f6ea25b4d1
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 |
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| .. | ||
| VectorPairHMM | ||
| c | ||
| chainFiles | ||
| doc | ||
| external-example | ||
| gatk-framework | ||
| gatk-package | ||
| gatk-queue-extgen | ||
| gsalib | ||
| java/config | ||
| package-tests | ||
| perl | ||
| queue-framework | ||
| queue-package | ||
| repo | ||
| sting-root | ||
| sting-utils | ||
| pom.xml | ||