Installation

gensep is a single self-contained C++17 command-line tool. There is no external library to install: Eigen is header-only and vendored under third_party/, and the program links statically. Use the prebuilt binary, or build from source with a plain make.

1. Prebuilt Linux executable #

A statically compiled executable for 64-bit Linux systems is available: gensep Linux Executable. It has no runtime dependencies (ldd ./gensep → “not a dynamic executable”), so it can be used directly on compatible systems:

chmod +x gensep
./gensep --help

This is the quickest option. To modify the code or rebuild for your environment, build from source instead (below).

2. Prerequisites #

• A C++17 compiler that can produce a static binary. The Makefile pins the system GCC (/usr/bin/g++) because it ships static libc / libm / libstdc++; the conda toolchain usually does not, so -static fails there.
• GNU make.
• (Optional) bash, to run the regression test suite.

No MKL, no BLAS, no Boost — the numerics use vendored header-only Eigen.

3. Build from source #

cd code/gensep
make            # -> ./gensep

make compiles everything under src/ and links a single executable, ./gensep. The binary is fully static (ldd ./gensep → “not a dynamic executable”, ~1.2 MB stripped), so it runs on any compatible Linux host with no runtime dependencies.

Overriding the compiler #

If the pinned /usr/bin/g++ is not what you want, override CXX on the command line:

make CXX=/path/to/your/g++

Note that the compiler you choose must be able to satisfy -static -static-libstdc++ -static-libgcc; otherwise the final link step will fail.

Threads (OpenMP) #

OpenMP is on by default, and the binary stays fully static. It runs single-threaded unless you ask for more with --max-threads N at run time (which parallelizes the block-jackknife loop across N cores) — no separate build needed. Each leave-one-block heritability solve is warm-started from the full-data fit, so it is already fast single-threaded. To build with no OpenMP at all:

make OMP=0

Eigen location #

Eigen is expected at third_party/eigen. In this repository that is a symlink to the Eigen copy vendored with fastgxe. If you relocate the project, point EIGEN at your Eigen headers:

make EIGEN=/path/to/eigen

The Makefile deliberately uses CXXFLAGS := (not ?=) so that a CXXFLAGS exported by a conda activate script cannot silently drop -Ithird_party/eigen.

4. Quick validation #

Confirm the executable starts and prints its usage:

./gensep --help

You should see the --se-method <jackknife|mc|delta|none> synopsis.

5. Run the regression tests #

A minimal, data-free regression suite is included. It exercises the three point-mode SE methods, point-value correctness, Monte-Carlo determinism, and every input-validation guard (bad numbers, negative SEs, --num-draws 0, malformed tagfile, …):

make test

All checks should report PASS and the run ends with N passed, 0 failed.

6. Troubleshooting #

• -static link errors (e.g. “cannot find -lc”): your compiler lacks the static runtime libraries. Use the system GCC (make CXX=/usr/bin/g++, the default) rather than a conda toolchain, or install the static glibc/libstdc++ packages.
• -Ithird_party/eigen seems ignored / Eigen headers not found: check that third_party/eigen exists (or pass make EIGEN=...), and make sure no environment CXXFLAGS is interfering.
• Rebuild from scratch: make clean && make.