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segfault with libMBD
Posted: Wed Feb 26, 2025 10:34 pm
by asrosen
I have compiled VASP 6.5.0 with libMBD 0.12.8 support using Intel OneAPI 2024.2. I ran a calculation with IVDW = 14 on one system, and everything worked as expected. However, when I try to model a primitive cell of Cu, it seg faults at geometry step 2.
Some things I tried that did not help:
- Switching to the master branch of libMBD
- Using only one core instead of the full node
- Using a full 1 TB of memory on the node
- Using a larger, off-equilibrium structure consisting of 8 Cu atoms (here it seg faulted at the first step)
- Using Ag instead of Cu
I have attached the relevant files. I used PAW_PBE Cu 22Jun2005 for the POTCAR.
Re: segfault with libMBD
Posted: Thu Feb 27, 2025 9:40 am
by ferenc_karsai
Please also post your used makefile.include and complete toolchain.
Re: segfault with libMBD
Posted: Thu Feb 27, 2025 12:48 pm
by asrosen
Of course. My makefile.include is shown below. For the toolchain, it's Intel OneAPI 2024.2 for the compilers, Intel OneAPI MPI 2021.13 for MPI, Intel OneAPI mkl 2024.2 for FFT, BLAS, LAPACK, ScaLAPACK, and hdf5 1.14.4 with Intel OneAPI 2024.2. I also built with DFTD4 3.7.0 support, although removing that does not seem to change anything.
Code: Select all
# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Dtbdyn \
-Dfock_dblbuf \
-D_OPENMP
CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)
FC = mpiifort -fc=ifx -qopenmp
FCL = mpiifort -fc=ifx
FREE = -free -names lowercase
FFLAGS = -assume byterecl -w
OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0
# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icx
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)
OBJECTS_LIB = linpack_double.o
# For the parser library
CXX_PARS = icpx
LLIBS = -lstdc++
##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##
# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -xHOST
FFLAGS += $(VASP_TARGET_CPU)
# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
# (Note: for Intel Parallel Studio's MKL use -mkl instead of -qmkl)
FCL += -qmkl
MKLROOT ?= /opt/intel/oneapi/mkl/2024.2
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw
# HDF5-support (optional but strongly recommended, and mandatory for some features)
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /usr/local/hdf5/oneapi-2024.2/intel-mpi/1.14.4
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS += -I$(HDF5_ROOT)/include
# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier
# For the fftlib library (hardly any benefit in combination with MKL's FFTs)
#FCL = mpiifort fftlib.o -qmkl
#CXX_FFTLIB = icpc -qopenmp -std=c++11 -DFFTLIB_USE_MKL -DFFTLIB_THREADSAFE
#INCS_FFTLIB = -I./include -I$(MKLROOT)/include/fftw
#LIBS += fftlib
# For machine learning library vaspml (experimental)
#CPP_OPTIONS += -Dlibvaspml
#CPP_OPTIONS += -DVASPML_USE_CBLAS
#CPP_OPTIONS += -DVASPML_USE_MKL
#CPP_OPTIONS += -DVASPML_DEBUG_LEVEL=3
#CXX_ML = mpiicpc -cxx=icpx -qopenmp
#CXXFLAGS_ML = -O3 -std=c++17 -Wall
#INCLUDE_ML =
# DFTD4
CPP_OPTIONS += -DDFTD4
LLIBS += $(shell pkg-config --libs dftd4) -lmulticharge -lmctc-lib -lmstore
INCS += $(shell pkg-config --cflags dftd4)
# LibMBD
CPP_OPTIONS += -DLIBMBD
LIBMBD_ROOT ?= /home/ROSENGROUP/software/libmbd/0.12.8
LLIBS += -L$(LIBMBD_ROOT)/lib64 -lmbd
INCS += -I$(LIBMBD_ROOT)/include/mbd
Re: segfault with libMBD
Posted: Thu Feb 27, 2025 7:55 pm
by asrosen
A note for debugging purposes: If you are using libMBD 0.12.8 with Intel OneAPI, you need to make the change described https://github.com/libmbd/libmbd/issues/65. Alternatively, you can use the master branch if you compile with -DCMAKE_BUILD_TYPE=Release.
In any case, here was how I build libMBD too:
Code: Select all
cmake -B build -DCMAKE_BUILD_TYPE=Release -DCMAKE_Fortran_COMPILER=ifx -DCMAKE_INSTALL_PREFIX=/home/ROSENGROUP/software/libmbd/0.12.8
make -C build install
The same error is obtained even with -DENABLE_SCALAPACK_MPI=ON.
Re: segfault with libMBD
Posted: Fri Feb 28, 2025 9:49 am
by ferenc_karsai
I've handed over this problem to a colleague who wrote the libMBD interface in VASP. He will post suggestions when he knows more.
Re: segfault with libMBD
Posted: Fri Feb 28, 2025 2:30 pm
by fabien_tran1
Hi,
I can reproduce the problem, for which it does not matter which compiler is used. This is probably the same problem that I encountered when I wrote the interface, and I think that the (vague) explanation was that libMBD stops when unphysical values are obtained. A solution would be to use the implementation of MBD@rsSCS in VASP (IVDW=202), which should be slower.
Re: segfault with libMBD
Posted: Fri Feb 28, 2025 2:41 pm
by asrosen
Thanks for confirming it was not a "me" issue!
Unfortunate about the crash. We probably can't afford to use the more expensive built-in approach, so we will have to forego using this method for the time being then.