Segmentation Error

2 posts / 0 new
Last post
sairamadugu
Segmentation Error

Hello All,

I have compiled chem shell successfully (at least no compilation issues so far). I have used the Intel-OneAPI compilers, MPI and MKL. When I try to run the tests from the tests folder and used as suggested by You in a different thread.

./run_validation.tcsh chemsh fragment

From the above command all the 12 tests fail. The .err file has the following issue.

chemsh.x:18204 terminated with signal 11 at PC=0 SP=7ffd66e99b78. Backtrace:
/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/psm-3.3-7an3buy/lib64/libinfinipath.so.4(+0x3f9c)[0x2b9174282f9c]
/lib64/libpthread.so.0(+0xf630)[0x2b915809f630]
0.147u 0.067s 0:00.99 20.2% 0+0k 0+48io 0pf+0w

-----

My compilation command: (I am not the system administrator of this machine). It is a cluster. Even the --mpi didnt do anything to resolve the issue.

./setup --fc ifort --cc icc --ld_path /opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/lib:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/lib/x64:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/lib/emu:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/lib/oclfpga/host/linux64/lib:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/lib/oclfpga/linux64/lib:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/compiler/lib/intel64_lin:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-compilers-2021.2.0-sapdob5/compiler/2021.2.0/linux/compiler/lib:/opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-mkl-2021.2.0-5koqho4/mkl/2021.2.0/lib/intel64 --mkl /opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-mkl-2021.2.0-5koqho4/mkl/2021.2.0/lib/intel64 --mkl_flags "-lmkl_sequential -lmkl_core -lmkl_intel_lp64" --scalapack /opt/ssoft/apps/2021.1/linux-centos7-x86_64/gcc-4.8.5/intel-oneapi-mkl-2021.2.0-5koqho4/mkl/2021.2.0/lib/intel64 --fftw /usr/share/apps/2021.1/arch/intel-2021.2.0/hdf5-1.10.7-mpi --pythonlib /usr/share/apps/2021.1/arch/intel-2021.2.0/python-3.8.8/lib --fhiaims /Users/sramadug/fhi-aims.210716_1/build/libaims.210716_1.meta.scalapack.mpi.so

sairamadugu
I have resolved this issue.

I have resolved this issue. The main problem was using the --pythonlib and linking the path of system level python library folder. I have still issue using

chemsh -np 2 example.py

but running

mpirun -np 2 chemsh.x example.py succeeds.

Log in or register to post comments