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 <[email protected]> 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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