Hi Junting, Hmm, it is weird. Could you check if the libcgns.so is correctly linked to other libraries? Mine is $ ldd ~/local/CGNS/build/lib/libcgns.so linux-vdso.so.1 => (0x00007ffe9c15d000) /opt/intel/mkl/lib/intel64/libmkl_core.so (0x00002b6f40c38000) /opt/intel/mkl/lib/intel64/libmkl_sequential.so (0x00002b6f44dc4000) libhdf5.so.8 => /usr/lib64/libhdf5.so.8 (0x00002b6f46370000) libsz.so.2 => /usr/lib64/libsz.so.2 (0x00002b6f46967000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002b6f46b6a000) libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002b6f46d80000) libm.so.6 => /usr/lib64/libm.so.6 (0x00002b6f46f85000) libc.so.6 => /usr/lib64/libc.so.6 (0x00002b6f47287000) libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002b6f47654000) libaec.so.0 => /usr/lib64/libaec.so.0 (0x00002b6f47871000) /lib64/ld-linux-x86-64.so.2 (0x000055d3ad492000)
Besides, could you just try $ export LD_LIBRARY_PATH=/data/sofrware/mesher/CGNS/build/src/:$LD_LIBRARY_PATH before reinstalling, executing etc? I would suspect that the libcgns.so is not correctly referred. Regards, Yoshiaki 2020年2月7日金曜日 7時05分50秒 UTC+9 Junting Chen: > > Thanks a lot, Yoshiaki. With your help I have successfully (no error > message) installed CGNS and linked it to HDF5, also reinstalled pyfr and > linked libcgns.so. I did exactly what you showed me. I have also read the > thread you provided. > > But still, when when i call "pyfr import yf17_hdf5.cgns aaa.pyfrm", there > is no output file with pyfrm extension generated, also no warning or error > reported. Can you tell me what went wrong? Thanks! > > jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ echo $LD_LIBRARY_PATH > /data/sofrware/mesher/CGNS/build/src/libcgns.so > jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ echo $PYFR_LIBRARY_PATH > /data/sofrware/mesher/CGNS/build/src/libcgns.so > jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ ls > yf17.cgns yf17_hdf5.cgns > jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ pyfr import -t cgns > yf17_hdf5.cgns aaa.pyfrm > jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ ls > yf17.cgns yf17_hdf5.cgns > > > Junting Chen > > On Tuesday, February 4, 2020 at 10:15:56 PM UTC-5, Yoshiaki Abe wrote: >> >> Hi Junting, >> >> I have succeeded to use the latest pyfr and CGNS3.4.0 to import both >> yf17.cgns.gz <http://cgns.github.io/CGNSFiles/Bruce/yf17_hdf5.cgns.gz> >> and yf17_hdf5.cgns.gz >> <http://cgns.github.io/CGNSFiles/Bruce/yf17_hdf5.cgns.gz>. >> So, I would recommend to build and install from the source using cmake: >> $ git clone https://github.com/CGNS/CGNS.git >> $ cd CGNS >> $ mkdir build >> $ cd build >> $ cmake .. >> $ ccmake . >> Then, followings are what I set. I have once experienced enabling 64bit >> caused error in CGNS3.3.0, so I have turned it off (but not sure if it's ok >> now). >> CGNS_BUILD_CGNSTOOLS ON >> >> CGNS_BUILD_SHARED ON >> >> CGNS_BUILD_TESTING OFF >> >> CGNS_ENABLE_64BIT OFF >> >> CGNS_ENABLE_BASE_SCOPE OFF >> >> CGNS_ENABLE_FORTRAN OFF >> >> CGNS_ENABLE_HDF5 ON >> >> CGNS_ENABLE_LEGACY OFF >> >> CGNS_ENABLE_MEM_DEBUG OFF >> >> CGNS_ENABLE_SCOPING OFF >> >> CGNS_ENABLE_TESTS OFF >> >> CGNS_USE_SHARED ON >> >> CMAKE_BUILD_TYPE Release >> >> CMAKE_INSTALL_PREFIX /data/home/yoshiaki/local/CGNS/build >> >> HDF5_C_LIBRARY_dl /usr/lib64/libdl.so >> >> HDF5_C_LIBRARY_hdf5 /usr/lib64/libhdf5.so >> >> HDF5_C_LIBRARY_m /usr/lib64/libm.so >> >> HDF5_C_LIBRARY_sz /usr/lib64/libsz.so >> >> HDF5_C_LIBRARY_z /usr/lib64/libz.so >> >> HDF5_NEED_MPI OFF >> >> HDF5_NEED_SZIP OFF >> >> HDF5_NEED_ZLIB OFF >> Then, export LD_LIBRARY_PATH=the path to libcgns.so, and install pyfr. >> Note that it is also important to appropriately link HDF5 library in >> libcgns.so, which is discussed in the following thread: >> https://groups.google.com/d/msg/pyfrmailinglist/qp5r3nlsONQ/4YzHuyGwEQAJ >> >> I hope it helps you. >> >> Regards, >> Yoshiaki >> >> >> 2020年1月23日木曜日 6時57分12秒 UTC+9 Junting Chen: >>> >>> hello, when trying to import a CGNS mesh (YF-17 from cgns website), I am >>> getting: >>> >>> jrcc@bilbo:/data/projects/JrcC/pyfr/cgns_test$ pyfr import yf17.cgns >>> qqq.pyfrm >>> Traceback (most recent call last): >>> File >>> "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/readers/cgns.py", line >>> 114, in _errcheck >>> raise self._statuses[status] >>> KeyError: 1 >>> >>> During handling of the above exception, another exception occurred: >>> >>> Traceback (most recent call last): >>> File "/usr/local/bin/pyfr", line 11, in <module> >>> load_entry_point('pyfr==1.9.0', 'console_scripts', 'pyfr')() >>> File "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/__main__.py", >>> line 110, in main >>> args.process(args) >>> File "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/__main__.py", >>> line 121, in process_import >>> reader = get_reader_by_extn(extn, args.inmesh) >>> File >>> "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/readers/__init__.py", >>> line 19, in get_reader_by_extn >>> return reader_map[extn](*args, **kwargs) >>> File >>> "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/readers/cgns.py", line >>> 375, in __init__ >>> self._file = file = cgns.open(msh.name) >>> File >>> "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/readers/cgns.py", line >>> 120, in open >>> self.lib.cg_open(bytes(name, 'utf-8'), self.CG_MODE_READ, file) >>> File >>> "/home/jrcc/.local/lib/python3.6/site-packages/pyfr/readers/cgns.py", line >>> 116, in _errcheck >>> raise CGNSError >>> pyfr.readers.cgns.CGNSError >>> >>> >>> I have CGNS 3.4 installed, also created a path variable >>> PYFR_LIBRARY_PATH and link to libcgns.so. Previously, it was complaining >>> libcgns.so not found. >>> >>> Thanks in advance! >>> >>> Junting Chen >>> >> -- 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 view this discussion on the web, visit https://groups.google.com/d/msgid/pyfrmailinglist/4b1ea114-b8f0-41be-8ac3-6770fce4abb1%40googlegroups.com.
