problems with my application. I’m not sure if we can trust the PASSED statement. This isn’t my area of expertise so I’m not sure what else I should try but its good someone else can replicate the behavior I’m seeing locally.
Thanks for your help, S. -- Si Hammond Scalable Computer Architectures Sandia National Laboratories, NM, USA On 1/11/16, 9:47 AM, "Hdf-forum on behalf of Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]" <[email protected] on behalf of [email protected]> wrote: >Simon, et al, > >I just built HDF5 1.8.15 using Intel 16.0.0.109 and Open MPI 1.10.0 (the >only combo available to me at present that is 16/1.10) and I can see the >same behavior. I also tried setting RUNPARALLEL='mpirun -np 6' in case >it was a mpiexec v mpirun issue. > >Indeed, if you run the exectuable yourself > >> (1094) $ mpirun -q -np 6 ./t_pflush1 >> Testing H5Fflush (part1) >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> (1095) $ echo $? >> 1 >> (1096) $ > >I would not expect a return code of 1 to correspond with a PASSED. If >one goes past that, everything else seems to "work" but can we trust it? > >> (1100) $ mpirun -q -np 6 ./t_pflush1 >> Testing H5Fflush (part1) >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> (1101) $ echo $? >> 1 >> (1102) $ mpirun -q -np 6 ./t_pflush2 >> Testing H5Fflush (part2 with flush) >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> Testing H5Fflush (part2 without flush) >>PASSED >> (1103) $ echo $? >> 0 >> (1104) $ mpirun -q -np 6 ./t_pshutdown >> Testing proper shutdown of HDF5 library >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> (1105) $ echo $? >> 0 >> (1106) $ mpirun -q -np 6 ./t_prestart >> Testing proper shutdown of HDF5 library >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> (1107) $ echo $? >> 0 >> (1108) $ mpirun -q -np 6 ./t_shapesame >> =================================== >> Shape Same Tests Start >> express_test = 1. >> =================================== >> MPI-process 3. hostname=borgo011 >> ...SKIP!... >> 980 of 1224 subtests skipped to expedite testing. >> >> >> >> >> All tests were successful. >> >> All tests were successful. >> >> =================================== >> Shape Same tests finished with no errors >> =================================== >> (1109) $ echo $? >> 0 >> (1110) $ >> > > >Matt > >On 01/10/2016 09:46 PM, Hammond, Simon David (-EXP) wrote: >> Hi HDF5 users/developers, >> >> I am trying to bring up HDF5 1.8.X (X = 14, 15, 16) on a new test bed >>system at Sandia using OpenMPI 1.10.1 and Intel 16.1.150 compilers. >> >> During the "make test" I get the following output for these libraries. >>Rather oddly, the tests are reported as a failure but the test being run >>is reported PASSED (see the output below). >> >> If I proceed to go ahead and install the libraries then I do receive >>I/O errors in my application. >> >> Has anyone tried this combination of HDF5, MPI and Intel compilers and >>had success or are there some pointers to what may need to be checked? >> >> Thanks for your help, >> >> Configure Line: >> >> ./configure >>--prefix=/home/projects/x86-64/hdf5/1.8.15/openmpi/1.10.1/intel/16.1.150 >>--enable-static --disable-shared --enable-parallel --enable-hl >>CC=/home/projects/x86-64/openmpi/1.10.1/intel/16.1.150/bin/mpicc >>CXX=/home/projects/x86-64/openmpi/1.10.1/intel/16.1.150/bin/mpicxx >>FC=/home/projects/x86-64/openmpi/1.10.1/intel/16.1.150/bin/mpif90 >>CFLAGS="-O3 -g -fPIC" CXXFLAGS="-O3 -g -fPIC" FCFLAGS="-O3 -g -fPIC" >>--enable-fortran --with-zlib=/home/projects/x86-64/zlib/1.2.8 >> >> Test Output: >> >> <.. Lots of Output ..> >> make[4]: Entering directory `/home/sdhammo/hdf5/hdf5-1.8.15/testpar' >> ============================ >> Testing t_pflush1 >> ============================ >> t_pflush1 Test Log >> ============================ >> Testing H5Fflush (part1) >>*** Hint *** >> You can use environment variable HDF5_PARAPREFIX to run parallel test >>files in a >> different directory or to add file type prefix. E.g., >> HDF5_PARAPREFIX=pfs:/PFS/user/me >> export HDF5_PARAPREFIX >> *** End of Hint *** >> PASSED >> >>------------------------------------------------------------------------- >>- >> mpiexec has exited due to process rank 0 with PID 91152 on >> node node17 exiting improperly. There are three reasons this could >>occur: >> >> 1. this process did not call "init" before exiting, but others in >> the job did. This can cause a job to hang indefinitely while it waits >> for all processes to call "init". By rule, if one process calls "init", >> then ALL processes must call "init" prior to termination. >> >> 2. this process called "init", but exited without calling "finalize". >> By rule, all processes that call "init" MUST call "finalize" prior to >> exiting or it will be considered an "abnormal termination" >> >> 3. this process called "MPI_Abort" or "orte_abort" and the mca parameter >> orte_create_session_dirs is set to false. In this case, the run-time >>cannot >> detect that the abort call was an abnormal termination. Hence, the only >> error message you will receive is this one. >> >> This may have caused other processes in the application to be >> terminated by signals sent by mpiexec (as reported here). >> >> You can avoid this message by specifying -quiet on the mpiexec command >>line. >> >> >>------------------------------------------------------------------------- >>- >> 21.72user 2.13system 0:08.38elapsed 284%CPU (0avgtext+0avgdata >>12960maxresident)k >> 9568inputs+3896outputs (1major+30976minor)pagefaults 0swaps >> make[4]: *** [t_pflush1.chkexe_] Error 1 >> make[4]: Leaving directory `/home/sdhammo/hdf5/hdf5-1.8.15/testpar' >> make[3]: *** [build-check-p] Error 1 >> make[3]: Leaving directory `/home/sdhammo/hdf5/hdf5-1.8.15/testpar' >> make[2]: *** [test] Error 2 >> make[2]: Leaving directory `/home/sdhammo/hdf5/hdf5-1.8.15/testpar' >> make[1]: *** [check-am] Error 2 >> make[1]: Leaving directory `/home/sdhammo/hdf5/hdf5-1.8.15/testpar' >> make: *** [check-recursive] Error 1 >> >> >> >> -- >> Simon Hammond >> Center for Computing Research (Scalable Computer Architectures) >> Sandia National Laboratories, NM >> [Sent from remote connection, please excuse typing errors] >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> Twitter: https://twitter.com/hdf5 >> > > >-- >Matt Thompson, SSAI, Sr Scientific Programmer/Analyst >NASA GSFC, Global Modeling and Assimilation Office >Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 >Phone: 301-614-6712 Fax: 301-614-6246 >http://science.gsfc.nasa.gov/sed/bio/matthew.thompson > >_______________________________________________ >Hdf-forum is for HDF software users discussion. >[email protected] >http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
