diff options
Diffstat (limited to 'INSTALL.md')
| -rw-r--r-- | INSTALL.md | 12 |
1 files changed, 6 insertions, 6 deletions
@@ -65,12 +65,12 @@ if you get an Eigen error you may need to override the include path. E.g. to build GEMMA on GNU Guix with shared libs the following may work - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 another example overriding optimization and LIB flags (so as to link against gslv1) would be - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 GCC_FLAGS="-Wall -isystem/$HOME/opt/gsl1/include" LIBS="$HOME/opt/gsl1/lib/libgsl.a $HOME/opt/gsl1/lib/libgslcblas.a -L$HOME/.guix-profile/lib -pthread -llapack -lblas -lz" + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 GCC_FLAGS="-Wall -isystem/$HOME/opt/gsl1/include" LIBS="$HOME/opt/gsl1/lib/libgsl.a $HOME/opt/gsl1/lib/libgslcblas.a -L$HOME/.guix-profile/lib -pthread -llapack -lblas -lz" to run GEMMA tests @@ -86,7 +86,7 @@ You can run gemma in the debugger with, for example Note that if you get <optimized out> warnings on inspecting variables you should compile with GCC_FLAGS="" to disable optimizations (-O3). E.g. - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 GCC_FLAGS= + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 GCC_FLAGS= If you get older OpenBlas errors you may need to add OPENBLAS_LEGACY=1. @@ -142,11 +142,11 @@ OpenBlas version gives problems around eigenvalues for some reason. We now have 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 unittests + 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" -j 4 unittests Latest (INT64, no gslcblas): - time env OPENBLAS_NUM_THREADS=4 make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/opt/gsl2/lib/libgsl.a ~/tmp/OpenBLAS/libopenblas_haswellp-r0.3.0.dev.a -pthread -lz -llapack" WITH_OPENBLAS=1 OPENBLAS_INCLUDE_PATH=~/tmp/OpenBLAS/ -j 4 fast-check + time env OPENBLAS_NUM_THREADS=4 make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/opt/gsl2/lib/libgsl.a ~/tmp/OpenBLAS/libopenblas_haswellp-r0.3.0.dev.a -pthread -lz -llapack" OPENBLAS_INCLUDE_PATH=~/tmp/OpenBLAS/ -j 4 fast-check ### OpenBlas 64-bit API @@ -165,6 +165,6 @@ setting for testing the 64-bit API. Note, for performance we want a 64-bit binary with threading. - make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/opt/gsl2/lib/libgsl.a ~/tmp/OpenBLAS/libopenblas_haswell-r0.3.0.dev.a ~/.guix-profile/lib/libgfortran.a ~/.guix-profile/lib/libquadmath.a -pthread -lz" WITH_OPENBLAS=1 OPENBLAS_INCLUDE_PATH=~/tmp/OpenBLAS/ -j 4 fast-check + make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 LIBS="~/opt/gsl2/lib/libgsl.a ~/tmp/OpenBLAS/libopenblas_haswell-r0.3.0.dev.a ~/.guix-profile/lib/libgfortran.a ~/.guix-profile/lib/libquadmath.a -pthread -lz" OPENBLAS_INCLUDE_PATH=~/tmp/OpenBLAS/ -j 4 fast-check Note we don't include standard lapack, because it is 32-bits. |