[Users] HDF5 and submission/runtime issues on a PBS cluster

[Haas, Roland]

Hello Vaishak,

as usual, I would suggest addressing the mailing list. Would you mind
if I forward this email to the list?

Your point 3 sounds like either an incorrectly set-up cluster or (if
this is a "private" cluster) missing passwordless ssh keys.

I would contact your cluster administrators and show them the output of trying to run something like:

mpirun -np 64 /usr/bin/hostname

which tries to start 64 copies of the "hostname" command. Make sure that 64 is more cores than a single node can provide.

Alternatively you can try and fix this yourself following for example

https://www.open-mpi.org/faq/?category=rsh#ssh-keys

but do leave the password blank (this implies you should only use this key-pair on the cluster and not do log into the cluster from the outside).

Yours,
Roland

> Dear Sir,
> 
> Thankyou very much for you reply. I will add the additional lines to
> LDFLAGS and try.
> 
> What do you think about the other issue point 3 in the document ? It looks
> like simfactory is unable to login to more than one compute node on the
> cluster.
> 
> 
> I have an additional related questions. What is the variable 'LIBDIRS' used
> for?
> 
> 
> Thankyou for you support again
> 
> Yours Sincerely
> Vaishak
> 
> On Fri, Sep 13, 2019 at 6:42 PM Haas, Roland <rhaas at illinois.edu> wrote:
> 
> > Hello Vaishak,
> >
> > looking at you .ini and .cfg files you need to add extra options to
> > make sure that the correct hdf5 libraries are found at runtime (not
> > just at compile time).
> >
> > Often on clusters there will be "environment modules" that you should
> > load to set the correct settings. The command to do so is the "module"
> > command, which you can test using "module avail" and then add the
> > correct "module load hdf5" command to the envsetup option in your ini
> > file. Something like this:
> >
> > envsetup = <<EOT
> > module load hdf5
> > EOF
> >
> > see eg the bluewaters.ini file in simfactory.
> >
> > If there are no modules or they don't work as expected or you would
> > like to not use them, then you can also add the following bit to your
> > LDFLAGS in your cfg file:
> >
> > -Wl,--rpath,/mnt/home/visitor/cvaishak/Installations/HDF5/hdf5-1.8.12/lib
> >
> > ie for each -L option that you have, add a "-Wl,--rpath," option (no
> > space between the commas) to instruct the linker (-Wl) to add an RPATH
> > (--rpath) value to the executable to tell it where to look for
> > libraries at runtime.
> >
> > Yours,
> > Roland
> >  
> > > Dear all,
> > >
> > > I am herewith attaching a document ( etk_setup_errors) and some relevant
> > > attachments concerning the issues I am facing in setting up ETK.
> > >
> > > I am looking forward to your help and support!
> > >
> > >
> > > Thanks
> > >  
> >
> >
> >
> > --
> > My email is as private as my paper mail. I therefore support encrypting
> > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >  
> 
> 



-- 
My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from http://pgp.mit.edu .
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