[CP2K-user] [CP2K:22410] Re: CP2K 2026.2 on ubuntu 22.04 + oneAPI: The MPI_Comm_c2f() function was called before MPI_INIT was invoked.

[Johann Pototschnig]

The Linker uses environment variables. So you can de-install the other MPI 
or modify the environment variables. 

on is LD_LIBRARY_PATH

best
johann

On Friday, August 21, 2026 at 6:35:50 PM UTC+2 Martin Konôpka wrote:

> Dear Johann,
>
> Thanks for your comment. Yes, it is so. And my yesterday's suspicion  that 
> I omitted to source the
>     /opt/intel/oneapi/2026.1/oneapi-vars.sh
> script was not true; I did source the script. Later I even  repeated the  
> whole toolchain + build procedure and the result was again a binary with 
> links to multiple MPI libraries. And not only MPI. I can see also a 
> non-oneAPI LAPACK and ScaLAPACK there. The mis-linked libraries are at 
> least these:
>
>    libscalapack-openmpi.so.2.1 => 
> /lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.1
>    liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3
>    libmpi.so.40 => /lib/x86_64-linux-gnu/libmpi.so.40
>
> I do now know where is a central config file in which I could disable 
> linking the undesired libraries. It will perhaps be  simpler for me to 
> uninstall the undesired MPI, LAPACK, etc libraries from the system. In the 
> past I needed them because I was using a CP2K version  installed from a 
> standard  ubuntu repository, similarly also a Quantum Espresso version. I 
> will no more need the old versions from the ubuntu repository so that I can 
> unistall them,  also the undesired libraries.
>
> Best,
> Martin.
>
> Dátum: piatok 21. augusta 2026, čas: 16:06:53 UTC+2, odosielateľ: Johann 
> Pototschnig
>
>> The linker links to two mpi libraries, the oneapi one and 
>> libmpi.so.40 => /lib/x86_64-linux-gnu/libmpi.so.40 (0x00007fa2f60c9000)
>>
>> This probably causes the problems. You need to remove the system mpi from 
>> the linker, so it only links the oneapi one. 
>>
>>
>> On Thursday, August 20, 2026 at 6:58:24 PM UTC+2 Martin Konôpka wrote:
>>
>>> Dear Frederick,
>>>
>>> Yes, you are right. Despite trying to be VERY careful, I perhaps (?) 
>>> forgot to run the script
>>>    /opt/intel/oneapi/2026.1/oneapi-vars.sh
>>> in the shell in which I subsequently launched  the toolchain script etc. 
>>> (Possibly I ran the intel script in a different shell mistakenly.) I now 
>>> clearly see the problems when  I look at the output of the
>>>     ldd /dalsie/cp2k-2026.2/install/bin/cp2k.psmp
>>> commands.
>>> I attach two ldd outputs, one with the correct build (Linux Mint Zena) , 
>>> the  other with the incorrect build (Ubuntu 22.04).
>>> I stress that I issued the ldd commands AFTER sourcing the scripts
>>>      /opt/intel/oneapi/2026.1/oneapi-vars.sh
>>>      /dalsie/cp2k-2026.2/install/cp2k_env
>>>
>>> I will rebuild the CP2K on  the ubuntu 22.04 and then I will do the 
>>> regression tests. (I have  not tried them yet.) As for  Spack, I have  not 
>>> used it for the CP2K 2026.2 build process. If possible to use,  I prefer 
>>> the toolchain to Spack.
>>>
>>> Once more thank you very much for helping me.
>>>
>>> Best,
>>> Martin.
>>> Dátum: štvrtok 20. augusta 2026, čas: 17:26:13 UTC+2, odosielateľ: 
>>> Frederick Stein
>>>
>>>> Dear Martin,
>>>> I guess, CP2K picked up the system-provided OpenMPI-implementation in 
>>>> some places (see the end of the cmake.log_Ubuntu_22.04.). Please 
>>>> double-check with your Spack-log files. Have you tried to run the 
>>>> regression tests beforehand? Without any further information it is hard to 
>>>> tell which library picked up the wrong MPI-installation. You can add the 
>>>> TRACE keyword to the &GLOBAL section of your input file and check where 
>>>> CP2K fails. If you are lucky, you may even see where it fails because a 
>>>> routine wasn't left.
>>>> Best,
>>>> Frederick
>>>>
>>>> Martin Konôpka schrieb am Donnerstag, 20. August 2026 um 16:54:24 UTC+2:
>>>>
>>>>> Dear Frederick,
>>>>>
>>>>> Thank you for the response. Yes, at the moment I have at hand all 
>>>>> such  files from my builds on the Linux Mint Zena and  on the Ubuntu 22.04. 
>>>>> I attach them, also the log files from  cmake and the files (or only parts 
>>>>> of them) which I created by copy-pasting my commands and  their standard 
>>>>> outputs printed on the terminal.
>>>>>
>>>>> If needed, I can later send such  files form my build on Ubuntu 26.04 
>>>>> (which is a notebook that I do not have at hand  at the  moment).
>>>>>
>>>>> BTW,  the toolchain script on 22.04 recommended to build the binaries 
>>>>> with the  command
>>>>>    ./build_cp2k.sh -j 18
>>>>> In my actual build I used only 16 (not 18). I hope this is not the 
>>>>> source of the reported problem.
>>>>>
>>>>> Best,
>>>>> Martin.
>>>>> Dátum: štvrtok 20. augusta 2026, čas: 15:56:02 UTC+2, odosielateľ: 
>>>>> Frederick Stein
>>>>>
>>>>>> Dear Martin,
>>>>>> Do you have log files from the build process? If you have a different 
>>>>>> MPI implementation on your system, it could be that one of those were 
>>>>>> picked up somewhere.
>>>>>> Best,
>>>>>> Frederick
>>>>>>
>>>>>> Martin Konôpka schrieb am Donnerstag, 20. August 2026 um 14:30:49 
>>>>>> UTC+2:
>>>>>>
>>>>>>> Dear CP2K experts,
>>>>>>>
>>>>>>> I have  built CP2K 2026.2 on  several Linux workstations and I am  
>>>>>>> trying to run it. In each case I used the Intel oneAPI 2026.1 compilers and 
>>>>>>> libraries installed in the same way. Also the  CP2K was built on each of 
>>>>>>> the workstations in the same way with one minor excpetion - see below. I 
>>>>>>> used the toolchain. The results are different however:
>>>>>>>
>>>>>>> Ubuntu 26.04:  My CP2K build works.
>>>>>>> Linux Mint Zena (based on ubuntu 24.04): My CP2K build works.
>>>>>>> Ubuntu 22.04: My CP2K build fails with the message
>>>>>>>
>>>>>>> *** The MPI_Comm_c2f() function was called before MPI_INIT was 
>>>>>>> invoked.
>>>>>>> *** This is disallowed by the MPI standard.
>>>>>>> *** Your MPI job will now abort.
>>>>>>> [oslik:116792] Local abort before MPI_INIT completed completed 
>>>>>>> successfully, but am not able to aggregate error messages, and not able to 
>>>>>>> guarantee that all other processes were killed!
>>>>>>>
>>>>>>> There is no error message in the usual output file. I attach it, as  
>>>>>>> well  as my script used to launch  the CP2K executable. As for the input 
>>>>>>> file, it is the  same as in my recent post here:
>>>>>>> https://groups.google.com/g/cp2k/c/_B6BE1Q78L0
>>>>>>>
>>>>>>> To configure the CP2K on the two  newer OSs, I issued the command
>>>>>>>
>>>>>>> ./install_cp2k_toolchain.sh  --mpi-mode=intelmpi  --math-mode=mkl 
>>>>>>>  --libint-lmax=6  --with-ifx=yes  --with-cmake=system  --with-eigen=install 
>>>>>>>  --with-dftd4=install
>>>>>>>
>>>>>>> On ubuntu 22.04 I used the  same with the exception of cmake; I used 
>>>>>>> install instead of system, because the system cmake was too old.
>>>>>>>
>>>>>>> As for the oneAPI environment one the ubuntu 22.04, I successfully 
>>>>>>> used it to build Quantum Espresso 7.5 (and  it works with the Intel MPI), 
>>>>>>> so I really do not know what is the cause of the problem with the CP2K and would 
>>>>>>> greatly appreciate your opinions and advices.
>>>>>>>
>>>>>>> Best regards
>>>>>>> Martin Konôpka
>>>>>>>
>>>>>>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cp2k/e7ece083-309e-41fd-b82d-cf33fa12a8bfn%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20260821/d8167e82/attachment.htm>