diff --git a/docs.it4i/software/chemistry/gaussian.md b/docs.it4i/software/chemistry/gaussian.md index b700638cd743753661fee8908ce1e2d644e640ec..0a87206e3b907c58700a5400b1d1e5a118730e2d 100644 --- a/docs.it4i/software/chemistry/gaussian.md +++ b/docs.it4i/software/chemistry/gaussian.md @@ -16,7 +16,7 @@ not in direct or indirect competition with the Gaussian Inc. company and have a The license includes GPU support and Linda parallel environment for Gaussian multi-node parallel execution. !!! note - You need to be a member of the **gaussian group**. Contact support@it4i.cz in order to get included in the gaussian group. + You need to be a member of the **gaussian group**. Contact [support\[at\]it4i.cz][b] in order to get included in the gaussian group. Check your group membership: @@ -27,16 +27,19 @@ uid=1000(user) gid=1000(user) groups=1000(user),1234(open-0-0),7310(gaussian) ## Installed Version -Gaussian is available on Salomon, Barbora, and DGX-2 systems in the latest version Gaussian 16 rev. c0. +Gaussian is available on Anselm, Salomon, Barbora, and DGX-2 systems in the latest version Gaussian 16 rev. c0. -| Module | CPU support | GPU support | Parallelization | Note | -|--------------------------------------|-------------|--------------|-----------------|---------------------| -| Gaussian/16_rev_c0-binary | AVX2 | Yes | SMP | Binary distribution | -| Gaussian/16_rev_c0-binary-Linda | AVX2 | Yes | SMP + Linda | Binary distribution | -| Gaussian/16_rev_c0-CascadeLake | AVX-512 | No | SMP | IT4I compiled | -| Gaussian/16_rev_c0-CascadeLake-Linda | AVX-512 | No | SMP + Linda | IT4I compiled | +| Module | CPU support | GPU support | Parallelization | Note | Anselm | Barbora | Salomon | DGX-2 | +|--------------------------------------|-------------|--------------|-----------------|---------------------|---------|---------|---------|-------| +| Gaussian/16_rev_c0-binary | AVX2 | Yes | SMP | Binary distribution | No | Yes | Yes | Yes | +| Gaussian/16_rev_c0-binary-Linda | AVX2 | Yes | SMP + Linda | Binary distribution | No | Yes | Yes | No | +| Gaussian/16_rev_c0-CascadeLake | AVX-512 | No | SMP | IT4I compiled | No | Yes | No | No | +| Gaussian/16_rev_c0-CascadeLake-Linda | AVX-512 | No | SMP + Linda | IT4I compiled | No | Yes | No | No | +| Gaussian/16_rev_c0-GPU-Linda | AVX-512 | Yes | SMP + Linda | IT4I compiled | No | Yes | No | No | +| Gaussian/16_rev_c0-GPU | AVX-512 | Yes | SMP | IT4I compiled | No | No | No | Yes | +| Gaussian/16_rev_c0-Linda | AVX | No | SMP + Linda | IT4I compiled | Yes | No | No | No | -Speedup may be observed on Barbora supercomputer when using the `CascadeLake` module compared to the `binary` module. +Speedup may be observed on Barbora and DGX-2 systems when using the `CascadeLake` and `GPU` modules compared to the `binary` module. ## Running @@ -44,7 +47,7 @@ Gaussian is compiled for single node parallel execution as well as multi-node pa GPU support for V100 cards is available on Barbora and DGX-2. !!! note - By default, the execution is single-core, single node, without GPU acceleration. + By default, the execution is single-core, single-node, and without GPU acceleration. ### Shared-Memory Multiprocessor Parallel Execution (Single Node) @@ -71,7 +74,7 @@ $ ml Gaussian/16_rev_c0-binary-Linda The network parallelization environment is **Linda**. In the input file Link0 header section, set the CPU cores (24 for Salomon, 36 for Barbora, 48 for DGX-2) and memory amount. -Include the **%UseSSH keyword**, as well. This enables Linda to spawn parallel workers. +Include the `%UseSSH` keyword, as well. This enables Linda to spawn parallel workers. ```bash %CPU=0-35 @@ -81,8 +84,8 @@ Include the **%UseSSH keyword**, as well. This enables Linda to spawn parallel w The number and placement of Linda workers may be controlled by %LindaWorkers keyword or by GAUSS_WDEF environment variable. When running multi-node job via the PBS batch queue, loading -the Linda-enabled module **automaticaly sets the `GAUSS_WDEF` variable** to the correct node-list, using one worker per node. -In combination with the %CPU keyword, this enables a full scale multi-node execution. +the Linda-enabled module **automatically sets the `GAUSS_WDEF` variable** to the correct node-list, using one worker per node. +In combination with the %CPU keyword, this enables a full-scale multi-node execution. ```bash $ echo $GAUSS_WDEF @@ -100,10 +103,16 @@ Load Linda-enabled binary module $ ml Gaussian/16_rev_c0-binary-Linda ``` +Or GPU-enabled module + +```bash +$ ml Gaussian/16_rev_c0-GPU-Linda +``` + In the input file Link0 header section, set the CPU cores (24 for Barbora GPU nodes) and memory. -To enable GPU acceleration, set the **%GPUCPU** keyword. This keyword activates GPU accelerators and dedicates CPU cores to drive the GPU accelerators. -On Barbora GPU nodes, we activate GPUs 0-3 and assign cores 0,2,12,14 (two from each CPU socket) to drive the accelerators. -If multi node computation is intended, Include the **%UseSSH keyword**, as well. This enables Linda to spawn parallel workers. +To enable GPU acceleration, set the `%GPUCPU` keyword. This keyword activates GPU accelerators and dedicates CPU cores to drive the GPU accelerators. +On Barbora GPU nodes, we activate GPUs 0-3 and assign cores 0, 2, 12, 14 (two from each CPU socket) to drive the accelerators. +If multi-node computation is intended, include the `%UseSSH` keyword, as well. This enables Linda to spawn parallel workers. ```bash %CPU=0-23 @@ -112,14 +121,20 @@ If multi node computation is intended, Include the **%UseSSH keyword**, as well. %UseSSH ``` -GPU accelerated caclulations on the **DGX-2** are supported -with Gaussian binary module. +GPU accelerated calculations on the **DGX-2** are supported +with Gaussian binary module ```bash $ ml Gaussian/16_rev_c0-binary ``` -In the input file Link0 header section, modify the %CPU keyword to 48 cores and the %GPUCPU keyword to 16 GPU accelerators. Omit the Linda. +Or IT4I-compiled module + +```bash +$ ml Gaussian/16_rev_c0-GPU +``` + +In the input file Link0 header section, modify the `%CPU` keyword to 48 cores and the `%GPUCPU` keyword to 16 GPU accelerators. Omit the Linda. ```bash %CPU=0-47 @@ -149,8 +164,6 @@ WATER H20 optimization R 0.96 A 109.471221 - - ``` ### Run Gaussian (All Modes) @@ -225,4 +238,5 @@ exit [1]: ../../salomon/storage.md [a]: https://gaussian.com/gaussian16/ +[b]: mailto:support@it4i.cz [c]: https://gaussian.com/man/ \ No newline at end of file