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

Haas, Roland rhaas at illinois.edu
Fri Sep 13 08:12:27 CDT 2019

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

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:


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.


> 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 .
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