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:
[email protected]
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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