Hello,
I'm trying to compile HDF5 with the new Intel tools, but while the
./config and make works without a problem, in the test phase (make
check), when reaching the Fortran API test, the test uses all my
machines memory (and the swap also), as you can see on this image:
http://img201.imageshack.us/img201/7406/cwk.png
The "scripts" that I used to compile szlib, zlib and the hdf5 are these:
SZLIB:
export CC=icc
export CXX=icpc
export F77=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FFLAGS='-O3 -xHost -ip'
tar -zxvf szip-2.1.tar.gz
cd szip-2.1
./configure --prefix=/home/user/Mohid/szip-2.1
make
make check
make install
ZLIB:
export CC=icc
export CFLAGS='-O3 -xHost -ip'
tar -zxvf zlib-1.2.8.tar.gz
cd zlib-1.2.8
./configure --prefix=/home/user/Mohid/zlib-1.2.8
make
make check
make install
hdf5:
export CC=icc
export FC='ifort -fpp -DDEC$=DEC_ -DMS$=MS_'
export CXX=icpc
tar -zxvf hdf5-1.8.11.tar.gz
cd hdf5-1.8.11
./configure --prefix=/home/user/Mohid/hdf5-1.8.11 --enable-fortran
--enable-fortran2003 --enable-cxx --enable-unsupported \
--with-szlib=/home/user/Mohid/szip-2.1
--with-zlib=/home/user/Mohid/zlib-1.2.8/include,/home/user/Mohid/zlib-1.2.8/lib
--enable-production
make
make check
make install
I used the '-fpp -DDEC$=DEC_ -DMS$=MS_' because it was refered here:
http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL
The 'result' of the ./config on the HDF5 is this:
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.11
Configured on: Thu Oct 31 09:53:29 WET 2013
Configured by: [email protected]
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux localhost.localdomain
3.11.6-200.fc19.x86_64 #1 SMP Fri Oct 18 22:34:18 UTC 2013 x86_64 x86_64
x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /home/user/Mohid/hdf5-1.8.11
Compiling Options:
------------------
Compilation Mode: production
C Compiler:
/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/icc ( Intel(R) C
Intel(R) 64 Compiler Version 14.0.0.080 Build 20130728)
CFLAGS:
H5_CFLAGS: -std=c99 -O
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG
-UH5_DEBUG_API
AM_CPPFLAGS: -I/home/user/Mohid/szip-2.1/include
-I/home/user/Mohid/zlib-1.2.8/include -D_LARGEFILE_SOURCE
-D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS: -L/home/user/Mohid/zlib-1.2.8/lib
-L/home/user/Mohid/szip-2.1/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler:
/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort -fpp -DDEC$=DEC_
-DMS$=MS_ ( Intel(R) Fortran Intel(R) 64 Compiler Version 14.0.0.080
Build 20130728)
Fortran 2003 Compiler: yes
Fortran Flags:
H5 Fortran Flags: -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler:
/opt/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc ( Intel(R) C++
Intel(R) 64 Compiler Version 14.0.0.080 Build 20130728)
C++ Flags:
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
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
Can you see some reason to this happens?
Any tip?
Thanks,
Best regards,
Eduardo Jauch.
--
TECNICO Lisboa - MARETEC
Secção de Ambiente e Energia
Av. Rovisco Pais
1049-001 Lisboa
Tel.: +351 21 8419424
Fax: +351 21 8417365
URL: www.mohid.com
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