Update file README.md

- The results of the tests if not performed by the client must be provided for inspection to ensure their validity.

- The tests have to be performed using Gromacs 2024.3 or newer - The program has a GPLv3 license and can be downloaded for free from the following [page](http://www.Gromacs.org/).

## General terms and abbreviations:

- Number of Nodes and their types

   - $N_{cpu}$ = Total number of computational nodes

   - $N_{mem}$ = Total number of big memory nodes

   - $N_{gpu}$ = Total number of GPU nodes

   - $N_{biggpu}$ = Total number of GPU-mem nodes

   - $N = N_{cpu}+N_{mem}+N_{gpu}+N_{biggpu}$= Total number of nodes in the cluster

   - $N^{test}_{task,job}$ = Number of nodes to be used in a job for a given task belonging to a test

- Number of jobs required to run simultaneously within a task

   - $J_{cpu}^{max} = \text{floor integer part of } (N_{cpu}/N^{test}_{task,job})$ (Maximum number of simultaneous jobs in a task using computing nodes)

   - $J_{mem}^{max} = \text{floor integer part of } (N_{mem}/N^{test}_{task,job})$ (Maximum number of simultaneous jobs in a task using big memory nodes

   - $J_{gpu}^{max} = \text{floor integer part of } (N_{gpu}/N^{test}_{task,job})$ (Maximum number of simultaneous jobs in a task using gpu nodes)

   - $J_{biggpu}^{max} = \text{floor integer part of } (N_{gpu}/N^{test}_{task,job})$ (Maximum number of simultaneous jobs in a task using gpu nodes)

## Template submission in slurm of a gromacs job for 1 hour

```bash

```

## General parameters of all tests (1 and 2)

- **Short description of the system**:  Molecular dynamics simulation of membrane interacting with a peripheral protein system in Gromacs.

- **Short description of the system:**  Molecular dynamics simulation of membrane interacting with a peripheral protein system in Gromacs.

- **tpr file:** sys1_150k_gmx2024.tpr 

- **Number atoms:** 149261

## Tests 1 (SCALING over network)

**Short description of the test**: Full (36 cores max) occupation of the computational nodes using 1 or more nodes per job.

**Short description of the test:** Full (36 cores max) occupation of the computational nodes using 1 or more nodes per job.

Tests 1.1 - 1.4 test performance scaling over multple nodes over the low-latency network. The tests 1.1 - 1.4 are identical, but target different sets of nodes (1.1 = cpu nodes, 1.2 = bigmem nodes, 1.3 = gpu nodes, 1.4 gpu-mem nodes). The tests 1.1 - 1.4 will be performed independently.

Each test consists of several tasks, defined by the "scaling factor", which is the number of computational nodes involved in each gromacs job.

The number of computational nodes per job in each task will be set to [1, 2, 4, 6, 8, 10, 12, 14, 16, 18 and 20] nodes (limited to the delivered number of nodes in tests 1.2 and 1.4.). Multiple jobs per task will be launched simultaneously such that the partition (cpu / bigmem / gpu / big-gpu) is filled as much as possible.

Tests 1.1 - 1.4 test performance scaling over multple nodes over the low-latency network. The tests 1.1 - 1.4 are identical, but target different sets of nodes (1.1 = cpu nodes, 1.2 = bigmem nodes, 1.3 = gpu nodes, 1.4 gpu-mem nodes).

The following results were obtained for the current cluster (2 x Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz per node).

| ------ | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

| ns/day |  13 |  25 |  48 |  71 |  90 | 104 | 130 | 152 | 167 | 175 | 188 |

The number of computational nodes per job in each task will be set to [1, 2, 4, 6, 8, 10, 12, 14, 16, 18 and 20] nodes (limited to the delivered number of nodes in tests 1.2 and 1.4.)

**Minimal required performance for passing each of the tests 1.1-1.4**:

**Minimal required performance for passing each of the tests 1.1-1.4:**

For each job, the results for the same number of nodes with the number of cores per node restricted to 36 should be at least 80% of the value obtained with our older aurum cluster, in the table above. For example, a job involving 10 nodes (360 cores) must report at least 0.8*104 = 83.2 ns/day.

**Aditional notes**

### 1.1 Tests scaling in the cpu nodes

- **Test name:** scaling_test_cpu

- **Results**:

- **Results:**

| Cores (Nodes)   |  36 (1) |  72 (2) | 144 (4) | 216 (6) | 288 (8) | 360 (10) | 432 (12) | 504 (14) | 576 (16)| 648 (18)| 720 (20)|

| ------ | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

### 1.2 Tests scaling in the bigmem nodes

- **Test name:** scaling_test_mem

- **Results**:

- **Results:**

| Cores (Nodes)   |  36 (1) |  72 (2) | 

| ------ | --- | --- |

### 1.3 Tests scaling in the gpu nodes

- **Test name:** scaling_test_gpu

- **Results**:

- **Results:**

| Cores (Nodes)   |  36 (1) |  72 (2) | 144 (4) | 216 (6) | 288 (8) | 360 (10) | 432 (12) | 504 (14) | 576 (16)| 648 (18)| 720 (20)|

| ------ | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |

### 1.4 Tests scaling in the gpu-mem nodes

- **Test name:** scaling_test_biggpu

- **Results**:

- **Results:**

| Cores (Nodes)   |  36 (1) |  72 (2) | 144 (4) | 216 (6) | 288 (8) |

| ------ | --- | --- | --- | --- | --- |