And I think the libcgns.so is definitely compiled from the source code, no pollution or ambiguity
[root@localhost cgns_file]# ll ` find / -name libcgns.so` -rwxr-xr-x 1 root root 715136 Jan 12 08:30 /root/CGNS-3.3.0/lib/libcgns.so -rw-r--r-- 1 root root 715136 Jan 12 08:27 /usr/local/lib/libcgns.so On Thursday, January 12, 2017 at 10:24:47 PM UTC+8, CatDog wrote: > > I am running into some confusions about the CGNS lib. > The CGNS 3.3.0 is too much newer than my CentOS 6. So I have to compile it > with hdf5 (and szip, I am not sure if it is necessary). However, after > that, when I tried to import CGNS grid. > > wget http://cgns.sourceforge.net/CGNSFiles/Chris/bump.cgns.gz > gunzip bump.cgns.gz > pyfr import -t cgns bump.cgns bump.pyfrm > > I got this error: > > Traceback (most recent call last): > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py" > , line 22, in load_library > File "/op/anaconda3/lib/python3.5/ctypes/__init__.py", line 347, in > __init__ > self._handle = _dlopen(self._name, mode) > OSError: /usr/local/lib/libcgns.so: undefined symbol: H5T_NATIVE_SCHAR_g > > > During handling of the above exception, another exception occurred: > > > Traceback (most recent call last): > File "/op/anaconda3/bin/pyfr", line 11, in <module> > load_entry_point('pyfr==1.5.0', 'console_scripts', 'pyfr')() > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py" > , line 110, in main > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/__main__.py" > , line 118, in process_import > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/__init__.py" > , line 11, in get_reader_by_name > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py" > , line 374, in __init__ > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/readers/cgns.py" > , line 34, in __init__ > File > "/op/anaconda3/lib/python3.5/site-packages/pyfr-1.5.0-py3.5.egg/pyfr/ctypesutil.py" > , line 31, in load_library > OSError: Unable to load cgns > > I googled "H5T_NATIVE_SCHAR_g", and I found the description at H5T: > Datatype Interface <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5T.html>. > It seems a fundamental part of hdf5. > > My compilation of CGNS is as follows: > #szip > wget https:// > support.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz > tar xf szip-2.1.tar.gz > cd szip-2.1 > ./configure --prefix=/usr/local > make > make install > cd > > > #hdf5 > wget -b https:// > support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar > tar xf hdf5-1.8.18.tar > cd hdf5-1.8.18 > ./configure --prefix=/usr/local --enable-parallel --with-szlib > make > make install > cd > > > #CGNS > wget https://github.com/CGNS/CGNS/archive/v3.3.0.tar.gz > tar xf v3.3.0.tar.gz > cd CGNS-3.3.0/src > export FC=gfortran > export FCFLAGS=-fPIC > #"--with-hdf5=/usr/local" in order to avoid "-I" flag. > ./configure --prefix=/usr/local --with-mpi --with-szip --with-hdf5=/usr/ > local --enable-64bit --enable-shared=all --enable-parallel > make > make install > cd > > I am using GCC 4.9.2 and CentOS 6 with OpenMPI > [root@localhost cgns_file]# mpicc --version > gcc (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6) > Copyright (C) 2014 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE > . > > > [root@localhost cgns_file]# uname -a > Linux localhost.localdomain 2.6.32-042stab120.11 #1 SMP Wed Nov 16 > 12:05:45 MSK 2016 x86_64 x86_64 x86_64 GNU/Linux > > [root@localhost cgns_file]# mpiexec --version > mpiexec (OpenRTE) 2.0.1 > > Report bugs to http://www.open-mpi.org/community/help/ > > Additionally, I want to know how important the threadsafety is to pyfr > when I need to use OpenMP? I found there is an threadsafety configure > option in HDF5 but I did not select it. > -- You received this message because you are subscribed to the Google Groups "PyFR Mailing List" group. To unsubscribe from this group and stop receiving emails from it, send an email to pyfrmailinglist+unsubscr...@googlegroups.com. To post to this group, send an email to pyfrmailinglist@googlegroups.com. Visit this group at https://groups.google.com/group/pyfrmailinglist. For more options, visit https://groups.google.com/d/optout.
