To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
The JNI treats shared memory as critical memory and doesn't allow any
parallel reads or writes to it until the native code finishes. This is
not a problem *per se* it is the right thing to do, but we need to
enable **-nct** when running the haplotype caller and with it have
multiple native PairHMM running for each map call.
Move to a copy based memory sharing where the JNI simply copies the
memory over to C++ and then has no blocked critical memory when running,
allowing -nct to work.
This version is slightly (almost unnoticeably) slower with -nct 1, but
scales better with -nct 2-4 (we haven't tested anything beyond that
because we know the GATK falls apart with higher levels of parallelism
* Make VECTOR_LOGLESS_CACHING the default implementation for PairHMM.
* Changed version number in pom.xml under public/VectorPairHMM
* VectorPairHMM can now be compiled using gcc 4.8.x
* Modified define-* to get rid of gcc warnings for extra tokens after #undefs
* Added a Linux kernel version check for AVX - gcc's __builtin_cpu_supports function does not check whether the kernel supports AVX or not.
* Updated PairHMM profiling code to update and print numbers only in single-thread mode
* Edited README.md, pom.xml and Makefile for users to pass path to gcc 4.8.x if necessary
* Moved all cpuid inline assembly to single function Changed info message to clog from cinfo
* Modified version in pom.xml in VectorPairHMM from 3.1 to 3.2
* Deleted some unnecessary code
* Modified C++ sandbox to print per interval timing
public/VectorPairHMM/src/main/c++ as per Khalid's suggestion
2. Use java.home in public/VectorPairHMM/pom.xml to pass environment
variable JRE_HOME to the make process. This is needed because the
Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among
others). Assuming that the Maven build process uses a JDK (and not just
a JRE), the variable java.home points to the JRE inside maven.
3. Dropped all pretense at cross-platform compatibility. Removed Mac
profile from pom.xml for VectorPairHMM
Geraldine Van der Auwera
David Roazen
Khalid Shakir
Karthik Gururaj