Hi Bill,
I have change the order of -I flag as suggested by you. After recompiling I am
getting a different error. PLOTSTUFF just quits whereas CGINS shows some
errors. Pasted are the errors that I am getting.
PLOTSTUFF ERROR
===================================================
A++ Internal_Index bounds checking: ON
Type: `plotStuff [-noplot] [-nopause] [-plot3d] [-ovText] fileName
[file[.cmd]]' to read the show file called fileName,
and optionally read a command file.
or: `plotStuff [-noplot] [-nopause] [-plot3d] [-ovText] file.cmd' to run the
command file (with first command the show file name).
Successfully opened /home/qamara/.overturerc for reading
Unknown keyword `ndwindow*width' in the .overturerc file.
Not using the colour `MEDIUMGOLDENROD'
User commands are being saved in the file `plotStuff.cmd'
mount the showfile: n.hdf
ShowFileReader::ERROR: unable to open an old file = n.hdf (or n.hdf.hdf) (or
n.hdf.show)
error
Overture::abort: I am now going to purposely abort so that you can get a
traceback from a debugger
Segmentation fault (core dumped)
=============================================================
CGINS ERROR
===============================================================
$grid
OvertureParser::result = [n.hdf]
readOrBuildTheGrid:Try to read the overlapping grid file : n.hdf
***** Mounting file n.hdf****
HDF5-DIAG: Error detected in HDF5 (1.8.8) MPI-process 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Sat Apr 27
13:54:24 2013
, name = 'n.hdf', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDmpio.c line 999 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#004: H5FDmpio.c line 999 in H5FD_mpio_open(): MPI_ERR_OTHER: known error not
in list
major: Internal error (too specific to document in detail)
minor: MPI Error String
getFromADataBase:ERROR: unable to open an old file = n.hdf (or n.hdf.hdf ),
(or n.hdf.show )
readOrBuildTheGrid:ERROR return from getFromADataBase
Error occured in file src/readOrBuildTheGrid.C line 50.
error
Overture::abort: I am now going to purposely abort so that you can get a
traceback from a debugger
Segmentation fault (core dumped)
==================================================================
Any suggestions to fix this.
Best,
-Adnan
Adnan Qamar, PhD
Mechanical Engineering,
Physical Sciences and Engineering Division,
Building 4, Room 3216,
4700 King Abdullah University of Science and Technology (KAUST),
Thuwal 23955-6900, KSA.
Email: Adnan.Qamar@xxxxxxxxxxxx
Ph: 966-2-8084896
Fax: 96628021077@xxxxxxxxxxxxxxxx
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*From:* overture-bounce@xxxxxxxxxxxxx [overture-bounce@xxxxxxxxxxxxx] on behalf
of Bill Henshaw [henshaw@xxxxxxxx]
*Sent:* Thursday, April 25, 2013 5:58 AM
*To:* overture@xxxxxxxxxxxxx
*Subject:* [overture] Re: HDF library version mismatch error
Hi Adnan,
As you noted, the problem occurs since the HDF version 1.8.5 library is being
found first
by the compiler when it compiles files, but the loader is finding the HDF 1.8.8
libraries.
Here is my compile line when the files in Overture/DataBase are compiled:
g++ -fPIC -I/home/henshaw.0/Overture.g/include -I. -DUSE_MESA -I/home/henshaw.0/A++P++/A++P++-4.3.2-64/A++/install/include -I/home/henshaw.0/software/OpenGL/Mesa-7.2.intel.gcc4.3.2/include
-I/usr/include -DBL_USE_DOUBLE -DBL_Solaris -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -g -DH5_USE_16_API -I/home/henshaw.0/software/hdf/hdf5-1.6.5-gcc4.3.2-64/include -c
GenericDataBase.C HDF_DataBase.C DataBaseBuffer.C dbAccess.C dbFunctions.f kk_ptr.cc
The -I flags tell the compiler where to look for .h files. In the above case,
if there were HDF .h files
in /usr/include then these would be found before the .h files in
/home/henshaw.0/software/hdf/hdf5-1.6.5-gcc4.3.2-64/include
You could edit the Overture/DataBase/Makefile and change the order of the -I
flags so that the HDF include
directory is found first. I think you can make the following change in this
file:
DataBase_date: $(Source)
# $(CC) $(CCFLAGS) -DH5_USE_16_API -I$(HDF)/include -c $?
$(CC) -DH5_USE_16_API -I$(HDF)/include $(CCFLAGS) -c $?
touch $@
Then in Overture/DataBase, type
rm *.o *_date
and then type "make" in the Overture directory.
...Bill
On 04/23/2013 01:42 AM, Adnan Qamar wrote:
Hi Bill,
I am trying to install parallel Overture/CG (PetSc=on) on one of our HPC cluster. Apparently, everything compiles smoothly and all executable are generated. However, when I run parallel ogen or
CGINS by utilising a grid file created by a serial version of ogen it gives me HDF5 library version mismatch error (error cut pasted below). The serial version of ogen is complied with same version
of HDF i.e 1.8.8 as used by parallel version.
I believe the HPC cluster already have HDF5 v 1.8.5 installed by root and somehow during compiling parallel or serial Overture/CG it is picking the original installed libraries of HDF5.v.1.8.5
instead of library path I am providing using HDF variable in defenv file. I would appreciate if you could point me to a possible fix to this issue.
Best,
Adnan
===================================================
Unknown keyword `ndwindow*width' in the .overturerc file.
Not using the colour `MEDIUMGOLDENROD'
User commands are being saved in the file `plotStuff.cmd'
mount the showfile: n.hdf
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.5, library is 1.8.8
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.8
Configured on: Sun Apr 21 10:12:00 AST 2013
Configured by: qamara@fen3
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux fen3 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed
Feb 20 12:17:37 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /home/qamara/over_p/hdf5-1.8.8
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/lib64/openmpi/bin/mpicc
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 -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked
-Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -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 -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG
-UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-D_BSD_SOURCE
Shared C Library: no
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lrt -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: mpicc
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE:
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
Bye...
Segmentation fault (core dumped)
==========================================================
Adnan Qamar, PhD
Mechanical Engineering,
Physical Sciences and Engineering Division,
Building 4, Room 3216,
4700 King Abdullah University of Science and Technology (KAUST),
Thuwal 23955-6900, KSA.
Email: Adnan.Qamar@xxxxxxxxxxxx
Ph: 966-2-8084896
Fax: 96628021077@xxxxxxxxxxxxxxxx
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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