qiqi / fds Goto Github PK

Currently there's no unit tests to run through the pbs / slurm interfaces. Need to figure out what packages (apt-get) we need to install in .travis.yml , to simulate these environments, and code up some unit tests.

Not much unit test coverage yet. Need to grab a file from cascade

Add support for adding a filtering parameter to LSS. Ideally has a way to automatically set it. Current implementation is equivalent to setting a zero filtering parameter. That may not work for very long trajectories

Cloned https://github.com/open-mpi/ompi.git

It looks like OpenMPI may also be looking for the PBS_NODEFILE environment variable when user calls mpiexec in a pbs/torque environment:

qiqi@ubuntu:~/git/ompi$ git grep PBS_NODEFILE
orte/mca/ras/tm/help-ras-tm.txt:No nodes were found in the PBS_NODEFILE:
orte/mca/ras/tm/ras_tm_component.c:    pbs_nodefile_env = getenv("PBS_NODEFILE");

Looking into the source, OpenMPI looks for pbs_nodefile under /var/torque/aux if the environment variable is not found. We have no machine to test this on. So just take note for now.

When in slurm, it may be also looking for SLURM_NODELIST environment variable:

qiqi@ubuntu:~/git/ompi$ git grep SLURM_NODELIST
orte/mca/ras/slurm/help-ras-slurm.txt:    SLURM_NODELIST
orte/mca/ras/slurm/help-ras-slurm.txt:    SLURM_NODELIST       value: %s
orte/mca/ras/slurm/ras_slurm_module.c:    slurm_node_str = getenv("SLURM_NODELIST");
orte/mca/ras/slurm/ras_slurm_module.c:                       "SLURM_NODELIST");
orte/mca/ras/slurm/ras_slurm_module.c: * @param *regexp A node regular expression from SLURM (i.e. SLURM_NODELIST)
orte/mca/ras/slurm/ras_slurm_module.c:                           1, regexp, tasks_per_node, "SLURM_NODELIST");
orte/mca/ras/slurm/ras_slurm_module.c:                               1, regexp, tasks_per_node, "SLURM_NODELIST");
orte/mca/ras/slurm/ras_slurm_module.c:                               1, regexp, tasks_per_node, "SLURM_NODELIST");
orte/mca/ras/slurm/ras_slurm_module.c:         * I would get SLURM_NODELIST=odin001 SLURM_TASKS_PER_NODE=4(x30)
orte/mca/schizo/slurm/schizo_slurm.c:    if (NULL == getenv("SLURM_NODELIST")) {

To run fds on Mira, we need to figure out what we need to do in a cobalt environment. What environment variable / file contains information about nodes / processors available for the current job?

One may be interested in the dynamics of a non-parameterized system, e.g., computing Lyapunov exponents, etc. Then, one may want to add a parameter for sensitivity analysis, and potentially add more parameters later one. Need to figure out an interface for this.

Easy: fds currently supports only one parameter. However, the same homogeneous solutions can be used to compute the tangent solution of many parameters simultaneously. fds should be modified to enable that.

Hi

I tried opening the tutorials

• Lorenz attractor in C
• Lorenz 96 in MPI and C

and the links direct me to empty documents. I tried changing branches but both tutorials seem to be empty in all of them. Van der Pol works though.