Auryn on a Fedora based cluster

[asinha]

This is a quick howto on how to run Auryn on a Fedora based cluster. I've used it on the Herts STRI cluster.

First - download auryn. It's best to checkout the lastest git commit. In general, the instructions present here should work just fine for you. You may need a couple of tweaks to the Makefile if the required libraries are not present in standard locations. For example, both, the required openmpi libraries and the mpic++ binary were placed in non standard locations in the cluster configuration. Therefore, I need to specify these during the build.

For the mpic++ binary, I simply needed to add its location to the PATH variable:

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export PATH=$PATH:/usr/mpi/gcc/openmpi-1.4.3/bin/:~/.local/bin/:~/bin:/soft/nrn/x86_64/bin/

to my ~/.bashrc was sufficient. Here, /usr/mpi/gcc/openmpi-1.4.3/bin is the location of the mpic++ executable.

Similarly, to specify the correct location of the libraries required to compile Auryn, I needed to modify the LDFLAGS variable in the Makefile. In my case, it now looks like this:

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LDFLAGS=-L/usr/lib64/openmpi/lib/ -lboost_program_options -lboost_mpi -lboost_serialization

I added the -L/usr/lib64/openmpi/lib/ fragment to tell the linker/compiler that it should look in this location also. You can read more about the -L on the internet, or the gcc etc. man pages.

Once it compiles, running it is quite easy if you're running it on the same node that you had compiled it on. In our cluster, like most, we need to submit jobs that a queue scheduler handles - using the qsub command. The other issue can arise if all the nodes on the cluster aren't exactly the same - maybe with different operating system versions or library versions. If the node that the scheduler will run your simulation on differs, you may need to provide some extra information to the qsub command. For example, I need to specify the location of the required shared objects in by job file:

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echo "---------------------- Simulation started -----------------------------"
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/mpi/gcc/openmpi-1.4.3/lib64/ ./auryn-0.4.1/build/home/sim_background
echo "---------------------- Simulation ended -----------------------------"

That's about it. For other issues, contact the cluster admin and he should be able to help you out - especially if you cannot find the required packages at all. The admins need to install these for you.

[zenke]

Thanks great for sharing this!

[afvincent]

(Disclaimer: if necrobumping threads is considered a bad practice, please tell me and I will open a new dedicated thread.)

Here is another solution that I found to install Auryn on a Fedora (27) workstation.

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# Script to download and set up Auryn from GitHub

module load mpi/openmpi-x86_64  # Fedora-specific? Add Open MPI to the path
cd $HOME/FOSS  # my custom directory for software installed through git
# From the official documentation
git clone https://github.com/fzenke/auryn.git
cd ./auryn/build/release
./bootstrap.sh
make

Putting the code from above in a bash script, I was able to successfully install Auryn following the tutorial in the official documentation. The key line is

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module load mpi/openmpi-x86_64

that makes the Open MPI libraries and executable files discoverable through the path. I guess that it simply does something similar to asinha's solution, but I wanted to share it, in case someone finds it better suited to their needs.