Page 1 of 1

"Segmentation fault" error while running a calculation with vasp.6.4.1 which was compiled with intel OneApi 2022

Posted: Wed May 31, 2023 9:34 am
by amihai_silverman1
Hello,
I get a "Segmentation fault" error when I run a sample calculation interactively on the cluster masternode.
I get the same error:

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 231279 RUNNING AT n023.zeus.technion.ac.il
= EXIT CODE: 11

when I submit this calculation to the cluster with a PBS script.

Below is the output of lspci, and file makefile.include which was used for the compilation.
As was suggested in a previous case, I replaced -xHOST with -march=core-avx2.
Thank you for your help. Amihai

$ lspci
00:00.0 Host bridge: Intel Corporation Sky Lake-E DMI3 Registers (rev 04)
00:04.0 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.1 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.2 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.3 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.4 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.5 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.6 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:04.7 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
00:05.0 System peripheral: Intel Corporation Sky Lake-E MM/Vt-d Configuration Registers (rev 04)
00:05.2 System peripheral: Intel Corporation Sky Lake-E RAS (rev 04)
00:05.4 PIC: Intel Corporation Sky Lake-E IOAPIC (rev 04)
00:08.0 System peripheral: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
00:08.1 Performance counters: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
00:08.2 System peripheral: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
00:11.0 Unassigned class [ff00]: Intel Corporation C620 Series Chipset Family MROM 0 (rev 09)
00:11.1 Unassigned class [ff00]: Intel Corporation C620 Series Chipset Family MROM 1 (rev 09)
00:14.0 USB controller: Intel Corporation C620 Series Chipset Family USB 3.0 xHCI Controller (rev 09)
00:14.2 Signal processing controller: Intel Corporation C620 Series Chipset Family Thermal Subsystem (rev 09)
00:16.0 Communication controller: Intel Corporation C620 Series Chipset Family MEI Controller #1 (rev 09)
00:16.4 Communication controller: Intel Corporation C620 Series Chipset Family MEI Controller #3 (rev 09)
00:1c.0 PCI bridge: Intel Corporation C620 Series Chipset Family PCI Express Root Port #1 (rev f9)
00:1c.4 PCI bridge: Intel Corporation C620 Series Chipset Family PCI Express Root Port #5 (rev f9)
00:1f.0 ISA bridge: Intel Corporation C621 Series Chipset LPC/eSPI Controller (rev 09)
00:1f.2 Memory controller: Intel Corporation C620 Series Chipset Family Power Management Controller (rev 09)
01:00.0 System peripheral: Hewlett-Packard Company Integrated Lights-Out Standard Slave Instrumentation & System Support (rev 07)
01:00.1 VGA compatible controller: Matrox Electronics Systems Ltd. MGA G200eH3 (rev 02)
01:00.2 System peripheral: Hewlett-Packard Company Integrated Lights-Out Standard Management Processor Support and Messaging (rev 07)
01:00.4 USB controller: Hewlett-Packard Company iLO5 Virtual USB Controller
02:00.0 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme BCM5719 Gigabit Ethernet PCIe (rev 01)
02:00.1 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme BCM5719 Gigabit Ethernet PCIe (rev 01)
02:00.2 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme BCM5719 Gigabit Ethernet PCIe (rev 01)
02:00.3 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme BCM5719 Gigabit Ethernet PCIe (rev 01)
11:00.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port A (rev 04)
11:05.0 System peripheral: Intel Corporation Sky Lake-E VT-d (rev 04)
11:05.2 System peripheral: Intel Corporation Sky Lake-E RAS Configuration Registers (rev 04)
11:05.4 PIC: Intel Corporation Sky Lake-E IOxAPIC Configuration Registers (rev 04)
11:08.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:08.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:09.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0a.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0a.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0e.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:0f.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:10.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:10.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:1d.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:1d.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:1d.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:1d.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
11:1e.0 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.1 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.2 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.3 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.4 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.5 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
11:1e.6 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
12:00.0 Infiniband controller: Mellanox Technologies MT27700 Family [ConnectX-4]
36:00.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port A (rev 04)
36:02.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port C (rev 04)
36:05.0 System peripheral: Intel Corporation Sky Lake-E VT-d (rev 04)
36:05.2 System peripheral: Intel Corporation Sky Lake-E RAS Configuration Registers (rev 04)
36:05.4 PIC: Intel Corporation Sky Lake-E IOxAPIC Configuration Registers (rev 04)
36:08.0 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:09.0 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.0 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.1 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.2 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.3 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.4 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0a.5 System peripheral: Intel Corporation Sky Lake-E LM Channel 1 (rev 04)
36:0a.6 System peripheral: Intel Corporation Sky Lake-E LMS Channel 1 (rev 04)
36:0a.7 System peripheral: Intel Corporation Sky Lake-E LMDP Channel 1 (rev 04)
36:0b.0 System peripheral: Intel Corporation Sky Lake-E DECS Channel 2 (rev 04)
36:0b.1 System peripheral: Intel Corporation Sky Lake-E LM Channel 2 (rev 04)
36:0b.2 System peripheral: Intel Corporation Sky Lake-E LMS Channel 2 (rev 04)
36:0b.3 System peripheral: Intel Corporation Sky Lake-E LMDP Channel 2 (rev 04)
36:0c.0 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0c.1 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0c.2 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0c.3 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0c.4 System peripheral: Intel Corporation Sky Lake-E Integrated Memory Controller (rev 04)
36:0c.5 System peripheral: Intel Corporation Sky Lake-E LM Channel 1 (rev 04)
36:0c.6 System peripheral: Intel Corporation Sky Lake-E LMS Channel 1 (rev 04)
36:0c.7 System peripheral: Intel Corporation Sky Lake-E LMDP Channel 1 (rev 04)
36:0d.0 System peripheral: Intel Corporation Sky Lake-E DECS Channel 2 (rev 04)
36:0d.1 System peripheral: Intel Corporation Sky Lake-E LM Channel 2 (rev 04)
36:0d.2 System peripheral: Intel Corporation Sky Lake-E LMS Channel 2 (rev 04)
36:0d.3 System peripheral: Intel Corporation Sky Lake-E LMDP Channel 2 (rev 04)
5b:00.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port A (rev 04)
5b:02.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port C (rev 04)
5b:05.0 System peripheral: Intel Corporation Sky Lake-E VT-d (rev 04)
5b:05.2 System peripheral: Intel Corporation Sky Lake-E RAS Configuration Registers (rev 04)
5b:05.4 PIC: Intel Corporation Sky Lake-E IOxAPIC Configuration Registers (rev 04)
5b:0e.0 Performance counters: Intel Corporation Sky Lake-E KTI 0 (rev 04)
5b:0e.1 System peripheral: Intel Corporation Sky Lake-E UPI Registers (rev 04)
5b:0f.0 Performance counters: Intel Corporation Sky Lake-E KTI 0 (rev 04)
5b:0f.1 System peripheral: Intel Corporation Sky Lake-E UPI Registers (rev 04)
5b:12.0 Performance counters: Intel Corporation Sky Lake-E M3KTI Registers (rev 04)
5b:12.1 Performance counters: Intel Corporation Sky Lake-E M3KTI Registers (rev 04)
5b:12.2 System peripheral: Intel Corporation Sky Lake-E M3KTI Registers (rev 04)
5b:15.0 System peripheral: Intel Corporation Sky Lake-E M2PCI Registers (rev 04)
5b:16.0 System peripheral: Intel Corporation Sky Lake-E M2PCI Registers (rev 04)
5b:16.4 System peripheral: Intel Corporation Sky Lake-E M2PCI Registers (rev 04)
5c:00.0 Serial Attached SCSI controller: Adaptec Smart Storage PQI 12G SAS/PCIe 3 (rev 01)
5d:00.0 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme II BCM57810 10 Gigabit Ethernet (rev 10)
5d:00.1 Ethernet controller: Broadcom Inc. and subsidiaries NetXtreme II BCM57810 10 Gigabit Ethernet (rev 10)
80:04.0 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.1 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.2 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.3 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.4 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.5 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.6 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:04.7 System peripheral: Intel Corporation Sky Lake-E CBDMA Registers (rev 04)
80:05.0 System peripheral: Intel Corporation Sky Lake-E MM/Vt-d Configuration Registers (rev 04)
80:05.2 System peripheral: Intel Corporation Sky Lake-E RAS (rev 04)
80:05.4 PIC: Intel Corporation Sky Lake-E IOAPIC (rev 04)
80:08.0 System peripheral: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
80:08.1 Performance counters: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
80:08.2 System peripheral: Intel Corporation Sky Lake-E Ubox Registers (rev 04)
85:00.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port A (rev 04)
85:05.0 System peripheral: Intel Corporation Sky Lake-E VT-d (rev 04)
85:05.2 System peripheral: Intel Corporation Sky Lake-E RAS Configuration Registers (rev 04)
85:05.4 PIC: Intel Corporation Sky Lake-E IOxAPIC Configuration Registers (rev 04)
85:08.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:08.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:09.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0a.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0a.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0e.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.4 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.5 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.6 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:0f.7 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:10.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:10.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:1d.0 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:1d.1 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:1d.2 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:1d.3 System peripheral: Intel Corporation Sky Lake-E CHA Registers (rev 04)
85:1e.0 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.1 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.2 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.3 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.4 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.5 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
85:1e.6 System peripheral: Intel Corporation Sky Lake-E PCU Registers (rev 04)
ae:00.0 PCI bridge: Intel Corporation Sky Lake-E PCI Express Root Port A (rev 04)


# cat makefile.include
# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf \
-D_OPENMP

CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC = mpiifort -qopenmp
FCL = mpiifort

FREE = -free -names lowercase

FFLAGS = -assume byterecl -w

OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0

OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS = icpc
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
VASP_TARGET_CPU ?= -march=core-avx2
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 = /usr/local/intel_oneapi2022/mkl/2022.0.2
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw

# HDF5-support (optional but strongly recommended)
#CPP_OPTIONS+= -DVASP_HDF5
#HDF5_ROOT ?= /path/to/your/hdf5/installation
#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

Re: "Segmentation fault" error while running a calculation with vasp.6.4.1 which was compiled with intel OneApi 2022

Posted: Wed May 31, 2023 3:29 pm
by martin.schlipf
Can you tell me which exact version of OneAPI you are using? Also, does this segmentation fault happen with any VASP calculation of do you need a specific setup to reproduce it? If the setup is important, please share the required input files, so that I can reproduce it.

Re: "Segmentation fault" error while running a calculation with vasp.6.4.1 which was compiled with intel OneApi 2022

Posted: Thu Jun 01, 2023 6:59 am
by amihai_silverman1
Hi,
The OneAPI version is 2021.5.0 20211109
Below is the INCAR file.
I may pack and send you all the input files, if you give me a link to a location to upload it.
Here is the full error message of this run :

]$ cat Pd.e465875
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
vasp_std 0000000001EE175A Unknown Unknown Unknown
libpthread-2.17.s 00002B9E468CF5F0 Unknown Unknown Unknown
vasp_std 0000000000E04B58 Unknown Unknown Unknown
vasp_std 0000000000DFE337 Unknown Unknown Unknown
libiomp5.so 00002B9E446BFC53 __kmp_invoke_micr Unknown Unknown
libiomp5.so 00002B9E4468F357 Unknown Unknown Unknown
libiomp5.so 00002B9E4468E9D5 Unknown Unknown Unknown
libiomp5.so 00002B9E446C0133 Unknown Unknown Unknown
libpthread-2.17.s 00002B9E468C7E65 Unknown Unknown Unknown
libc-2.17.so 00002B9E46EDC88D clone Unknown Unknown

]$ find /usr/local/intel_oneapi2022/ -name libiomp5.so
/usr/local/intel_oneapi2022/compiler/2022.0.2/linux/compiler/lib/ia32_lin/libiomp5.so
/usr/local/intel_oneapi2022/compiler/2022.0.2/linux/compiler/lib/intel64_lin/libiomp5.so
/usr/local/intel_oneapi2022/inspector/2022.0.0/lib32/libiomp5.so
/usr/local/intel_oneapi2022/inspector/2022.0.0/lib64/libiomp5.so
/usr/local/intel_oneapi2022/clck/2021.5.0/provider/share/common/lib/intel64/libiomp5.so

]$ cat INCAR
SYSTEM = Li2O2 GAS PHASE MOLECULE

Electronic relaxation:
ENCUT = 500.0 ! Cutoff energy for plane waves basis set in eV (determines NGX,Y,Z).
ALGO = Normal !
NELMIN = 6 ! Minimum number of eletronic selfconsistency (SC) steps
NELM = 60 ! Maximum number of electronic SC steps
NELMDL = -12 ! Number of NON-selfconsistency steps
EDIFF = 1.0E-6 ! Global-break condition for the electronic SC-loop (ELM)
AMIX = 0.01000
BMIX = 0.000100

Calculation mode:
PREC = Normal ! Calcululation level (Changes FFT-grids)
ISPIN = 2 ! non-spin-polarized calculations
ADDGRID = .TRUE. ! PAW flag
LASPH = .TRUE. ! non-spherical elements in the PAW method
LREAL = AUTO

IDIPOL = 3

Ionic relaxation:
NSW = 500 ! Number of ionic steps
EDIFFG = -0.0200 ! stop if all forces are smaller than |EDIFFG|
IBRION = 2 !
ISIF = 0 ! Calculate FORCE and Relaxa Ions
POTIM = 0.50

ISTART = 0
ICHARG = 2

Integration over the Brillouin zone (BZ):
ISMEAR = 2 ! Fermi smearing
SIGMA = 0.2

OUTCAR size:
NWRITE = 1 ! Determines how much information will be written in OUTCAR
LWAVE = .FALSE.
LCHARG = .FALSE.

Key for parallel mode calculation:
NPAR = 1
LPLANE = .TRUE.

Re: "Segmentation fault" error while running a calculation with vasp.6.4.1 which was compiled with intel OneApi 2022

Posted: Thu Jun 01, 2023 8:29 am
by martin.schlipf
I need all the input files, please. You can upload them to this forum if you zip all of them.

Did you try to run a different example as well, perhaps from the testsuite or one of the tutorials? This is an important information for me, because it determines whether I need to look for a potential bug in the code or a potential incompatibility with a certain compiler.