If you are using these libraries often and they exist on a remote server
(NFS or whatever) you may want to use the "libraries" or "prestage"
directives in Scyld's config to put them on compute nodes instead.
Jeff White - GNU+Linux Systems Administrator
University of Pittsburgh - CSSD
On 01/15/2015 06:22 PM, Don Kirkby wrote:
I'm new to the list, so please let me know if I'm asking in the wrong place.
We're running a Scyld Beowulf cluster on CentOS 5.9, and I'm trying to
run some Django admin commands on a compute node. The problem is that it
can take three to five minutes to launch ten MPI processes across the
four compute nodes and the head node. (We're using OpenMPI.)
I traced the delay to smaller and smaller parts of the code until I
created two example scripts that just import a Python library and print
out timing information. Here's the first script that imports the
collections module:
from datetime import datetime
t0 = datetime.now()
print 'started at {}'.format(t0)
import collections
print 'imported at {}'.format(datetime.now() - t0)
When I run that with mpirun -host n0 python
cached_imports_collections.py, it initially takes about 10 seconds to
import. However, repeated runs take less time, until it takes less than
0.01 seconds to import.
Running an equivalent script to import the decimal module takes about 30
seconds, and never speeds up like that. It may be too large to get
cached completely. I ran beostatus while the script was running, and I
didn't see the network traffic go over 100 kBps. For comparison, running
wc on a 100MB file on a compute node causes the network traffic to go
over 3000 kBps.
I looked in the Scyld admin guide (PDF) and the reference guide (PDF),
and found the bplib command that manages which libraries are cached and
not transmitted with the job processes. However, its list of library
directories already includes the Python installation.
Is there some way to increase the size of the bplib cache, or am I doing
something inefficient in the way I launch my Python processes?
Thanks,
Don Kirkby
British Columbia Centre for Excellence in HIV/AIDS
cfenet.ubc.ca
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