 Re: Cannot finish the NEGF testrun ( No.1 ) |
- Date: 2020/01/07 21:46
- Name: T. Ozaki
- Hi,
Could you copy work/negf_example/Lead-L-8ZGNR-NC.dat to your work directory, and
perform openmx with the input file directly without the runtestNEGF command?
Since we do not have an account on the machine installed at Kyoto Univ., unfortunately,
it might be difficult to fix the problem.
Regards,
TO
|
| Re: Cannot finish the NEGF testrun ( No.2 ) |
- Date: 2020/01/08 23:30
- Name: K. Yamaguchi
- Dear Ozaki-sensei,
Thank you very much for your advises.
I've solved this MPI error.
I changed Intel Compiler(19.0.5) and Intel MPI Library(2019.5)
from Intel Compiler(18.0.5) and Intel MPI Library(2018.4).
Then I complied the whole software again.
Finally, I was able to finish NEGFruntest normally.
The MPI error seems to be caused by Intel MPI Library,
however, it's not sure what the problem is.
Best regards,
K. Yamaguchi
|
| Re: Cannot finish the NEGF testrun ( No.3 ) |
- Date: 2020/01/16 20:01
- Name: K. Yamaguchi
- Dear Ozaki-sensei,
The DFT calculation for NC systems is unstable on my simulation environment.
****Makefile****
FFTW = /opt/app/fftw/3.3.5/intel-17.0-impi-2017.1
CC = mpiicc -O3 -xHOST -ip -no-prec-div -mcmodel=medium -shared-intel -qopenmp -I${FFTW}/include -fp-model precise -g
FC = mpiifort -O3 -xHOST -ip -no-prec-div -mcmodel=medium -shared-intel -qopenmp -I${FFTW}/include -fp-model precise -g
LIB= -L${FFTW}/lib -lfftw3 -L$(MKLROOT)/lib/intel64 -mkl=parallel -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -lifcore -lmpi -liomp5 -lpthread -lm -ldl
****************
The error occurred again at lead-l-8zgnr-nc.dat or lead-r-8zgnr-nc.dat.
I checked the problem using the debugger software(Arm DDT).
****Error Message****
Process stopped in make_NC_v_eff (Occupation_Number_LDA_U.c:5120) with signal SIGSEGV (Segmentation fault).
Reason/Origin: address not mapped to object (attempt to access invalid address)
5120: time_per_atom[Gc_AN] += Etime_atom - Stime_atom;
Etime_atom: 1578738274.145021
Stime_atom: 4.9406564584124654e-324
openmx:110521 terminated with signal 11 at PC=711388 SP=7fffad93e680. Backtrace:
openmx[0x711388]
openmx[0x6f5b05]
openmx[0x4b8340]
openmx[0x996029]
openmx[0x994291]
openmx[0x405ff2]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b1f232be495]
openmx[0x405379]
**********************
I compiled OpenMX3.8.5 used the same condition(ScaLAPACK).
However, the error never happen.
Do you have any solutions for this problem?
Thank you in advance.
Best regards,
K. Yamaguchi
 |
| Re: Cannot finish the NEGF testrun ( No.4 ) |
- Date: 2020/01/18 12:34
- Name: T. Ozaki
- Hi,
I cannot reproduce your problem on my environment.
So, it might be difficult to fix the problem.
Could you modify the code "Occupation_Number_LDA_U.c" as follows:?
for the line 5120
Present:
time_per_atom[Gc_AN] += Etime_atom - Stime_atom;
Modified:
// time_per_atom[Gc_AN] += Etime_atom - Stime_atom;
for the line 3379
Present:
void make_NC_v_eff(int SCF_iter, int SucceedReadingDMfile, double dUele, double ECE[])
Modified:
#pragma optimization_level 1
void make_NC_v_eff(int SCF_iter, int SucceedReadingDMfile, double dUele, double ECE[])
Please modfify the code as shown above, and recompile the code.
Please let us know what happens after the modification.
Regards,
TO
|
|
This thread is locked.Only browsing is available.
Cannot finish the NEGF testrun