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@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
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