diff --git a/docs/examples.rst b/docs/examples.rst index 99fbf2d..392ee66 100644 --- a/docs/examples.rst +++ b/docs/examples.rst @@ -73,13 +73,13 @@ acceleration, we refer to the Table as seen below. * - System - Execution time (averaged) - * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + * - Intel(R) Core(TM) i9-10900K (20 threads) - 172.58s - * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + RTX 4090 + * - Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090 - 90.18s - * - Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz (6 threads) + * - Intel(R) Core(TM) i5-8400 (6 threads) - 311.84s - * - Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz (6 threads) + RTX 2070 + * - Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070 - 125.08s Co HCP 11-21 @@ -196,7 +196,15 @@ acceleration, we refer to the Table as seen below. * - System - Execution time (averaged) - * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + * - Intel(R) Core(TM) i9-10900K (20 threads) - 5207.93s (1h26m47s) - * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + RTX 4090 + * - Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090 - 2368.63s (39m28s) + * - Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070 + - 2986.00s (49m46s) + * - Intel(R) Xeon(R) Gold 6234 (16 threads) + A5000 + - 3912.19 (65m12s) + * - Intel(R) Core(TM) i5-12400F (12 threads) + 1x GTX 1080 Ti + - 2759.49 (45m59s) + * - Intel(R) Core(TM) i5-12400F (12 threads) + 2x GTX 1080 Ti + - 2067.24s (34m27s) diff --git a/docs/execution_model.rst b/docs/execution_model.rst index f065dc2..7cc4274 100644 --- a/docs/execution_model.rst +++ b/docs/execution_model.rst @@ -9,6 +9,12 @@ acceleration to speed up the execution. This is especially beneficial when performing a similarity analysis. :program:`Bramble` supports multi-GPU setups, so one can use multiple GPUs if more than one GPU is available. +.. warning:: + :program:`Bramble` requires a GPU with at least 8Gb of memory. :program:`Bramble` + will check whether the GPU supports the calculation prior to execution and throws + an error when the GPU is not supported. You can also check the memory available + on your GPU by running ``bramblecuda``. + When performing the similarity analysis, an inventory of all the jobs is made. ``N+1`` OpenMP threads are being spawned where ``N`` equals the number of GPUs. Each GPU gets assigned a CPU thread and jobs are relayed to the GPU via the CPU diff --git a/docs/installation.rst b/docs/installation.rst index 59278ea..54090e2 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -23,7 +23,8 @@ On Debian-based operating systems, one can run the following:: The compilation instructions below can be readily used. .. warning:: - In order to compile for GPU using CUDA, one needs Eigen3 version **3.4.0** or higher. + * In order to compile for GPU using CUDA, one needs Eigen3 version **3.4.0** or higher. + * Your GPU needs at least 8Gb of memory in order to use Bramble. Compilation ----------- @@ -55,11 +56,9 @@ The similarity analysis functionality of :program:`Bramble` can benefit from the availability of a graphical card. To compile :program:`Bramble` with CUDA support, run CMake with:: - cmake ../src -DMOD_CUDA=1 -DCUDA_ARCH= + cmake ../src -DMOD_CUDA=1 -wherein `` is replaced with the architecture of your graphical card. For -example, if you use an RTX 4090, you would use ``-DCUDA_ARCH=sm_89``. To -test that :program:`Bramble` can use your GPU, you can run the ``bramblecuda`` +To test that :program:`Bramble` can use your GPU, you can run the ``bramblecuda`` tool whose sole function is to test for the availability of a GPU on the system:: ./bramblecuda @@ -127,3 +126,11 @@ Typical output should look as follows:: 100% tests passed, 0 tests failed out of 9 Total Test time (real) = 1.73 sec + +EasyBuild Installation +---------------------- + +For HPC infrastructure, there is also the option to install :program:`Bramble` using EasyBuild. +Make a copy of `bramble-1.1.0.eb` and run:: + + eb bramble-1.1.0.eb --minimal-toolchains --add-system-to-minimal-toolchains --robot