Re: [HTCondor-users] Unable to start Abaqus MPI Jobs with HTCondor

[Greg Thain <gthain@xxxxxxxxxxx>]

On 2/6/21 3:05 PM, felix.koelzow@xxxxxx wrote:
> Just as a short answer. The abaqus job within the interactive session is
> running fine, i.e.:
Hi Felix:

I don't know anything about Abaqus, but typically when this happens, it 
means there is an environment variable missing that the job needs. My 
first guess would be HOME. In your runAbaqus.sh script, can you add a 
line like

export HOME=$_CONDOR_SCRATCH_DIR

if you are running without a shared filesystem, or the path to the 
correct home if you are?

Thanks,


-greg

> $ condor_submit -i
> Submitting job(s).
> 1 job(s) submitted to cluster 80.
> Waiting for job to start...
> Welcome to slot1@kallisto
> You will be logged out after 7200 seconds of inactivity.
> $ abq2017 input=test_06_400_1_90 job=test_06_400_1_90.inp cpus=32
> user=uamp_x64_v5_KpKonst_amp_extern.f interr
> Analysis initiated from SIMULIA established products
> Abaqus JOB test_06_400_1_90
> Abaqus 3DEXPERIENCE R2017x
> Abaqus License Manager checked out the following licenses:
> Begin Compiling Abaqus/Standard User Subroutines
> Sat 06 Feb 2021 09:53:11 PM CET
> End Compiling Abaqus/Standard User Subroutines
> Begin Linking Abaqus/Standard User Subroutines
> GNU ld version 2.27-44.base.el7
> End Linking Abaqus/Standard User Subroutines
> Sat 06 Feb 2021 09:53:13 PM CET
> Begin Analysis Input File Processor
> Sat 06 Feb 2021 09:53:13 PM CET
> Run pre
> Sat 06 Feb 2021 09:53:23 PM CET
> End Analysis Input File Processor
> Begin Abaqus/Standard Analysis
> Sat 06 Feb 2021 09:53:23 PM CET
> Run standard
> Sat 06 Feb 2021 09:58:19 PM CET
> End Abaqus/Standard Analysis
> Begin MFS->SFS and SIM cleanup
> Sat 06 Feb 2021 09:58:19 PM CET
> Run SMASimUtility
> Sat 06 Feb 2021 09:58:19 PM CET
> End MFS->SFS and SIM cleanup
> Abaqus JOB test_06_400_1_90 COMPLETED
>
> I will spend more time for testing and analysis. This is just a quick
> reponse in order to provide feedback.
>
> Maybe this result indicates the right direction for debugging.
>
>
> Regards,
>
> Felix
>
>
>
>
> On 06/02/2021 00:20, Greg Thain wrote:
> > If you start an interactive shell via condor with submit -i, and then
> > run abaqus "by hand", do you get the same error?
> >
> >
> > -greg
> >
> > On 2/5/21 4:30 PM, felix.koelzow@xxxxxx wrote:
> > > At first,
> > >
> > > I would like to say thank you to everyone who contributed and/or still
> > > contributes in any sense to
> > >
> > > htcondor, I am really impressed about the capabilities and 
> > > possibilities
> > > of htcondor.
> > >
> > >
> > > Currently, I am struggeling with htcondor while running abaqus jobs. In
> > > short, I am able to run
> > >
> > > abaqus jobs on each host if it is started WITHOUT condor. But if condor
> > > is involed, after a short
> > >
> > > successfull runtime, the abaqus job terminates with
> > >
> > >
> > > *** buffer overflow detected ***:
> > > /opt/Abaqus/V6R2017x/linux_a64/code/bin/standard terminated
> > > ======= Backtrace: =========
> > > /lib64/libc.so.6(__fortify_fail+0x37)[0x2af27504a607]
> > > /lib64/libc.so.6(+0x116782)[0x2af275048782]
> > > /lib64/libc.so.6(+0x115c8b)[0x2af275047c8b]
> > > /lib64/libc.so.6(_IO_default_xsputn+0xe1)[0x2af274faefa1]
> > > /lib64/libc.so.6(_IO_vfprintf+0x28c5)[0x2af274f7cec5]
> > > /lib64/libc.so.6(__vsprintf_chk+0x88)[0x2af275047d18]
> > > /lib64/libc.so.6(__sprintf_chk+0x7d)[0x2af275047c6d]
> > > /opt/Abaqus/V6R2017x/linux_a64/code/bin/libifcoremt.so.5(fname_from_piped_fd+0xa3)[0x2af273bda993] 
> > >
> > >
> > >
> > > ...
> > >
> > >
> > > Actually, I am absolutely without ideas and any help is appreciated.
> > >
> > >
> > > I guess you need more information, so please feel free to ask for more.
> > >
> > >
> > > OS: CentOS7.9
> > >
> > > Condor Version: Stable 8.8.12
> > >
> > >
> > > Regards,
> > >
> > > Felix
> > >
> > >
> > > --------
> > >
> > > submit file:
> > >
> > > universe = parallel
> > > executable = runAbaqus.sh
> > > request_cpusÂÂÂÂ = 1
> > > machine_countÂÂÂ = 1
> > > requirements = ( machine == "specifichost")
> > >
> > > jobname = somename
> > > usersubroutine = uamp.f
> > > arguments= job=$(jobname) input=$(jobname).inp user=$(usersubroutine)
> > > cpus=$(request_cpus) inter
> > >
> > > outputÂÂÂÂÂÂ = outputfile
> > > errorÂÂÂÂÂÂÂ = errorfile
> > > logÂÂÂÂÂÂÂÂÂ = abq2017.log
> > > concurrency_limits = abaqus_tokens:5
> > > getenv = True
> > > should_transfer_files = no
> > > queue
> > >
> > > runAbaqus.sh file
> > >
> > > cat runAbaqus.sh
> > > #!/usr/bin/bash
> > > /opt/Abaqus/Commands/abq2017 "$@"
> > >
> > >
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