-- Closes GSA-515 Nanoscheduler GSA-542 Good interface to nanoScheduler
-- Old -nt means dataThreads
-- New -cnt (--num_cpu_threads_per_data_thread) gives you n cpu threads for each data thread in the system
-- Cleanup logic for handling data and cpu threading in HMS, LMS, and MS
-- GATKRunReport reports the total number of threads in use by the GATK, not just the nt value
-- Removed the io,cpu tags for nt. Stupid system if you ask me. Cleaned up the GenomeAnalysisEngine and ThreadAllocation handling to be totally straightforward now
-- GATKRunReports contain itemized information about the numThreads used to execute the GATK, as well as the efficiency of the use of those threads to get real work done, including time spent running, waiting, blocking, and waiting for IO
-- See https://jira.broadinstitute.org/browse/GSA-506 for more details
Move the RunReport S3 upload process onto a separate thread with a timeout allowing the parent to continue.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
Now looks like:
<GATK-run-report>
<id>D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz</id>
<start-time>2012/03/10 20.21.19</start-time>
<end-time>2012/03/10 20.21.19</end-time>
<run-time>0</run-time>
<walker-name>CountReads</walker-name>
<svn-version>1.4-483-g63ecdb2</svn-version>
<total-memory>85000192</total-memory>
<max-memory>129957888</max-memory>
<user-name>depristo</user-name>
<host-name>10.0.1.10</host-name>
<java>Apple Inc.-1.6.0_26</java>
<machine>Mac OS X-x86_64</machine>
<iterations>105</iterations>
</GATK-run-report>
No longer capturing command line or directory information, to minimize people's concerns with phone home and privacy
-Running the GATK with the -et NO_ET or -et STDOUT options now
requires a key issued by us. Our reasons for doing this, and the
procedure for our users to request keys, are documented here:
http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home
-A GATK user key is an email address plus a cryptographic signature
signed using our private key, all wrapped in a GZIP container.
User keys are validated using the public key we now distribute with
the GATK. Our private key is kept in a secure location.
-Keys are cryptographically secure in that valid keys definitely
came from us and keys cannot be fabricated, however keys are not
"copy-protected" in any way.
-Includes private, standalone utilities to create a new GATK user key
(GenerateGATKUserKey) and to create a new master public/private key
pair (GenerateKeyPair). Usage of these tools will be documented on
the internal wiki shortly.
-Comprehensive unit/integration tests, including tests to ensure the
continued integrity of the GATK master public/private key pair.
-Generation of new user keys and the new unit/integration tests both
require access to the GATK private key, which can only be read by
members of the group "gsagit".
-- This is a partial fix for the problem with uploading S3 logs reported by Mauricio. There the problem is that the java.io.tmpdir is not accessible (network just hangs). Because of that the s3 upload fails because the underlying system uses tmpdir for caching, etc. As far as I can tell there's no way around this bug -- you cannot overload the java.io.tmpdir programmatically and even if I could what value would we use? The only solution seems to me is to detect that tmpdir is hanging (how?!) and fail with a meaningful error.
-- Cannot reproduce the very long waits reported by some users.
-- Fixed problem that exception might result in an undeleted file, which is now fixed with deleteOnExit()
Mark DePristo
Eric Banks
David Roazen
Chris Saunders