[CP2K-user] [CP2K:22411] Re: CP2K 2026.2 on ubuntu 22.04 + oneAPI: The MPI_Comm_c2f() function was called before MPI_INIT was invoked.

[Martin Konôpka]

Greetings,

I did as I have  written (on  the Ubuntu 22.04): uninstalled the non-oneAPI 
software and I built CP2K 2026.2 again using the toolchain. The resulting 
CP2K binary works better but still unsatisfactorily. A simple single-point 
calculation ran succesfully. A more involved task crashed. I used also the 
TRACE keyword. It told me that some library (or perhaps two libraries) was 
not configured. I remember that (one of) the  mentioned libs was libxsmm. I 
somehow lost or cannot find the files from  that run so that I cannot 
attach them. I however did the regression tests and they also showed 
errors. I attach the error summary.

I will likely give up my toolchain efforts and will try to use Spack to get 
CP2K 2026.2 working on the Ubuntu 22.04 workstation.

Best,
Martin.
Dátum: piatok 21. augusta 2026, čas: 18:52:52 UTC+2, odosielateľ: 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
>>>>>>>>
>>>>>>>

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