These are chat archives for dereneaton/ipyrad
@dereneaton @isaacovercast Hey guys, I'm still trying to use ipcluster on a multi-node MPI setup. When I try to connect to an ipyparallel cluster, I get
TimeoutErrorTraceback (most recent call last) <ipython-input-10-2db68591f40a> in <module>() 4 5 ## connect to the client ----> 6 ipyclient = ipp.Client(profile="MPI96") 7 8 ## print how many engines are connected /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/client/client.pyc in __init__(self, url_file, profile, profile_dir, ipython_dir, context, debug, sshserver, sshkey, password, paramiko, timeout, cluster_id, **extra_args) 493 494 try: --> 495 self._connect(sshserver, ssh_kwargs, timeout) 496 except: 497 self.close(linger=0) /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/client/client.pyc in _connect(self, sshserver, ssh_kwargs, timeout) 613 evts = poller.poll(timeout*1000) 614 if not evts: --> 615 raise error.TimeoutError("Hub connection request timed out") 616 idents, msg = self.session.recv(self._query_socket, mode=0) 617 if self.debug: TimeoutError: Hub connection request timed out
mpiruncommand. Instead, ipcluster itself will attempt to make the appropriate MPI call when you tell it
--engines=MPIto start engines across available cores using MPI.
@Wind-ant Also, unless you tell ipyrad to use the launched ipcluster instance with
--ipcluster it will not look for it and instead attempt to automatically launch its own ipcluster instance.
A simpler way to run ipyrad across 8 cores is with the following command:
ipyrad -p params-c70m80.txt -s 67 -f
Or, if the ipcluster autolaunch is not working, then launch it yourself like this:
ipcluster start --n=8 --daemonize sleep 10 ipyrad -p params-c70m80.txt -s 67 -f --ipcluster
The way you were running I'm guessing that it may have started many ipcluster instances all at once with the same name/profile, and that might have confused things and caused everything to totally bog down.