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HDF5 Parallel Build (PGI 14.6/Fedora 20) Test Failures

 
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WCAPEHART



Joined: 07 Jun 2007
Posts: 5

PostPosted: Sun Jul 13, 2014 1:34 pm    Post subject: HDF5 Parallel Build (PGI 14.6/Fedora 20) Test Failures Reply with quote

Hello All:

I am getting a failure when testing what appears otherwise to be a
successful build of a Parallel PGI Build of HDF5 1.18.13 at the ≥make
check≤ phase of building HDF5.

(Note that this error also happens when I build without MPICH and
--enable-parallel enabled and without čenable-fortran).

Details:

OS: Fedora 20 64-bit

HDF5 Version 1.18.13

PGI Version 14.6 (with the MPICH 3.0.4 executables and libraries that come
with PGI, not a separate MPICH build)

Configure optons: ./configure --prefix=/usr/local --enable-parallel
--enable-parallel-tests --enable-fortran

FC, F90 and F77 = mpif90, CC = mpicc, CXX = mpicxx

The build happens without incident. But when I test, I get the following
error with make check:


% make check
Making check in src
make[1]: Entering directory `/usr/local/hdf5-1.8.13/src'
make check-TESTS
make[2]: Entering directory `/usr/local/hdf5-1.8.13/src'
make[3]: Entering directory `/usr/local/hdf5-1.8.13/src'
make[4]: Entering directory `/usr/local/hdf5-1.8.13/src'
make[4]: Nothing to be done for `_exec_check-s'.
make[4]: Leaving directory `/usr/local/hdf5-1.8.13/src'
make[3]: Leaving directory `/usr/local/hdf5-1.8.13/src'
make[3]: Entering directory `/usr/local/hdf5-1.8.13/src'
make[3]: Leaving directory `/usr/local/hdf5-1.8.13/src'
make[2]: Leaving directory `/usr/local/hdf5-1.8.13/src'
make[1]: Leaving directory `/usr/local/hdf5-1.8.13/src'
Making check in test
make[1]: Entering directory `/usr/local/hdf5-1.8.13/test'
make testhdf5 lheap ohdr stab gheap cache cache_api pool accum hyperslab
istore bittests dt_arith dtypes dsets cmpd_dset filter_fail extend
external efc objcopy links unlink big mtime fillval mount flush1 flush2
app_ref enum set_extent ttsafe getname vfd ntypes dangle dtransform
reserved cross_read freespace mf btree2 fheap file_image unregister
error_test err_compat tcheck_version testmeta links_env testerror.sh
testlibinfo.sh testcheck_version.sh testlinks_env.sh
make[2]: Entering directory `/usr/local/hdf5-1.8.13/test'
make[2]: `testhdf5' is up to date.
make[2]: `lheap' is up to date.
make[2]: `ohdr' is up to date.
make[2]: `stab' is up to date.
make[2]: `gheap' is up to date.
make[2]: `cache' is up to date.
make[2]: `cache_api' is up to date.
make[2]: `pool' is up to date.
make[2]: `accum' is up to date.
make[2]: `hyperslab' is up to date.
make[2]: `istore' is up to date.
make[2]: `bittests' is up to date.
make[2]: `dt_arith' is up to date.
make[2]: `dtypes' is up to date.
make[2]: `dsets' is up to date.
make[2]: `cmpd_dset' is up to date.
make[2]: `filter_fail' is up to date.
make[2]: `extend' is up to date.
make[2]: `external' is up to date.
make[2]: `efc' is up to date.
make[2]: `objcopy' is up to date.
make[2]: `links' is up to date.
make[2]: `unlink' is up to date.
make[2]: `big' is up to date.
make[2]: `mtime' is up to date.
make[2]: `fillval' is up to date.
make[2]: `mount' is up to date.
make[2]: `flush1' is up to date.
make[2]: `flush2' is up to date.
make[2]: `app_ref' is up to date.
make[2]: `enum' is up to date.
make[2]: `set_extent' is up to date.
make[2]: `ttsafe' is up to date.
make[2]: `getname' is up to date.
make[2]: `vfd' is up to date.
make[2]: `ntypes' is up to date.
make[2]: `dangle' is up to date.
make[2]: `dtransform' is up to date.
make[2]: `reserved' is up to date.
make[2]: `cross_read' is up to date.
make[2]: `freespace' is up to date.
make[2]: `mf' is up to date.
make[2]: `btree2' is up to date.
make[2]: `fheap' is up to date.
make[2]: `file_image' is up to date.
make[2]: `unregister' is up to date.
make[2]: `error_test' is up to date.
make[2]: `err_compat' is up to date.
make[2]: `tcheck_version' is up to date.
make[2]: `testmeta' is up to date.
make[2]: `links_env' is up to date.
make[2]: `testerror.sh' is up to date.
make[2]: `testlibinfo.sh' is up to date.
make[2]: `testcheck_version.sh' is up to date.
make[2]: `testlinks_env.sh' is up to date.
make[2]: Leaving directory `/usr/local/hdf5-1.8.13/test'
make check-TESTS
make[2]: Entering directory `/usr/local/hdf5-1.8.13/test'
make[3]: Entering directory `/usr/local/hdf5-1.8.13/test'
===Serial tests in test begin Sun Jul 13 20:29:11 UTC 2014===
make[4]: Entering directory `/usr/local/hdf5-1.8.13/test'
============================
No need to test testhdf5 again.
============================
No need to test lheap again.
============================
No need to test ohdr again.
============================
No need to test stab again.
============================
No need to test gheap again.
============================
No need to test cache again.
============================
No need to test cache_api again.
============================
No need to test pool again.
============================
No need to test accum again.
============================
No need to test hyperslab again.
============================
No need to test istore again.
============================
No need to test bittests again.
============================
No need to test dt_arith again.
============================
No need to test dtypes again.
============================
No need to test dsets again.
============================
No need to test cmpd_dset again.
============================
No need to test filter_fail again.
============================
No need to test extend again.
============================
No need to test external again.
============================
No need to test efc again.
============================
No need to test objcopy again.
============================
No need to test links again.
============================
No need to test unlink again.
============================
No need to test big again.
============================
No need to test mtime again.
============================
No need to test fillval again.
============================
No need to test mount again.
============================
No need to test flush1 again.
============================
No need to test flush2 again.
============================
No need to test app_ref again.
============================
No need to test enum again.
============================
No need to test set_extent again.
============================
No need to test ttsafe again.
============================
No need to test getname again.
============================
No need to test vfd again.
============================
No need to test ntypes again.
============================
No need to test dangle again.
============================
No need to test dtransform again.
============================
No need to test reserved again.
============================
No need to test cross_read again.
============================
No need to test freespace again.
============================
No need to test mf again.
============================
No need to test btree2 again.
============================
No need to test fheap again.
============================
No need to test file_image again.
============================
No need to test unregister again.
============================
No need to test testerror.sh again.
============================
============================
No need to test testlibinfo.sh again.
============================
============================
Testing testcheck_version.sh
============================
testcheck_version.sh Test Log
============================
Tests for the H5check_version function.
Note that abort messages may appear due to the expected termination
of the program when it is tested with mis-matched version numnbers.
tcheck_version
PASSED
tcheck_version -tM
*FAILED*
Expected exit code (6) differs from actual code (0)
tcheck_version -tm
*FAILED*
Expected exit code (6) differs from actual code (0)
tcheck_version -tr
*FAILED*
Expected exit code (6) differs from actual code (0)
env HDF5_DISABLE_VERSION_CHECK= tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK= tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK= tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK= tcheck_version -tr
PASSED
env HDF5_DISABLE_VERSION_CHECK=-1 tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK=-1 tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK=-1 tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK=-1 tcheck_version -tr
PASSED
env HDF5_DISABLE_VERSION_CHECK=0 tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK=0 tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK=0 tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK=0 tcheck_version -tr
PASSED
env HDF5_DISABLE_VERSION_CHECK=1 tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK=1 tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK=1 tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK=1 tcheck_version -tr
PASSED
env HDF5_DISABLE_VERSION_CHECK=2 tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK=2 tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK=2 tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK=2 tcheck_version -tr
PASSED
env HDF5_DISABLE_VERSION_CHECK=3 tcheck_version
PASSED
env HDF5_DISABLE_VERSION_CHECK=3 tcheck_version -tM
PASSED
env HDF5_DISABLE_VERSION_CHECK=3 tcheck_version -tm
PASSED
env HDF5_DISABLE_VERSION_CHECK=3 tcheck_version -tr
PASSED
***3 errors encountered***
0.03user 0.08system 0:00.26elapsed 46%CPU (0avgtext+0avgdata
3632maxresident)k
0inputs+360outputs (0major+45451minor)pagefaults 0swaps
make[4]: *** [testcheck_version.sh.chkexe_] Error 1
make[4]: Leaving directory `/usr/local/hdf5-1.8.13/test'
make[3]: *** [build-check-s] Error 2
make[3]: Leaving directory `/usr/local/hdf5-1.8.13/test'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/usr/local/hdf5-1.8.13/test'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/usr/local/hdf5-1.8.13/test'
make: *** [check-recursive] Error 1
%




Ideas?

Thanks Muchä
================================================================
Bill Capehart <William.Capehart@sdsmt.edu> Associate Professor
Atmospheric & Environmental Sciences Program Coordinator
213 Mineral Industries Building Hydrometeorology
South Dakota School of Mines and Technology Skype: wcapehart
501 East Saint Joseph Street Ph: +1-605-394-1994
Rapid City, SD 57701-3995 Mobile: +1-605-484-5692
=================== http://capehart.sdsmt.edu ==================
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cparrott



Joined: 02 May 2011
Posts: 142

PostPosted: Mon Jul 14, 2014 11:14 am    Post subject: Reply with quote

Hi Bill,

Thanks so much for the report. I will investigate the issue here, and follow up when I have more information.

Best regards,

+chris
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cparrott



Joined: 02 May 2011
Posts: 142

PostPosted: Mon Jul 21, 2014 4:14 pm    Post subject: Reply with quote

Hi Bill,

Our Fedora 20 system is down due to an office move right now, but I was able to build HDF5 1.8.13 on a Red Hat 6.2 system with PGI 14.6 and MPICH 3.0.4 internally. I then ran the test suite here, and did not see the problem you observed with the test failure.

One thing you might try is adding the following settings: CPP=cpp LD=ld.

This tells the build to use the standard Linux preprocessor and linker. Sometimes, ./configure scripts behave badly when using the PGI drivers for these functions.

When our Fedora 20 system comes back, I will try again there just to see if I can reproduce the issue you reported.

Best regards,

+chris
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