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Diffstat (limited to 'INSTALL.md')
| -rw-r--r-- | INSTALL.md | 44 |
1 files changed, 43 insertions, 1 deletions
@@ -14,7 +14,7 @@ GEMMA runs on Linux and MAC OSX and the runtime has the following dependencies: * C++ tool chain >= 4.9 -* GNU Science library (GSL) 1.x (GEMMA does not currently work with GSL >= 2). +* GNU Science library (GSL) 1.x (note that 2.x is not yet supported) * blas/openblas * lapack * [Eigen3 library](http://eigen.tuxfamily.org/dox/) @@ -88,6 +88,9 @@ should compile with GCC_FLAGS="" to disable optimizations (-O3). E.g. make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 GCC_FLAGS= +If you get older OpenBlas errors you may need to add +OPENBLAS_LEGACY=1. + Other options, such as compiling with warnings, are listed in the Makefile. @@ -100,3 +103,42 @@ GEMMA includes the shunit2 test framework (version 2.0). or ./run_tests.sh + +## Optimizing performance + +### OpenBlas + +Linking against a built-from-source OpenBlas is a first optimization +step because it will optimize code for the local architecture (on my +workstation it easily doubles speed). When you check the output .log +file of GEMMA after a run, it will tell you how the linked-in OpenBlas +was compiled. + +To link a new version, compile OpenBlas as per +[instructions](http://www.openblas.net/). You can start with the default: + + make -j 4 + +or play with the switches + + make USE_THREAD=1 NUM_THREADS=16 -j 4 + +rendering for example: + + OpenBLAS build complete. (BLAS CBLAS) + OS ... Linux + Architecture ... x86_64 + BINARY ... 64bit + C compiler ... GCC (command line : gcc) + Library Name ... libopenblas_haswellp-r0.3.0.dev.a (Multi threaded; Max num-threads is 16) + + To install the library, you can run "make PREFIX=/path/to/your/installation install". + +This generates a static library which you can link using the full path +with using the GEMMA Makefile: + + time env OPENBLAS_NUM_THREADS=4 make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/tmp/OpenBLAS/libopenblas_haswellp-r0.3.0.dev.a -lgsl -lgslcblas -pthread -lz -llapack" WITH_OPENBLAS=1 -j 4 fast-check + + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/tmp/OpenBLAS/libopenblas_haswellp-r0.3.0.dev.a -lgsl -lgslcblas -pthread -lz -llapack" WITH_OPENBLAS=1 -j 4 unittests + +NOTE: we should make this easier. |