Hi Richard,
I used "configure" with the following options:
--prefix=/some/dir --enable-parallel
Platform:
Linux atlasz 3.2.0-4-amd64 #1 SMP Debian 3.2.68-1+deb7u1 x86_64 GNU/Linux
The libhdf5.settings file is attached.
Thanks!
Regards,
Joseph
Idézet (Richard van Hees <[email protected]>):
Hi Joseph ,
It would be helpful if you would indicate which way you configured
HDF5. Using cmake? Using configure? Which options did you use? On
which platform?
Helpful also be the content of the file
<HDF5_DIR>/lib/libhdf5.settings, where <HDF5_DIR> is the
installation directory for HDF5, default "/usr/local" or specified
by you using PREFIX or --prefix
Greetings, Richard
On 11/24/2015 12:40 PM, Kóbori József wrote:
Hi Mohamad,
I compiled the latest version of HDF5: hdf5-1.8.16
After compiling (make) I simply typed the "make check" command,
and I got the error below, so I don't have a particular test case.
If You need more info please let me know!
Thank You!
Regards,
Joseph
Idézet (Mohamad Chaarawi <[email protected]>):
Hi Joseph,
Could you please indicate the version of the HDF5 library and
Open-MPI that you are using?
Furthermore, could you provide a test case that replicates the
failure below?
You are correct that it seems that we are constructing a derived
datatype that the ADIO driver in ROMIO doesn't seem to be able to
parse properly. We don't test however much with Open-MPI, at lease
to the extent that we do with MPICH. I'd be curious if you can try
the same program with MPICH and see if it gives the same error.
Thanks,
Mohamad
-----Original Message-----
From: Hdf-forum [mailto:[email protected]] On Behalf
Of Kóbori József
Sent: Monday, November 16, 2015 5:30 AM
To: [email protected]
Subject: [Hdf-forum] unsupported data type
Dear All,
when trying to test the previously compiled (with mpicc) HDF5 source I
encountered the following error message:
"MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on exactly
when Open MPI kills them.
-------------------------------------------------------------------------- Error: Unsupported datatype passed to
ADIOI_Count_contiguous_blocks,
combiner = 17
Error: Unsupported datatype passed to ADIOI_Count_contiguous_blocks,
combiner = 17
Error: Unsupported datatype passed to ADIOI_Count_contiguous_blocks,
combiner = 17
Error: Unsupported datatype passed to ADIOI_Count_contiguous_blocks,
combiner = 17
Error: Unsupported datatype passed to ADIOI_Count_contiguous_blocks,
combiner = 17
Error: Unsupported datatype passed to ADIOI_Count_contiguous_blocks,
combiner = 17
-------------------------------------------------------------------------- mpiexec has exited due to process rank 1 with PID 17756 on node
XXXX
exiting without calling "finalize". This may have caused other
processes in the
application to be terminated by signals sent by mpiexec (as
reported here)."
As I learnt it has to do something with a particular data type
(as the error
message indicates it), but I'm stuck, I don't know how to proceed.
Could You give some help?
Best regards,
Joseph
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
-------------------------------------------
József Kóbori
PhD Student - Particle Physics and Astronomy Program
Room: Building North, Number 5.91, Phone: +36 30-266-5673
Eötvös Loránd University
1117 Budapest, Pázmány P. stny. 1/A
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
-------------------------------------------
József Kóbori
PhD Student - Particle Physics and Astronomy Program
Room: Building North, Number 5.91, Phone: +36 30-266-5673
Eötvös Loránd University
1117 Budapest, Pázmány P. stny. 1/A
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.16
Configured on: Thu Nov 19 12:32:16 CET 2015
Configured by: jkobori@xxxx
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux atlasz 3.2.0-4-amd64 #1 SMP Debian
3.2.68-1+deb7u1 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /xxx/jkobori/hdf5/hdf5-1.8.16
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/mpicc ( Configured with:
../src/configure -v --with-pkgversion='Debian 4.7.2-5'
--with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs
--enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.7 --enable-shared --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7
--libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu
--enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object
--enable-plugin --enable-objc-gc --with-arch-32=i586 --with-tune=generic
--enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu
--target=x86_64-linux-gnu built with gcc version 4.7.2 (Debian 4.7.2-5))
CFLAGS:
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef
-Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align
-Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes
-Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs
-Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked
-Wdisabled-optimization -Wformat=2 -Wendif-labels -Wdeclaration-after-statement
-Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self
-Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros
-Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op
-Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384
-Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init
-Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const
-Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance
-Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -O3
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L
-DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lrt -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: yes
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
MPE:
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
