[CP2K-user] [CP2K:16788] Re: Cannot use CP2K via Docker/Singularity

[Lenard Carroll]

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.schuett 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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>>>>>>
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