I hope someone help me and give me tips.
I tried to install Code_saturne6.0.5 on Ubunts18.04 in Virtual Box.
I used an automated installer (install_saturne.py).
I found this problem when importing MED (med3.2, 3.3, 4.0) file into Code_saturne
because some errors happened.
"Preprocessor.log" indicated as following:
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/home/tsubasa/Code_Saturne/6.0.5/code_saturne-6.0.5/arch/Linux_x86_64/libexec/code_saturne/cs_preprocess
--log --out mesh_input /home/tsubasa/Desktop/test/MESH/cube_med30.med
.------------------------------.
| |
| Code_Saturne Preprocessor |
| |
`------------------------------'
code_saturne version 6.0.5 (built jeu. 19 nov. 2020 05:08:28 CET)
Error in preprocessor execution
===============================
/home/tsubasa/saturne/code_saturne-6.0.5/preprocessor/pre-post/ecs_pre.c:486: Fatal error.
File format "MED" support not available in this
installation (file "/home/tsubasa/Desktop/test/MESH/cube_med30.med").
Call stack
1: 0x55dde37d618a <ecs_pre__type_format+0x41a> (cs_preprocess)
2: 0x55dde37d1669 <ecs_cmd__lit_arg+0x3c9> (cs_preprocess)
3: 0x55dde37ceded <main+0x9d> (cs_preprocess)
4: 0x7f0369d78bf7 <__libc_start_main+0xe7> (libc.so.6)
5: 0x55dde37cf76a <_start+0x2a> (cs_preprocess)
End of stack
Therefore, I tried to install MED package in automatic installation process.
I edit a "setup" file in automatic installation process as following:
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# Name Use Install Path
#
hdf5 yes yes /home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
cgns yes yes /home/tsubasa/Code_Saturne/6.0.5/cgns-4.1.1/arch/Linux_x86_64
med yes yes /home/tsubasa/Code_Saturne/6.0.5/med-4.0.0/arch/Linux_x86_64
scotch yes yes /home/tsubasa/Code_Saturne/6.0.5/scotch-6.0.9/arch/Linux_x86_64
parmetis yes yes /home/tsubasa/Code_Saturne/6.0.5/parmetis-4.0.3/arch/Linux_x86_64
#
#========================================================
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../code_saturne-6.0.5/install_saturne.py
Code: Select all
tsubasa@tsubasa-VirtualBox:~/saturne/code_saturne-6.0.5.build$ ../code_saturne-6.0.5/install_saturne.py
Installation of Code_Saturne
____________________________
The process will take several minutes.
You can have a look at the log file meanwhile.
Check the setup file and some utilities presence.
o Checking for cc... /usr/bin/cc
o Checking for f95... /usr/bin/f95
o Checking for python3... /usr/bin/python3
Python version is 3.6
o Checking for make... /usr/bin/make
HDF5 (Hierarchical Data Format)
version: 1.10.6
url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz
package: hdf5
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
config_opts: --enable-build-mode=production
Extract of HDF5
Installation of HDF5
HDF5 (Hierarchical Data Format)
version: 1.10.6
url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz
package: hdf5
source_dir: /home/tsubasa/saturne/code_saturne-6.0.5.build/hdf5-1.10.6
install_dir: /home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
config_opts: --enable-build-mode=production
o Configure...
o Compile...
o Install...
o Clean...
CGNS (CFD General Notation System)
version: 4.1.1
url: https://github.com/CGNS/CGNS/archive/v4.1.1.tar.gz
package: cgns
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/cgns-4.1.1/arch/Linux_x86_64
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64 -DHDF5_INCLUDE_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64/include
Extract of CGNS
Installation of CGNS
CGNS (CFD General Notation System)
version: 4.1.1
url: https://github.com/CGNS/CGNS/archive/v4.1.1.tar.gz
package: cgns
source_dir: /home/tsubasa/saturne/code_saturne-6.0.5.build/CGNS-4.1.1
install_dir: /home/tsubasa/Code_Saturne/6.0.5/cgns-4.1.1/arch/Linux_x86_64
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64 -DHDF5_INCLUDE_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64/include
o Configure...
o Compile...
o Install...
o Clean...
MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome/other/med-4.0.0.tar.gz
package: med
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/med-4.0.0/arch/Linux_x86_64
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
Extract of MED
Traceback (most recent call last):
File "../code_saturne-6.0.5/install_saturne.py", line 1357, in <module>
setup.install()
File "../code_saturne-6.0.5/install_saturne.py", line 1105, in install
p.extract()
File "../code_saturne-6.0.5/install_saturne.py", line 295, in extract
tar.extractall()
File "/usr/lib/python2.7/tarfile.py", line 2083, in extractall
self.extract(tarinfo, path)
File "/usr/lib/python2.7/tarfile.py", line 2120, in extract
self._extract_member(tarinfo, os.path.join(path, tarinfo.name))
File "/usr/lib/python2.7/tarfile.py", line 2196, in _extract_member
self.makefile(tarinfo, targetpath)
File "/usr/lib/python2.7/tarfile.py", line 2236, in makefile
with bltn_open(targetpath, "wb") as target:
IOError: [Errno 13] Permission denied: './med-4.0.0/doc/jpg/xmdump.jpg'
tsubasa@tsubasa-VirtualBox:~/saturne/code_saturne-6.0.5.build$
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tsubasa@tsubasa-VirtualBox:~/saturne/code_saturne-6.0.5.build/med-4.0.0/doc$ chmod 777 -R jpg/
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tsubasa@tsubasa-VirtualBox:~/saturne/code_saturne-6.0.5.build$ ../code_saturne-6.0.5/install_saturne.py
Installation of Code_Saturne
____________________________
The process will take several minutes.
You can have a look at the log file meanwhile.
Check the setup file and some utilities presence.
o Checking for cc... /usr/bin/cc
o Checking for f95... /usr/bin/f95
o Checking for python3... /usr/bin/python3
Python version is 3.6
o Checking for make... /usr/bin/make
HDF5 (Hierarchical Data Format)
version: 1.10.6
url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz
package: hdf5
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
config_opts: --enable-build-mode=production
CGNS (CFD General Notation System)
version: 4.1.1
url: https://github.com/CGNS/CGNS/archive/v4.1.1.tar.gz
package: cgns
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/cgns-4.1.1/arch/Linux_x86_64
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64 -DHDF5_INCLUDE_PATH=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64/include
MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome/other/med-4.0.0.tar.gz
package: med
source_dir: None
install_dir: /home/tsubasa/Code_Saturne/6.0.5/med-4.0.0/arch/Linux_x86_64
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
Extract of MED
Installation of MED
MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome/other/med-4.0.0.tar.gz
package: med
source_dir: /home/tsubasa/saturne/code_saturne-6.0.5.build/med-4.0.0
install_dir: /home/tsubasa/Code_Saturne/6.0.5/med-4.0.0/arch/Linux_x86_64
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64
o Configure...
Error during configure stage of MED.
See install_saturne.log for more information.
tsubasa@tsubasa-VirtualBox:~/saturne/code_saturne-6.0.5.build$
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checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1000' is supported by ustar format... yes
checking whether GID '1000' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
configure: Trying /home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64 home path for searching H5pubconf.h file.
checking for a sed that does not truncate output... /bin/sed
checking whether to compile C using MPI... no
checking for style of include used by make... GNU
checking for gcc... /usr/bin/cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/cc accepts -g... yes
checking for /usr/bin/cc option to accept ISO C89... none needed
checking whether /usr/bin/cc understands -c and -o together... yes
checking dependency style of /usr/bin/cc... gcc3
checking for /usr/bin/cc option to accept ISO C99... none needed
checking whether to compile FC using MPI... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: HDF version is not a parallel one.
checking for grep that handles long lines and -e... /bin/grep
checking how to run the C preprocessor... /usr/bin/cc -E
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking absolute name of <H5public.h>... checking H5public.h usability... yes
checking H5public.h presence... yes
checking for H5public.h... yes
///home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64/include/H5public.h
checking absolute name of <H5Ipublic.h>... checking H5Ipublic.h usability... yes
checking H5Ipublic.h presence... yes
checking for H5Ipublic.h... yes
///home/tsubasa/Code_Saturne/6.0.5/hdf5-1.10.6/arch/Linux_x86_64/include/H5Ipublic.h
checking for H5open in -lhdf5... no
configure: error: Can't find hdf5 library, either use HDF5HOME env. var. , --with-hdf5=<path> or --with-hdf5-lib=<libpath>