I just found the following phenomena:
[root@localhost cgns_file]# nm -g /usr/local/lib/libcgns.so nm: /usr/local/lib/libcgns.so: no symbols [root@localhost cgns_file]# nm -gC /usr/local/lib/libcgns.so nm: /usr/local/lib/libcgns.so: no symbols [root@localhost cgns_file]# objdump -T /usr/local/lib/libcgns.so /usr/local/lib/libcgns.so: file format elf64-x86-64 DYNAMIC SYMBOL TABLE: 0000000000017848 l d .init 0000000000000000 .init 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.3 __ctype_toupper_loc 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 getenv 0000000000000000 D *UND* 0000000000000000 *H5T_NATIVE_SCHAR_g* 0000000000000000 D *UND* 0000000000000000 H5Tget_native_type 0000000000000000 D *UND* 0000000000000000 ompi_mpi_comm_world 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 free 0000000000000000 D *UND* 0000000000000000 H5Pset_link_creation_order 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 putchar 0000000000000000 D *UND* 0000000000000000 H5Sget_simple_extent_npoints 0000000000000000 D *UND* 0000000000000000 H5Fget_access_plist 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 __errno_location 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 unlink 0000000000000000 D *UND* 0000000000000000 H5T_IEEE_F64LE_g 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 strncpy 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 strncmp 0000000000000000 w D *UND* 0000000000000000 _ITM_deregisterTMCloneTable 0000000000000000 DO *UND* 0000000000000000 GLIBC_2.2.5 stdout 0000000000000000 D *UND* 0000000000000000 H5Tcopy 0000000000000000 D *UND* 0000000000000000 H5Fopen 0000000000000000 D *UND* 0000000000000000 H5Gunlink 0000000000000000 D *UND* 0000000000000000 H5Awrite 0000000000000000 DF *UND* 0000000000000000 GLIBC_2.2.5 strcpy ... Because there are two errors, I am not sure which one is the essential one, the *OSError: Unable to load cgns* or *OSError: /usr/local/lib/libcgns.so: undefined symbol: H5T_NATIVE_SCHAR_g* ? 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 [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.
