[Wien] NMR Integration crashes when using nmr_integ:localhost:4 in .machines Link error

Mon Sep 1 09:30:12 CEST 2025

Hello all,

thanks again  for all your advise. I now used ifort 2021.1.1 and icc 
2021.4.0 for compilation (with flag -no-gcc) but the SIGSEV is still 
there. As you can see it is a C-Library related communication error

The new GLIBC 2.42 core library does not work together correctly with 
Intels mpi (all versions, see error reports below). It will be difficult 
to solve that problem, a downgrade of a Core library is not 
recommendable, so I use as a work around the sequential integration on 
one core. The integration step does not really take long and the 
parallel calculation of the electron current is still working.

I am sure that problem  will arise soon for most who use mpirun and have 
GLIBC 2.42 in their LINUX operating system.

Best regards,

Michael

------------------------------------

EXECUTING:     mpirun -np 4 -machinefile .machine_nmrinteg 
/usr/local/WIEN2k/nmr_mpi -case MgF2 -mode integ -green

/usr/local/WIEN2k/nmr_mpi: Relink 
`/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with 
`/lib64/libm.so.6' for IFUNC symbol `modff'
/usr/local/WIEN2k/nmr_mpi: Relink 
`/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with 
`/lib64/libm.so.6' for IFUNC symbol `modff'
/usr/local/WIEN2k/nmr_mpi: Relink 
`/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with 
`/lib64/libm.so.6' for IFUNC symbol `modff'
/usr/local/WIEN2k/nmr_mpi: Relink 
`/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with 
`/lib64/libm.so.6' for IFUNC symbol `modff'

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 391888 RUNNING AT localhost
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 1 PID 391889 RUNNING AT localhost
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 2 PID 391890 RUNNING AT localhost
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 3 PID 391891 RUNNING AT localhost
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

stop

/opt/fftw-3.3.10/mpi/.libs/mpi-bench: Relink 
`/opt/intel/oneapi/mpi/2021.1.1//lib/release/libmpi.so.12' with 
`/lib64/libm.so.6' for IFUNC symbol `modff'

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 66889 RUNNING AT Marlowe
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================
FAILED mpirun -np 1 /opt/fftw-3.3.10/mpi/mpi-bench:

Am 30.08.2025 um 10:15 schrieb Michael Fechtelkord via Wien:
> Hello Peter,
>
>
> lapw0 crashes with the same error:
>
> /usr/local/WIEN2k/lapw0_mpi: Relink 
> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with 
> `/lib64/libm.so.6' for IFUNC symbol `modff'
> /usr/local/WIEN2k/lapw0_mpi: Relink 
> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with 
> `/lib64/libm.so.6' for IFUNC symbol `modff'
> /usr/local/WIEN2k/lapw0_mpi: Relink 
> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with 
> `/lib64/libm.so.6' for IFUNC symbol `modff'
> /usr/local/WIEN2k/lapw0_mpi: Relink 
> `/opt/intel/oneapi/mpi/2021.13/lib/libmpi.so.12' with 
> `/lib64/libm.so.6' for IFUNC symbol `modff'
> [1]    Exitcode 255                      mpirun -np 4 -machinefile 
> .machine0 /usr/local/WIEN2k/lapw0_mpi lapw0.def >> .time00
>
> OMP_NUM_THREADS=1 does not change anything.
>
>
> I will try the 2021.1.0 version of oneapi soon and get back with the 
> results soon.
>
>
> Best regards,
>
> Michael
>
>
> Am 29.08.2025 um 16:10 schrieb Peter Blaha:
>> Just for some more info:
>>
>> Does this crash also occur in  an mpirun of lapw0 ?? (would point to 
>> fftw)
>>
>> What is your OMP_NUM_THREADS  variable ? Set it to one (also in 
>> .bashrc).
>>
>>
>>
>> Am 29.08.2025 um 12:54 schrieb Michael Fechtelkord via Wien:
>>> Dear all,
>>>
>>>
>>> I am back now to ifort 2021.13 because it crashes much less as the 
>>> new ifx compiler, also it produces omp errors using fftw3 during 
>>> compilation.
>>>
>>> All worked fine since the last Open Suse Tumbleweed version using 
>>> Kernel 6.16.3-1 (Opensuse Tumbleweed 202250827). Parallel Jobs 
>>> terminate when using "mpirun" with the following error. The same 
>>> error appears when I have compiled fftw 3.10 with gcc 15.1 and run 
>>> "make check" the check routine crashes when using mpirun with the 
>>> same error.
>>>
>>>
>>> Does somebody  know what that relink error means and how to solve 
>>> it? Is it maybe the opensuse libm.so.6 library (glibc version 
>>> 2.42.1) causing the error, because the new version does not contain 
>>> the symbol, libmpi is reqeusting?
>>>
>>>
>>>
>>> Best  regards,
>>>
>>> Michael
>>>
>>> ---------------
>>>
>>>   EXECUTING:     mpirun -np 4 -machinefile .machine_nmrinteg 
>>> /usr/local/ WIEN2k/nmr_mpi -case MgF2 -mode integ -green
>>>
>>> /usr/local/WIEN2k/nmr_mpi: Relink 
>>> `/opt/intel/oneapi/mpi/2021.13/lib/ libmpi.so.12' with 
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/nmr_mpi: Relink 
>>> `/opt/intel/oneapi/mpi/2021.13/lib/ libmpi.so.12' with 
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/nmr_mpi: Relink 
>>> `/opt/intel/oneapi/mpi/2021.13/lib/ libmpi.so.12' with 
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>> /usr/local/WIEN2k/nmr_mpi: Relink 
>>> `/opt/intel/oneapi/mpi/2021.13/lib/ libmpi.so.12' with 
>>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>>
>>> =================================================================================== 
>>>
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   RANK 0 PID 396989 RUNNING AT localhost
>>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>> =================================================================================== 
>>>
>>>
>>> =================================================================================== 
>>>
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   RANK 1 PID 396990 RUNNING AT localhost
>>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>> =================================================================================== 
>>>
>>>
>>> =================================================================================== 
>>>
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   RANK 2 PID 396991 RUNNING AT localhost
>>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>> =================================================================================== 
>>>
>>>
>>> =================================================================================== 
>>>
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   RANK 3 PID 396992 RUNNING AT localhost
>>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>> =================================================================================== 
>>>
>>>
>>> stop
>>>
>>> /opt/fftw-3.3.10/mpi/.libs/mpi-bench: Relink `/opt/intel/oneapi/ 
>>> mpi/2021.13/lib/libmpi.so.12' with `/lib64/libm.so.6' for IFUNC 
>>> symbol `modff'
>>>
>>> =================================================================================== 
>>>
>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>> =   RANK 0 PID 183831 RUNNING AT planck
>>> =   KILLED BY SIGNAL: 11 (Segmentation fault)
>>> =================================================================================== 
>>>
>>> FAILED mpirun -np 1 /opt/fftw-3.3.10/mpi/mpi-bench:
>>>
>>>
>>
-- 
Dr. Michael Fechtelkord

Institut für Geowissenschaften
Ruhr-Universität Bochum
Universitätsstr. 150
D-44780 Bochum

Phone: +49 (234) 32-24380
Fax:  +49 (234) 32-04380
Email:Michael.Fechtelkord at ruhr-uni-bochum.de
Web Page:https://www.ruhr-uni-bochum.de/kristallographie/kc/mitarbeiter/fechtelkord/