[Wien] NMR Integration crashes when using nmr_integ:localhost:4 in .machines Link error
Michael Fechtelkord
Michael.Fechtelkord at ruhr-uni-bochum.de
Thu Oct 9 20:13:10 CEST 2025
I think, I fixed the mpi error by using mpich 4.3.2
configuring by
CC=gcc CXX=g++ F77=ifx FC=ifx MPIF77=mpiifx MPIF90=mpiifx MPIFC=mpiifx
MPICC=mpigcc \
../configure --prefix=/usr/local --with-device=ch3 --with-pm=hydra
--enable-shared --enable-fast=all,O3 MPICHLIB_CFLAGS="-O3 -march=native
-mavx2" \
MPICHLIB_FFLAGS="-O3 -xCORE-AVX2 -march=native" MPICHLIB_CXXFLAGS="-O3
-march=native -mavx2" MPICHLIB_FCFLAGS="-O3 -xCORE-AVX2 -march=native" \
CFLAGS="-O3 -march=native -mavx2" FCFLAGS="-O3 -xCORE-AVX2 -march=native"
Am 01.09.2025 um 15:26 schrieb Michael Fechtelkord via Wien:
> Hello Gavin,
>
>
> thanks for your comprehensive report on this issue. I was using Open
> Suse LEAP 15.6 before which uses an older kernel and also older
> libraries. Tumbleweed uses the most recent developments and thus
> things like this can happen. I have good experiences with Tumbleweed,
> cause it supports the newest hardware. I am still using the latest
> ifort version because it produces nearly no SIGSEV errors with WIEN2k
> compared to the newest ifx version.
>
> I think maybe the easiest is to switch mpi to mpiich (which updated
> quite often) for WIEN2k and ELPA or use the workaround, I described.
>
>
> Anyway, thanks for your advise again!
>
>
> Best regards,
>
> Michael
>
>
> Am 01.09.2025 um 13:23 schrieb Gavin Abo:
>> At [1], the current latest version of oneAPI is 2025.2. There it has
>> under supported Linux distributions "SuSE LINUX Enterprise Server* 15
>> SP4, SP5, SP6". Those look like they might be more aligned with the
>> openSUSE Leap 15.x versions seen in the list at [2]. The openSUSE
>> Tumbleweed looks like it's a rolling release that might always be
>> ahead of what Intel is developing the oneAPI with. If that is the
>> case, incompatibility risks are probably going to be higher using
>> Tumbleweed than one of the distributions in Intel's oneAPI supported
>> list.
>>
>> The error message has:
>>
>> `/lib64/libm.so.6' for IFUNC symbol `modff'
>>
>> The modff is a function in the libm library [3] that looks to be a
>> part of the identified GLIBC. I see that you mentioned downgrading
>> the GLIBC (which could need using an older OpenSUSE Leap version) is
>> not a solution for you.
>>
>> A few other ideas below that you may or may not want to consider.
>>
>> Intel has a libimf Compiler Math Library [4] that seems to contain a
>> modff function [5]. So, static linking to the libimf.a might be a
>> possibility. There is a post about a RELINK error that might be of
>> interest at [6].
>>
>> IFUNC in the above message is likely a GNU indirect function that
>> resolves a function implementation picked by a resolver at runtime
>> where glibc uses this to provide multiple implementations optimized
>> for different architecture levels [7]. I don't recall what
>> architecture was targeted for your compile, but say it was AVX and
>> the new glibc has an issue with it. Maybe falling back to an
>> architecture (see [8]) were optimization isn't as good if the
>> processor your using also supports it, say SSE3, might be something
>> to try.
>>
>> If the Intel MPI source code for libmpi.so.12 has to be compiled with
>> the GLIBC 2.42 by Intel in a future release to fix the issue, an
>> alternate solution might be to use a different Message Passing
>> Interface (MPI) such as MPICH or OpenMPI [9].
>>
>> [1]
>> https://www.intel.com/content/www/us/en/developer/articles/system-requirements/oneapi-base-toolkit/2025.html
>> [2] https://en.wikipedia.org/wiki/OpenSUSE#Version_history
>> [3] https://sourceware.org/newlib/libm.html#modf
>> [4]
>> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/compiler-math-library.html
>> [5]
>> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/nearest-integer-functions.html
>> [6]
>> https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Trouble-linking-libimf-a-on-Linux/td-p/1342415
>> [7] https://maskray.me/blog/2021-01-18-gnu-indirect-function
>> [8]
>> https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2025-2/arch.html
>> [9] https://en.wikipedia.org/wiki/MPICH#MPICH_derivatives
>>
>> Kind Regards,
>>
>> Gavin
>> WIEN2k user
>>
>> On 9/1/2025 1:30 AM, Michael Fechtelkord via Wien wrote:
>>> 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:
>>>>>>
>>>>>>
>>>>>
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>
--
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/
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