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]
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--
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
_______________________________________________
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