error when writing Charge Density

[Dukhyun Choe]

Hello Elk users,

I am new to Elk and currently complining and testing the code.

I successfully compiled the code using mpi settings.

The test calculation was also successfull, but when I try to writh the charge density using the following

tasks
0
1
33

I get the following message.

Can you help me with this?

Thank you very much!

Info(elk): current task : 33
Info(elk): MPI process 1 idle for task 33
Info(elk): MPI process 3 idle for task 33
Info(elk): MPI process 9 idle for task 33
Info(elk): MPI process 11 idle for task 33
Info(elk): MPI process 4 idle for task 33
Info(elk): MPI process 7 idle for task 33
Info(elk): MPI process 8 idle for task 33
Info(elk): MPI process 2 idle for task 33
Info(elk): MPI process 5 idle for task 33
Info(elk): MPI process 6 idle for task 33
Info(elk): MPI process 10 idle for task 33
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
elk 0000000001027A09 Unknown Unknown Unknown
elk 00000000010262DE Unknown Unknown Unknown
elk 0000000000FC9E72 Unknown Unknown Unknown
elk 0000000000F69D88 Unknown Unknown Unknown
elk 0000000000F6E7AB Unknown Unknown Unknown
libpthread.so.0 000000361F60EB10 Unknown Unknown Unknown
elk 00000000005685BD Unknown Unknown Unknown
libiomp5.so 00002AAAAB377233 Unknown Unknown Unknown

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 174
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
salloc: Relinquishing job allocation 104602

[Jinkai Wang]

the same situation occured with elk.5.2.14.
but everything goes well with elk.4.0.15

[mfechner]

could you post your makefile and give more insights in your elk.in ?

[Jinkai Wang]

Hi mfechner,
thanks for the reply. any information is appreciated.

this is the make.inc, which i copy from the example.
I used it to compile elk-4 and elk-5. All the tests are passed in elk-4 while some failed in elk-5.

---

MKLROOT = /data/soft/compiler/intel/v2013/composer_xe_2013_sp1.0.080/mkl/
MAKE = make
F90 = mpif90
F90_OPTS = -O3 -ip -axCORE-AVX2,AVX,SSE4.2 -openmp -I$(MKLROOT)/include
F77 = mpif90
F77_OPTS = -O3 -ip -axCORE-AVX2,AVX,SSE4.2 -openmp
AR = xiar
LIB_SYS =
LIB_LPK = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_i
ntel_thread.a -Wl,--end-group -lpthread -lm -openmp
SRC_MPI =
SRC_libxc = libxcifc_stub.f90
SRC_FFT = zfftifc.f90
LIB_LPK = lapack.a blas.a
LIB_FFT = fftlib.a

---

I test the task 33 in test-001 dirctory. elk-4 goes well while elk-5 throws the error message

---

tasks
0
33

plot3d
0 0 0
1 0 0
0 1 0
0 0 0
10 10 10

mixtype
3

! small cut-off for testing purposes
rgkmax
5.0

gmaxvr
0.0

maxscl
200

avec
7.2246 0.0 0.0
0.0 7.3442 0.0
0.0 0.0 22.0733

[mfechner]

I would suggest first to try a simplified version of the make file. Take out the MKL stuff and
compile with ifort

thus you should go with

MAKE = make
F90 = mpif90
F90_OPTS = -O3 -ip -unroll -no-prec-div -qopenmp
F77 = mpif90
F77_OPTS = -O3 -ip -unroll -no-prec-div -qopenmp -assume protect_parens
AR = ar
LIB_SYS =.
LAPACK and BLAS libraries
LIB_LPK = lapack.a blas.a
LIB_FFT = fftlib.a

SRC_OMP =
SRC_libxc = libxcifc_stub.f90
SRC_FFT = zfftifc.f90

does this run without crashing than ?

best
Michael

[Jinkai Wang]

Hi Michael,

elk-5 compiled without mkl lib still gave the error message within task 53 and 33.

---

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
elk 0000000000DF2DA9 Unknown Unknown Unknown
elk 0000000000DF1720 Unknown Unknown Unknown
elk 0000000000D8ECE2 Unknown Unknown Unknown
elk 0000000000D2EDC8 Unknown Unknown Unknown
elk 0000000000D337FB Unknown Unknown Unknown
libpthread.so.0 000000311CC0F500 Unknown Unknown Unknown

[Anonymous]

Okay,

could you try to go to the serial version and hence replace

mpif90 with ifort
and introduce
SRC_MPI = mpi_stub.f90

than

make clean
and
make

again and check if the linear version at least runs through

best
Michael

[Jinkai Wang]

Hi Michael

I think i know the problem source

Since ifort of version 14 is provided in our platform only, i change the flag qopmp into opmp.(sorry for the wrong information)
it may be the problem source. but i dont have a higher version of ifort to check whether it is.

I use gfortran to compile elk-5. convergence were reahced well and task 33 or 53 finished as expected.
the make.inc are generatd by ./setup with option 2.
( but i remember i have tested the make.inc generated by ./setup with option 1 and 2 very early, )

Anyway, problem solved most. thanks for the answers.

Kai.

Best

From: noreply@sourceforge.net
Date: 2019-05-08 22:18:36
To: "[elk:discussion] " 897820@discussion.elk.p.re.sourceforge.net
Subject: [elk:discussion] error when writing Charge Density
Okay,
could you try to go to the serial version and hence replace
mpif90 with ifort
and introduce
SRC_MPI = mpi_stub.f90
than
make clean
and
make
again and check if the linear version at least runs through
best
Michael
error when writing Charge Density
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