[CP2K-user] [CP2K:16797] Re: Cannot use CP2K via Docker/Singularity

[Ole Schütt]

Hi Lenard,

I've  uploaded a new docker image 
<https://hub.docker.com/layers/cp2k/cp2k/cp2k/dev20220330/images/sha256-a78bd270ca09ef64df5e80e034b22ed92671632ea5ed37ef88951a1268b8df50>, 
which is based on the latest 
<https://github.com/cp2k/cp2k/commit/aa9c8d9962e810d991202283608a233847e566fc> 
developer version and uses the novel Dockerfile.prod_generic_psmp 
<https://github.com/cp2k/cp2k/blob/master/tools/docker/Dockerfile.prod_generic_psmp>. 
I've also moved the symlink creation to the build phase.

Please give it a try:

  docker pull cp2k/cp2k:dev20220330
  docker run cp2k/cp2k:dev20220330 cp2k --version

-Ole

On Tuesday, March 29, 2022 at 8:30:42 PM UTC+2 lenardc... at gmail.com wrote:

> I don't know, I got rid of the /opt/cp2k/prod_entrypoint.sh: line 20:   
> 443 Illegal instruction     "$@" and the ln: failed to create symbolic link 
> '/opt/cp2k/exe/local/cp2k': errors now, but it tells me for both docker and 
> singularity error while loading shared libraries: libgfortran.so.5: cannot 
> open shared object file: No such file or directory
>
>
> On Tue, Mar 29, 2022 at 8:25 PM Ole Schütt <ole.s... at cp2k.org> wrote:
>
>> Your CPUs might indeed be a bit too old to run the current docker image.
>>
>> We recently added the ability to build generic binaries 
>> <https://github.com/cp2k/cp2k/pull/1854>, which I plan to use for the 
>> next release.
>>
>> -Ole
>>
>>
>>
>> On Tuesday, March 29, 2022 at 5:11:27 PM UTC+2 lenardc... at gmail.com 
>> wrote:
>>
>>> Not sure about all of them, but they are definitely intel. One is a low 
>>> budget Intel G4400 and another is an Intel Xeon processor (Haswell 
>>> architecture I believe). 
>>>
>>> On Tue, Mar 29, 2022 at 4:40 PM Ole Schütt <ole.s... at cp2k.org> wrote:
>>>
>>>> > docker pull cp2k/cp2k
>>>> > docker run cp2k/cp2k cp2k --version
>>>>
>>>> Well, it works for me (tm).
>>>>
>>>> > /opt/cp2k/prod_entrypoint.sh: line 20:   443 Illegal instruction     
>>>> "$@"
>>>>
>>>> May I ask what kind of CPU you are using? I've built the container on 
>>>> an AMD Ryzen Threadripper 3970X.
>>>>
>>>> -Ole
>>>>
>>>>
>>>>
>>>> On Tuesday, March 29, 2022 at 3:33:42 PM UTC+2 lenardc... at gmail.com 
>>>> wrote:
>>>>
>>>>> If I make that change (on singularity), I no longer get the ln error, 
>>>>> but:
>>>>> error while loading shared libraries: libgfortran.so.5: cannot open 
>>>>> shared object file: No such file or directory
>>>>>
>>>>> On Tuesday, March 29, 2022 at 2:06:29 PM UTC+2 ASSIDUO Network wrote:
>>>>>
>>>>>> For Docker I just did:
>>>>>> docker pull cp2k/cp2k
>>>>>> docker run cp2k/cp2k cp2k --version
>>>>>>
>>>>>> then I get the error. I tried it on my PCs and two HPC servers.
>>>>>>
>>>>>> Since I am also new to docker and singularity, I don't know quite how 
>>>>>> to edit that information in the container already, I'll see what I can find.
>>>>>>
>>>>>> On Tue, Mar 29, 2022 at 12:54 PM Ole Schütt <ole.s... at cp2k.org> 
>>>>>> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> how exactly did you try to run via Docker?
>>>>>>> Note that the docker image is pretty new and you are one of the 
>>>>>>> first to use it. So any feedback is appreciated.
>>>>>>>
>>>>>>> > Then when using singularity instead of docker, I get the following 
>>>>>>> error message:
>>>>>>>
>>>>>>> Unfortunately, I don't have any experience with Singularity. You 
>>>>>>> could try commenting those lines in the prod_entrypoint.sh 
>>>>>>> <https://github.com/cp2k/cp2k/blob/master/tools/docker/scripts/prod_entrypoint.sh#L17> 
>>>>>>> script and instead use the absolute path of the binary.
>>>>>>> If that works, I'll move the creation of those symlinks to the build 
>>>>>>> phase (or replace them with aliases).
>>>>>>>
>>>>>>> -Ole
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Sunday, March 27, 2022 at 6:57:12 PM UTC+2 lenardc... at gmail.com 
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi there, I hope you are doing well. 
>>>>>>>>
>>>>>>>> I tried using CP2K via Docker following this 
>>>>>>>> https://hub.docker.com/r/cp2k/cp2k
>>>>>>>> but I get the following error message:
>>>>>>>> /opt/cp2k/prod_entrypoint.sh: line 20:   443 Illegal instruction   
>>>>>>>>   "$@"
>>>>>>>>
>>>>>>>> Then when using singularity instead of docker, I get the following 
>>>>>>>> error message:
>>>>>>>> ln: failed to create symbolic link '/opt/cp2k/exe/local/cp2k': 
>>>>>>>> Read-only file system
>>>>>>>>
>>>>>>>> Can you help me resolve this? I've been trying to get CP2K working 
>>>>>>>> for a month now at my local HPC. I have failed, so I turned to asking help 
>>>>>>>> from admin, but they too cannot get it right. So now I am trying to go for 
>>>>>>>> a container, but I get the above error messages.
>>>>>>>>
>>>>>>>>
>>>>>>>>
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