"make check" failure in testphdf5 for impi

christopher.w.harrop · January 16, 2014, 10:41pm

Hello,

I am attempting to build parallel HDF5 using Intel MPI. The ./configure and make steps succeed, but I am getting an error in the "make check" step (see below). Has anyone else tried impi? Anyone know how to overcome this issue? My searches have not turned up anything so I am posting here. I hope I've provided enough information for folks to ponder this, but if not, please do let me know. Any/all ideas are appreciated.

Here are the configure details:

export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort
export RUNPARALLEL='mpiexec.hydra -n $${NPROCS:=6}'

./configure --with-szlib=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/szip/2.1/gnu/4.4.6 \
--enable-parallel --enable-fortran --enable-fortran2003 --enable-shared \
--prefix=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG

I am building HDF5 1.8.11 with Intel version 12.0.4.191 on a Linux 2.6.32-279.32.1.el6.x86_64 system.

I am doing the ./configure, make, and make check on a Lustre filesystem with tons of free space, so the HDF5_PARAPREFIX setting should not be needed.

Here is the output of the testphdf5 part of the "make check":

testphdf5 Test Log

···

============================

PHDF5 TESTS START

MPI-process 3. hostname=r26i1n2
MPI-process 1. hostname=r26i1n2
MPI-process 4. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 5. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 2. hostname=r26i1n2
MPI-process 0. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
*** 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 ***
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
11.51user 18.99system 0:11.70elapsed 260%CPU (0avgtext+0avgdata 458448maxresident)k
616inputs+1265704outputs (30major+155431minor)pagefaults 0swaps
make[5]: *** [testphdf5.chkexe_] Error 1
make[5]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[4]: *** [build-check-p] Error 1
make[4]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[3]: *** [test] Error 2
make[3]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG'
make: *** [/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG] Error 2
[Christopher.W.Harrop@Zeus:r26i1n2 bass.r21]$

Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303

Mohamad_Chaarawi · January 16, 2014, 10:59pm

Hi Christopher,

I have not tried building HDF5 with Intel MPI; but I have a clue on what the problem that you are seeing might be.

In PHDF5 we have a very complicated use of MPI Derived Datatypes. Initially it exposed bugs in many MPI implementations and had to work around those for a while. As those bugs were fixed and "enough (~2-3 years)" time passed by, there was no need for those workarounds, so they were removed. Since we do not support Intel MPI as a library for our development, we don't test with it, and so we don't see this problem.

My suggestion is to check what the latest version of Intel MPI and update to that if your current version is considerably old - maybe that would fix it. But again since it is not supported, my answer comes with a certain amount of uncertainty.

Thanks,
Mohamad

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Christopher Harrop - NOAA Affiliate
Sent: Thursday, January 16, 2014 4:41 PM
To: HDF Users Discussion List
Subject: [Hdf-forum] "make check" failure in testphdf5 for impi

Hello,

I am attempting to build parallel HDF5 using Intel MPI. The ./configure and make steps succeed, but I am getting an error in the "make check" step (see below). Has anyone else tried impi? Anyone know how to overcome this issue? My searches have not turned up anything so I am posting here. I hope I've provided enough information for folks to ponder this, but if not, please do let me know. Any/all ideas are appreciated.

Here are the configure details:

export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort
export RUNPARALLEL='mpiexec.hydra -n $${NPROCS:=6}'

./configure --with-szlib=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/szip/2.1/gnu/4.4.6 \
--enable-parallel --enable-fortran --enable-fortran2003 --enable-shared \
--prefix=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG

I am building HDF5 1.8.11 with Intel version 12.0.4.191 on a Linux 2.6.32-279.32.1.el6.x86_64 system.

I am doing the ./configure, make, and make check on a Lustre filesystem with tons of free space, so the HDF5_PARAPREFIX setting should not be needed.

Here is the output of the testphdf5 part of the "make check":

testphdf5 Test Log

===================================
PHDF5 TESTS START

MPI-process 3. hostname=r26i1n2
MPI-process 1. hostname=r26i1n2
MPI-process 4. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 5. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 2. hostname=r26i1n2
MPI-process 0. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
*** 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 ***
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
11.51user 18.99system 0:11.70elapsed 260%CPU (0avgtext+0avgdata 458448maxresident)k
616inputs+1265704outputs (30major+155431minor)pagefaults 0swaps
make[5]: *** [testphdf5.chkexe_] Error 1
make[5]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[4]: *** [build-check-p] Error 1
make[4]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[3]: *** [test] Error 2
make[3]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG'
make: *** [/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG] Error 2
[Christopher.W.Harrop@Zeus:r26i1n2 bass.r21]$

Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov<mailto:christopher.w.harrop@noaa.gov>
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303

christopher.w.harrop · January 16, 2014, 11:07pm

Mohamad,

Thank you very much for that idea. In fact, I did have to work around that exact problem for our SGI MPT build. The "make check" will fail for Intel/MPT unless I do "export MPI_TYPE_DEPTH=1024 ". Fortunately, that was an easy one because the resulting error message actually told me what to do to fix it.

I'll do a search and see if there are any derived type depth settings for Intel MPI. And I'll also see if there's a newer version of impi that we could get installed.

If there are any others out there who know what environment setting or version of impi that would fix the problem, please do chime in.

Thank you for your time,

Chris

···

Hi Christopher,

I have not tried building HDF5 with Intel MPI; but I have a clue on what the problem that you are seeing might be.

In PHDF5 we have a very complicated use of MPI Derived Datatypes. Initially it exposed bugs in many MPI implementations and had to work around those for a while. As those bugs were fixed and “enough (~2-3 years)” time passed by, there was no need for those workarounds, so they were removed. Since we do not support Intel MPI as a library for our development, we don’t test with it, and so we don’t see this problem.

My suggestion is to check what the latest version of Intel MPI and update to that if your current version is considerably old - maybe that would fix it. But again since it is not supported, my answer comes with a certain amount of uncertainty.

Thanks,
Mohamad

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Christopher Harrop - NOAA Affiliate
Sent: Thursday, January 16, 2014 4:41 PM
To: HDF Users Discussion List
Subject: [Hdf-forum] "make check" failure in testphdf5 for impi

Hello,

I am attempting to build parallel HDF5 using Intel MPI. The ./configure and make steps succeed, but I am getting an error in the "make check" step (see below). Has anyone else tried impi? Anyone know how to overcome this issue? My searches have not turned up anything so I am posting here. I hope I've provided enough information for folks to ponder this, but if not, please do let me know. Any/all ideas are appreciated.

Here are the configure details:

export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort
export RUNPARALLEL='mpiexec.hydra -n $${NPROCS:=6}'

./configure --with-szlib=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/szip/2.1/gnu/4.4.6 \
--enable-parallel --enable-fortran --enable-fortran2003 --enable-shared \
--prefix=/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG

I am building HDF5 1.8.11 with Intel version 12.0.4.191 on a Linux 2.6.32-279.32.1.el6.x86_64 system.

I am doing the ./configure, make, and make check on a Lustre filesystem with tons of free space, so the HDF5_PARAPREFIX setting should not be needed.

Here is the output of the testphdf5 part of the "make check":

testphdf5 Test Log

===================================
PHDF5 TESTS START

MPI-process 3. hostname=r26i1n2
MPI-process 1. hostname=r26i1n2
MPI-process 4. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 5. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
MPI-process 2. hostname=r26i1n2
MPI-process 0. hostname=r26i1n2

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11

For help use: /scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.8 release 11
*** 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 ***
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Test filenames are:
    ParaTest.h5
Testing -- fapl_mpio duplicate (mpiodup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- fapl_mpiposix duplicate (posixdup)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset using split communicators (split)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent write (idsetw)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset independent read (idsetr)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective write (cdsetw)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- dataset collective read (cdsetr)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent write (eidsetw)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset independent read (eidsetr)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective write (ecdsetw)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset collective read (ecdsetr)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- extendible dataset independent write #2 (eidsetw2)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- chunked dataset with none-selection (selnone)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel extend Chunked allocation on serial file (calloc)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- parallel read of dataset written serially with filters (fltread)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- compressed dataset collective read (cmpdsetr)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple datasets write (ndsetw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups write (ngrpw)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- multiple groups read (ngrpr)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- compact dataset test (compact)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- collective group and dataset write (cngrpw)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- independent group and dataset read (ingrpr)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- big dataset test (bigdset)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- dataset fill value (fill)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- simple collective chunk io (cchunk1)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- noncontiguous collective chunk io (cchunk2)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- multi-chunk collective chunk io (cchunk3)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- collective chunk io with partial non-selection (cchunk4)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- linked chunk collective IO without optimization (cchunk5)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- multi-chunk collective IO with direct request (cchunk6)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO with optimization (cchunk7)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- linked chunk collective IO transferring to multi-chunk (cchunk8)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO with optimization (cchunk9)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- multiple chunk collective IO transferring to independent IO (cchunk10)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous write (ccontw)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular contiguous read (ccontr)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk write (cschunkw)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular simple chunk read (cschunkr)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk write (ccchunkw)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- collective irregular complex chunk read (ccchunkr)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- null dataset test (null)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- I/O mode confusion test -- hangs quickly on failure (I/Omodeconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- round robin object header flush confusion test (rrobjflushconf)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
Testing -- test lower dim size comp in span tree to mpi derived type (tldsc)
APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
11.51user 18.99system 0:11.70elapsed 260%CPU (0avgtext+0avgdata 458448maxresident)k
616inputs+1265704outputs (30major+155431minor)pagefaults 0swaps
make[5]: *** [testphdf5.chkexe_] Error 1
make[5]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[4]: *** [build-check-p] Error 1
make[4]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[3]: *** [test] Error 2
make[3]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG/testpar'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/build/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG'
make: *** [/scratch1/portfolios/BMC/nesccmgmt/Christopher.W.Harrop/bass.r21/opt/hdf5-impi/1.8.11/intel/12.0.4.191/impi/4.0.4.008.ORIG] Error 2
[Christopher.W.Harrop@Zeus:r26i1n2 bass.r21]$

Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303

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"make check" failure in testphdf5 for impi

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PHDF5 TESTS START

testphdf5 Test Log

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testphdf5 Test Log

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