VASP6.3.2 forrtl: severe (174): SIGSEGV, segmentation fault occurred
Posted: Wed Jan 25, 2023 4:44 pm
I used instructions from here to build VASP https://www.intel.com/content/www/us/en ... ilers.html
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
1 TB of RAM 10 GB of swap 128 cores.
ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4126170
max locked memory (kbytes, -l) 65536
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4126170
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
uname -a
Linux hostname 5.15.0-52-generic #58~20.04.1-Ubuntu SMP Thu Oct 13 13:09:46 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
head /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 25
model : 1
model name : AMD EPYC 7773X 64-Core Processor
stepping : 2
microcode : 0xa001229
cpu MHz : 2195.894
SCRIPT_THAT_STARTS_MPIRUN & VASP6.3.2
#!/bin/bash
cores=126
executable='/var/tmp/intel_vasp_build/vasp.6.3.2/bin/vasp_std'
source /opt/intel/oneapi/setvars.sh
echo "Running VASP with executable at: "$executable
export OMP_NUM_THREADS=1
/usr/local/spack/opt/spack/linux-ubuntu20.04-zen3/aocc-3.2.0/openmpi-4.1.1-y2ogf3bkk3syj5oiz5ep554fs2kuvjsz/bin/mpirun -np $cores $executable 2>&1 | tee vasp_try${1}.out
wait
source /opt/intel/oneapi/setvars.sh
:: initializing oneAPI environment ...
bash: BASH_VERSION = 5.0.17(1)-release
args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: clck -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: inspector -- latest
:: ipp -- latest
:: ippcp -- latest
:: ipp -- latest
:: itac -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vpl -- latest
:: vtune -- latest
:: oneAPI environment initialized ::
makefile.include started off as a copy of makefile.include.linux_intel
Makefile.include
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf
CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)
FC = mpiifort
FCL = mpiifort -mkl=sequential
FREE = -free -names lowercase
FFLAGS = -assume byterecl -w
OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0 -traceback
OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /opt/intel/oneapi/mkl/2023.0.0/interfaces/fftw3xf/libfftw3xf_intel.a
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)
OBJECTS_LIB = linpack_double.o
CXX_PARS = icpc
LLIBS = -lstdc++
VASP_TARGET_CPU ?= -march=core-avx2
FFLAGS += $(VASP_TARGET_CPU) -traceback -debug -g
FCL += -qmkl=sequential
MKLROOT ?= /opt/intel/oneapi/mkl/2023.0.0/lib/intel64
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw
70% of the time MPIRUN & VASP crash with this error
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libpthread-2.31.s 00007FADD5EA6420 Unknown Unknown Unknown
vasp_std 00000000008BF0D0 hamil_mp_hamiltmu 1626 hamil.F
vasp_std 00000000010BA5A9 david_mp_eddav_ 505 davidson.F
vasp_std 000000000115D063 elmin_ 499 electron.F
vasp_std 0000000001CB3E5F vamp_IP_electroni 5384 main.F
vasp_std 0000000001C8C1CD MAIN__ 3142 main.F
vasp_std 000000000040959D Unknown Unknown Unknown
libc-2.31.so 00007FADD5B75083 __libc_start_main Unknown Unknown
vasp_std 00000000004094BE Unknown Unknown Unknown
--------------------------------------------------------------------------
any help would be appreciated.
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
1 TB of RAM 10 GB of swap 128 cores.
ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4126170
max locked memory (kbytes, -l) 65536
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4126170
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
uname -a
Linux hostname 5.15.0-52-generic #58~20.04.1-Ubuntu SMP Thu Oct 13 13:09:46 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
head /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 25
model : 1
model name : AMD EPYC 7773X 64-Core Processor
stepping : 2
microcode : 0xa001229
cpu MHz : 2195.894
SCRIPT_THAT_STARTS_MPIRUN & VASP6.3.2
#!/bin/bash
cores=126
executable='/var/tmp/intel_vasp_build/vasp.6.3.2/bin/vasp_std'
source /opt/intel/oneapi/setvars.sh
echo "Running VASP with executable at: "$executable
export OMP_NUM_THREADS=1
/usr/local/spack/opt/spack/linux-ubuntu20.04-zen3/aocc-3.2.0/openmpi-4.1.1-y2ogf3bkk3syj5oiz5ep554fs2kuvjsz/bin/mpirun -np $cores $executable 2>&1 | tee vasp_try${1}.out
wait
source /opt/intel/oneapi/setvars.sh
:: initializing oneAPI environment ...
bash: BASH_VERSION = 5.0.17(1)-release
args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: clck -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: inspector -- latest
:: ipp -- latest
:: ippcp -- latest
:: ipp -- latest
:: itac -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vpl -- latest
:: vtune -- latest
:: oneAPI environment initialized ::
makefile.include started off as a copy of makefile.include.linux_intel
Makefile.include
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf
CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)
FC = mpiifort
FCL = mpiifort -mkl=sequential
FREE = -free -names lowercase
FFLAGS = -assume byterecl -w
OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0 -traceback
OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /opt/intel/oneapi/mkl/2023.0.0/interfaces/fftw3xf/libfftw3xf_intel.a
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)
OBJECTS_LIB = linpack_double.o
CXX_PARS = icpc
LLIBS = -lstdc++
VASP_TARGET_CPU ?= -march=core-avx2
FFLAGS += $(VASP_TARGET_CPU) -traceback -debug -g
FCL += -qmkl=sequential
MKLROOT ?= /opt/intel/oneapi/mkl/2023.0.0/lib/intel64
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw
70% of the time MPIRUN & VASP crash with this error
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libpthread-2.31.s 00007FADD5EA6420 Unknown Unknown Unknown
vasp_std 00000000008BF0D0 hamil_mp_hamiltmu 1626 hamil.F
vasp_std 00000000010BA5A9 david_mp_eddav_ 505 davidson.F
vasp_std 000000000115D063 elmin_ 499 electron.F
vasp_std 0000000001CB3E5F vamp_IP_electroni 5384 main.F
vasp_std 0000000001C8C1CD MAIN__ 3142 main.F
vasp_std 000000000040959D Unknown Unknown Unknown
libc-2.31.so 00007FADD5B75083 __libc_start_main Unknown Unknown
vasp_std 00000000004094BE Unknown Unknown Unknown
--------------------------------------------------------------------------
any help would be appreciated.