[Wien] LAPW1 segmentation fault WIEN2k.19.1
Luigi Maduro - TNW
L.A.Maduro at tudelft.nl
Thu Jun 27 14:53:26 CEST 2019
Dear WIEN2k users,
I recently updated from WIEN2k.18.1 to WIEN2k.19.1.
Both versions were compiled with the same intel compilers, intel_xe_2016.
The FFTW3 (fftw-3.3.4) and LIBXC(libxc-4.3.4) packages were also compiled with the same intel compilers as the WIEN2k versions and
WIEN2k.19.1 compiles without any error. Each individual node is a shared memory machine, and runs CentOS 7<http://www.centos.org/>, where PBS/torque is used to schedule jobs. I have the following compiler options for WIEN2k.19.1
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M OpenMP switch: -qopenmp
O Compiler options: -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include
L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -lpthread -lm -ldl -liomp5
P Preprocessor flags '-DParallel'
R R_LIBS (LAPACK+BLAS): -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
F FFTW options: -DFFTW3 -DFFTW_OMP -I/home/lamaduro/2FFTW3/FFTW/include
FFTW-LIBS: -L/home/lamaduro/2FFTW3/FFTW/lib -lfftw3 -lfftw3_omp
FFTW-PLIBS: -lfftw3_mpi
X LIBX options: -DLIBXC -I/home/lamaduro/LIBXC_4_3_4/LIBXC/LIBXC/include
LIBXC-LIBS: -L/home/lamaduro/LIBXC_4_3_4/LIBXC/LIBXC/lib/ -lxcf03 -lxc
C Parallel Compiler: mpiifort
FP Parallel Compiler Options: -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include
MP MPIRUN command: /opt/ud/openmpi-1.8.8/bin/mpirun
Sp SCALAPACK: -L$(MKLROOT)/lib/intel64
-lmkl_scalapack_lp64
-L$(MKLROOT)/lib/intel64 -lmkl_blacs_intelmpi_lp64
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When running the code in serial mode on a unit cell of MoS2 everything runs fine on one node and one cpu. However, when I use more than one cpu then lapw1 gives the following error(in the case below 1 node and 2 cpus were used as a test)
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NLVDW END
[1] Done mpirun -np 2 -machinefile .machinenlvdw /home/lamaduro/WIEN2k_19_2/nlvdw_mpi nlvdw.def >> .time00
LAPW0 END
[1] Done mpirun -np 2 -machinefile .machine0 /home/lamaduro/WIEN2k_19_2/lapw0_mpi lapw0.def >> .time00
w2k_dispatch_signal(): received: Segmentation fault
w2k_dispatch_signal(): received: Segmentation fault
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1
[1] + Done ( cd $PWD; $t $ttt; rm -f .lock_$lockfile[$p] ) >> .time1_$loop
grep: lapw2*.error: No such file or directory
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When I change to the WIEN2k.18.1 version lapw1 runs fine.
Following the advice giving in this link http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017209.html
I changed the blacs library to mkl_blacs_openmpi_lp64 and got the following errors when recompiling lapw1
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/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_null'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_f2c'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblcplex'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_packed'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_max'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_maxloc'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_min'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_byte'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_world'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_float'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_request_null'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_cplex'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_unsigned_short'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_c2f'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double_int'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_int'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_long_long_int'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_integer'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblprec'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_f2c'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_f2c'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_sum'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_c2f'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_real'
/opt/ud/intel_xe_2016/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_c2f'
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I'm not sure how to proceed. Any help would be appreciated.
Kind regards,
Luigi Maduro
PhD candidate
Kavli Institute of Nanoscience
Department of Quantum Nanoscience
Faculty of Applied Sciences
Delft University of Technology
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