72 lines
4.6 KiB
Markdown
72 lines
4.6 KiB
Markdown
|
Implementation overview:
|
||
|
|
Created a new Java class called VectorLoglessPairHMM which extends LoglessPairHMM and
|
||
|
|
overrides functions from both LoglessPairHMM and PairHMM.
|
||
|
|
1. Constructor: Call base class constructors. Then, load the native library located in this
|
||
|
|
directory and call an init function (with suffix 'jniInitializeClassFieldsAndMachineMask') in the
|
||
|
|
library to determine fields ids for the members of classes JNIReadDataHolder and
|
||
|
|
JNIHaplotypeDataHolders. The native code stores the field ids (struct offsets) for the classes and
|
||
|
|
re-uses them for subsequent computations. Optionally, the user can disable the vector
|
||
|
|
implementation, by using the 'mask' argument (see comments for a more detailed explanation).
|
||
|
|
2. When the library is loaded, it invokes the constructor of the class LoadTimeInitializer (because
|
||
|
|
a global variable g_load_time_initializer is declared in the library). This constructor
|
||
|
|
(LoadTimeInitializer.cc) can be used to perform various initializations. Currently, it initializes
|
||
|
|
two global function pointers to point to the function implementation that is supported on the
|
||
|
|
machine (AVX/SSE/un-vectorized) on which the program is being run. The two pointers are for float
|
||
|
|
and double respectively. The global function pointers are declared in utils.cc and are assigned in
|
||
|
|
the function initialize_function_pointers() defined in utils.cc and invoked from the constructor of
|
||
|
|
LoadTimeInitializer.
|
||
|
|
Other initializations in LoadTimeInitializer:
|
||
|
|
* ConvertChar::init - sets some masks for the vector implementation
|
||
|
|
* FTZ for performance
|
||
|
|
* stat counters = 0
|
||
|
|
* debug structs (which are never used in non-debug mode)
|
||
|
|
This initialization is done only once for the whole program.
|
||
|
|
3. initialize(): To initialize the region for PairHMM. Pass haplotype bases to native code through
|
||
|
|
the JNIHaplotypeDataHolder class. Since the haplotype list is common across multiple samples in
|
||
|
|
computeReadLikelihoods(), we can pass the haplotype bases to the native code once and re-use across
|
||
|
|
multiple samples.
|
||
|
|
4. computeLikelihoods(): Copies array references for readBases/quals etc to array of
|
||
|
|
JNIReadDataHolder objects. Invokes the JNI function to perform the computation and updates the
|
||
|
|
likelihoodMap.
|
||
|
|
The JNI function copies the byte array references into an array of testcase structs and invokes the
|
||
|
|
compute_full_prob function through the function pointers initialized earlier.
|
||
|
|
The primary native function called is
|
||
|
|
Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods. It uses
|
||
|
|
standard JNI calls to get and return data from/to the Java class VectorLoglessPairHMM. The last
|
||
|
|
argument to the function is the maximum number of OpenMP threads to use while computing PairHMM in
|
||
|
|
C++. This option is set when the native function call is made from JNILoglessPairHMM
|
||
|
|
computeLikelihoods - currently it is set to 12 (no logical reason).
|
||
|
|
Note: OpenMP has been disabled for now - insufficient #testcases per call to computeLikelihoods() to
|
||
|
|
justify multi-threading.
|
||
|
|
5. finalizeRegion(): Releases the haplotype arrays initialized in step 3 - should be called at the
|
||
|
|
end of every region (line 351 in PairHMMLikelihoodCalculationEngine).
|
||
|
|
|
||
|
|
Note: Debug code has been moved to a separate class DebugJNILoglessPairHMM.java.
|
||
|
|
|
||
|
|
Compiling:
|
||
|
|
Make sure you have icc (Intel C compiler) available. Currently, gcc does not seem to support all AVX
|
||
|
|
intrinsics.
|
||
|
|
This native library is called libVectorLoglessPairHMM.so
|
||
|
|
Using Maven:
|
||
|
|
Type 'mvn install' in this directory - this will build the library (by invoking 'make') and copy the
|
||
|
|
native library to the directory
|
||
|
|
${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm
|
||
|
|
The GATK maven build process (when run) will bundle the library into the StingUtils jar file from
|
||
|
|
the copied directory.
|
||
|
|
Simple build:
|
||
|
|
cd src/main/c++
|
||
|
|
make
|
||
|
|
|
||
|
|
Running:
|
||
|
|
The default implementation of PairHMM is now VECTOR_LOGLESS_CACHING in HaplotypeCaller.java. To use
|
||
|
|
the Java version, use the command line argument "--pair_hmm_implementation LOGLESS_CACHING". (see
|
||
|
|
run.sh in src/main/c++).
|
||
|
|
The native library is bundled with the StingUtils jar file. When HaplotypeCaller is invoked, then
|
||
|
|
the library is unpacked from the jar file, copied to the /tmp directory (with a unique id) and
|
||
|
|
loaded by the Java class VectorLoglessPairHMM in the constructor (if it has not been loaded
|
||
|
|
already).
|
||
|
|
The default library can be overridden by using the -Djava.library.path argument (see
|
||
|
|
src/main/c++/run.sh for an example) for the JVM to pass the path to the library. If the library
|
||
|
|
libVectorLoglessPairHMM.so can be found in java.library.path, then it is loaded and the 'packed'
|
||
|
|
library is not used.
|