[Clas_offline] similar problem on batch farm

[Nick Tyler]

Hi Nikolai,

You have to load the singularity module both interactively and in batch scripts before you can use it.

To do this either run this command or add it to your .cshrc/.bashrc file:

module load singularity/3.4.0

This will load the singularity command into your path so that you can use it.

Nick

> On Feb 19, 2020, at 9:07 AM, Nikolai Pivnyuk <pivnyuk at jlab.org> wrote:
> 
> Hi Nick,
> 
> I am a bit confused and upset. ifarm180i as well as the batch farm nodes
> do not understand what does the command "singularity" mean. Could you please
> check that from your account.
> ----------------------------------------------------------------
> pivnyuk at ifarm1801.jlab.org> pwd
> /u/home/pivnyuk/g10/mc/qf_2020/fsgen_gsim_gpp_recsis
> pivnyuk at ifarm1801.jlab.org> date
> Wed Feb 19 08:55:24 EST 2020
> pivnyuk at ifarm1801.jlab.org> singularity exec
> /work/clas/clase1/tylern/clas6.img bosdump
> singularity: Command not found.
> pivnyuk at ifarm1801.jlab.org>
> -----------------------------------------------------------------------------------
> It seems that ifarm180i have been rebooted a few hours ago.
> 
> Regards,
> 
> Nikolai
> 
> 
>> Hi Nikolai,
>> 
>> All of these programs you mention work with the singularity image as well,
>> and in theory all the the clas6 executables should work inside of the
>> image in this way. I have the code used to build everything and a bit of a
>> readme about using it on the farm as a slurm submission available on my
>> GitHub. (https://github.com/tylern4/clas6
>> <https://github.com/tylern4/clas6>) You can think of the singularity image
>> as a light weight virtual machine that is running centos6 and has all the
>> clas6 software built inside of it.
>> 
>> Or you can modify your job submission simply by appending "singularity
>> exec /work/clas/clase1/tylern/clas6.img” before the executable you want to
>> run with all the same arguments afterwards.
>> 
>> For example:
>> gsim_bat … => singularity exec /work/clas/clase1/tylern/clas6.img gsim_bat
>> …
>> gpp … =>  singularity exec /work/clas/clase1/tylern/clas6.img gpp …
>> Etc.
>> 
>> If you want I’m happy to help you get started using it on the farm.
>> 
>> Nick
>> 
>> 
>>> On Feb 18, 2020, at 10:52 AM, Nikolai Pivnyuk <pivnyuk at jlab.org> wrote:
>>> 
>>> Hi,
>>> 
>>> it is not only the "bosdump" affected by centos77 !?
>>> My executables in simulations also failed IN THE SIMILAR WAY as bosdump
>>> did.
>>> 
>>> Below ARE the lines from my ".err" output file from farm batch (Auger)
>>> job
>>> with "OS: centos77" specification.
>>> 
>>> -----------------------------------------------------------------------------------------------------------------------------------
>>> gsim_bat: error while loading shared libraries: libXbae.so.4: cannot
>>> open
>>> shared object file: No such file or directory
>>> gpp: error while loading shared libraries: libmysqlclient.so.20: cannot
>>> open shared object file: No such file or directory
>>> mv: cannot stat ‘gpp.hbook’: No such file or directory
>>> -----------------------------------------------------------------------------------------------------------------------------------
>>> user_ana: error while loading shared libraries: libmysqlclient.so.20:
>>> cannot open shared object file: No such file or directory
>>> /home/claseg2/bin/LinuxRHEL7/user_ana: error while loading shared
>>> libraries: libmysqlclient.so.20: cannot open shared object file: No such
>>> file or directory
>>> -------------------------------------------------------------------------------------------------------------------------------------
>>> 
>>> Hard times begin for the simple ordinary user ?
>>> May be it might be reasonable to keep some nodes untouchable in 'old' OS
>>> conditions until 'new' start working perfectly ?
>>> 
>>> Nikolai
>>> 
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>>> Clas_offline at jlab.org
>>> https://mailman.jlab.org/mailman/listinfo/clas_offline
>> 
>> 
> 
>