Hi Andreas, On Fri, Jul 24, 2020 at 12:29 PM Andreas Tille <[email protected]> wrote:
> Hi Pranav, > > seems ampliconnoise will keep us busy longer than other packages. The > fact that now no extra data are shipped somehow made my motivation to > put them into an extra package somehow void. So I reverted this and in > addition used xz compression for the data file shipped by upstream. That sounds great. > Unfortunately there are issues with the test (which I ignored formerly > since I'm used to the fact that inside the pbuilder environment root > is executing the test which does not work for mpi). I've now tried > to run /usr/share/doc/ampliconnoise/run-unit-test on my local machine > which ended in: > > C005.dat > Calculating .fdist file > -------------------------------------------------------------------------- > There are not enough slots available in the system to satisfy the 4 > slots that were requested by the application: > > PyroDist > > Either request fewer slots for your application, or make more slots > available for use. > > A "slot" is the Open MPI term for an allocatable unit where we can > launch a process. The number of slots available are defined by the > environment in which Open MPI processes are run: > > 1. Hostfile, via "slots=N" clauses (N defaults to number of > processor cores if not provided) > 2. The --host command line parameter, via a ":N" suffix on the > hostname (N defaults to 1 if not provided) > 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.) > 4. If none of a hostfile, the --host command line parameter, or an > RM is present, Open MPI defaults to the number of processor cores > > In all the above cases, if you want Open MPI to default to the number > of hardware threads instead of the number of processor cores, use the > --use-hwthread-cpus option. > > Alternatively, you can use the --oversubscribe option to ignore the > number of available slots when deciding the number of processes to > launch. > -------------------------------------------------------------------------- > Exit code: 1 > > > Seems mpi needs some initialisation before it runs on the local > machine. My machine has > > $ nproc > 4 > > So 4 processors should not be a problem. > Any idea what might be wrong here? > It didn't seem to require any initialization for me. Maybe we should just try it with the --use-hwthread-cpus option. I've tried it inside and outside the chroot and it works for me. Could you please try it too? I've edited the commands and pushed. Regards, Pranav ᐧ
