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 [email protected]. To post to this group, send an email to [email protected]. Visit this group at https://groups.google.com/group/pyfrmailinglist. For more options, visit https://groups.google.com/d/optout.
