FAQ

SMP Cluster FAQs

If the answer to your question isn't here, ask on the smp-hpc mailing list.

General questions

How do I get a cluster account?

Staff members and research students in SMP can apply for a getafix and dogmatix cluster accounts by sending a request to the ITS Help Desk attn: ITS Research Infrastructure.

Running graphical programs

I am trying to run mathematica (or some other graphical program) and it is asking me for a password, and then it doesn't work anyway.

You need to add an ssh key. See Howto.Slurm

Compiling

How do I compile with the intel compilers?

To compile with the intel compilers load the intel module and any other modules you need. For example:

module add intel mkl fftw icc ...

How do I compile with intel and mpi?

We now have a license for intel mpi but there's also an intel compiled openmpi installed:

module add intel mkl openmpi_eth

How do I get the Intel compiler to work with XMDS2?

To configure XMDS2 to use the intel compiler:

module add intel fftw mkl openmpi_eth
CXX=icc xmds2 --reconfigure
xmds2  ...

XMDS2 might not generate the correct linker command for intel, so if you get a linker error try adding -ldl at the appropriate place in the Makefile:

... -L/usr/lib64 -lz -lm '''-ldl''' -Wl,-Bstatic

My code compiles and runs on the login node so why does it get an "Illegal Instruction" error when I submit it to the queue?

The login node is running on an FC430 which is the newest hardware so if your code is compiled with -march=native it will get that error if you run it on older hardware. There are four possible solutions:

Compile your code with -mtune=generic instead and it will be runnable on all nodes.
Submit your job to the FC430 nodes it was compiled for with #SBATCH --constraint=FC430 in your submission script.
Compile your code on the hardware you plan to run it on. For example if you plan to run it on the C6220 and C8220 nodes start an interactive job with --constraint='[C6220,C8220]' and compile your code there.
Compile your code on the oldest hardware which currently is F720, C6220 and C8220: start an interactive job with --constraint='[C6220,C8220,R720]' and compile your code there.

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Page last modified on February 26, 2021, at 10:41 AM