Segment fault when getting element property with MKL built Julia
Forgive me if this is a kind of problem among multiple sources but I would post here first.
I would like to get the element property as below in Julia 1.1.1 with Gmsh SDK v4.4:
include("/home/pshi/codes/GmshTools.jl/deps/usr/lib/gmsh.jl") # where I download the SDK gmsh.initialize() gmsh.model.mesh.getElementProperties(5) # this line crash gmsh.finalize()
Excuting it will show segment fault. Then I use Julia-debug which shows:
(gdb) r Starting program: /home/pshi/bin/julia ./mytest.jl [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". warning: File "/opt/gcc8/lib64/libstdc++.so.6.0.25-gdb.py" auto-loading has been declined by your `auto-load safe-path' set to "$debugdir:$datadir/auto-load:/usr/bin/mono-gdb.py". To enable execution of this file add add-auto-load-safe-path /opt/gcc8/lib64/libstdc++.so.6.0.25-gdb.py line to your configuration file "/home/pshi/.gdbinit". To completely disable this security protection add set auto-load safe-path / line to your configuration file "/home/pshi/.gdbinit". For more information about this security protection see the "Auto-loading safe path" section in the GDB manual. E.g., run from the shell: info "(gdb)Auto-loading safe path" [New Thread 0x7fffed026700 (LWP 201337)] [New Thread 0x7fffdf677700 (LWP 201340)] [New Thread 0x7fffdee76700 (LWP 201341)] [New Thread 0x7fffde675700 (LWP 201342)] [New Thread 0x7fffdde74700 (LWP 201343)] [New Thread 0x7fffcfbff700 (LWP 201344)] [New Thread 0x7fffce7fd700 (LWP 201345)] [New Thread 0x7fffcd3fb700 (LWP 201346)] [New Thread 0x7fffa3620700 (LWP 201477)] [New Thread 0x7fffa2e1f700 (LWP 201478)] [New Thread 0x7fffa061e700 (LWP 201479)] [New Thread 0x7fff9de1d700 (LWP 201480)] [New Thread 0x7fff9b61c700 (LWP 201483)] [New Thread 0x7fff98e1b700 (LWP 201484)] [New Thread 0x7fff9661a700 (LWP 201485)] [New Thread 0x7fff91c18780 (LWP 201583)] [New Thread 0x7fff91816800 (LWP 201585)] [New Thread 0x7fff91414880 (LWP 201586)] [New Thread 0x7fff91012900 (LWP 201588)] [New Thread 0x7fff90c10980 (LWP 201589)] [New Thread 0x7fff9080ea00 (LWP 201590)] [New Thread 0x7fff9040ca80 (LWP 201591)] [New Thread 0x7fff73ffeb00 (LWP 201592)] [New Thread 0x7fff73bfcb80 (LWP 201593)] [New Thread 0x7fff737fac00 (LWP 201594)] [New Thread 0x7fff733f8c80 (LWP 201595)] [New Thread 0x7fff72ff6d00 (LWP 201596)] [New Thread 0x7fff72bf4d80 (LWP 201597)] [New Thread 0x7fff727f2e00 (LWP 201598)] [New Thread 0x7fff723f0e80 (LWP 201599)] [New Thread 0x7fff71feef00 (LWP 201600)] [New Thread 0x7fff717ecf80 (LWP 201602)] [New Thread 0x7fff713eb000 (LWP 201603)] [New Thread 0x7fff70fe9080 (LWP 201605)] [New Thread 0x7fff70be7100 (LWP 201606)] [New Thread 0x7fff707e5180 (LWP 201608)] [New Thread 0x7fff3bfff200 (LWP 201610)] [New Thread 0x7fff3bbfd280 (LWP 201611)] Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fff3bbfd280 (LWP 201611)] 0x00007fffacf632f3 in mkl_blas_avx512_xdscal () from /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_avx512.so Missing separate debuginfos, use: debuginfo-install bzip2-libs-1.0.6-13.el7.x86_64 expat-2.1.0-10.el7_3.x86_64 fontconfig-2.13.0-4.3.el7.x86_64 freetype-2.8-12.el7_6.1.x86_64 glibc-2.17-260.el7_6.6.x86_64 libX11-1.6.5-2.el7.x86_64 libXau-1.0.8-2.1.el7.x86_64 libXcursor-1.1.15-1.el7.x86_64 libXext-1.3.3-3.el7.x86_64 libXfixes-5.0.3-1.el7.x86_64 libXft-2.3.2-2.el7.x86_64 libXinerama-1.1.3-2.1.el7.x86_64 libXrender-0.9.10-1.el7.x86_64 libpng-1.5.13-7.el7_2.x86_64 libuuid-2.23.2-59.el7_6.1.x86_64 libxcb-1.13-1.el7.x86_64 mesa-libGLU-9.0.0-4.el7.x86_64 zlib-1.2.7-18.el7.x86_64 (gdb) backtrace full #0 0x00007fffacf632f3 in mkl_blas_avx512_xdscal () from /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_avx512.so No symbol table info available. #1 0x00007fffb3f52609 in mkl_blas_xdscal () from /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_core.so No symbol table info available. #2 0x00007fffb1a8b5b2 in mkl_blas_dscal () from /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64/libmkl_intel_thread.so No symbol table info available. #3 0x00007fffbcb80ed3 in __kmp_invoke_microtask () from /opt/intel/compilers_and_libraries/linux/lib/intel64/libiomp5.so No symbol table info available. #4 0x00007fffbcb43726 in __kmp_invoke_task_func (gtid=1002390336) at ../../src/kmp_runtime.cpp:7421 this_thr = 0x7fff71bb4f00 team = 0x7fff91df2b00 dummy = 0x7fff3bbf4790 exit_runtime_p = 0x7fff3bbf3ed0 #5 0x00007fffbcb4271c in __kmp_launch_thread (this_thr=0x7fff3bbf4340) at ../../src/kmp_runtime.cpp:6008 gtid = 1908100928 pteam = 0x7fff71bb4f40 thread_data = 0x17 #6 0x00007fffbcb8130b in _INTERNAL_26_______src_z_Linux_util_cpp_20354e55::__kmp_launch_worker ( thr=0x7fff3bbf4340) at ../../src/z_Linux_util.cpp:585 status = 0 old_type = 0 old_state = 0 padding = 0x7fff3bbf4850 gtid = 23 #7 0x00007ffff6e6fdd5 in start_thread () from /lib64/libpthread.so.0 No symbol table info available. #8 0x00007ffff6b9902d in clone () from /lib64/libc.so.6 No symbol table info available.
I am not knowledgeable about these but I got no such issue with OpenBLAS built Julia. So I sense it's related to some incompatibility with MKL, especially the AVX512, based on the debugging information.
So far I only find
getElementProperties would crash, others like
getEntitiesForPhysicalGroup all work perfectly. Again sorry for this mess. I would be appreciated for any insight to help me deal with it.
I also notice generate 3D mesh (using demo
t3.jl) would cause `Intel MKL ERROR: Parameter 11 was incorrect on entry to DGESVD.