Commit 170b1a2e authored by Ondrej Tichacek's avatar Ondrej Tichacek
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Update file README.md

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@@ -64,13 +64,13 @@ srun gmx_mpi mdrun -deffnm ${NAME} -nsteps -1 -v -maxh 1

```

## General parameters of all tests (1-5)
## 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.
- **tpr file:** sys1_150k_gmx2024.tpr 
- **Number atoms:** 149261


## Tests 1-4 (SCALING over network)
## Tests 1 (SCALING over network)
- **Special test conditions:**
   - All tasks in the test need to be run sequentially without interruption to ensure that some jobs eventually use nodes placed in different sections of the cluster.
   - Only 36 cores can be used for each node in this test.
@@ -79,7 +79,7 @@ srun gmx_mpi mdrun -deffnm ${NAME} -nsteps -1 -v -maxh 1
- **Short description of the test**: Full (36 cores max) occupation of the computational nodes using 1 or more nodes per job. There might be few unallocated nodes if the number of computational nodes is not a multiple of number of computational nodes per job in each task.
- **Storage for tasks:** This test must try all 5 different NFS shares in storage1, storage2, scratch1,  scratch2, cryo2.

### 1. Tests scaling in the cpu nodes
### 1.1 Tests scaling in the cpu nodes
- **Test name:** scaling_test_cpu
- **Nodes involved**: cpu computational nodes
- **Number of tasks:** 11 x 5
@@ -99,7 +99,7 @@ srun gmx_mpi mdrun -deffnm ${NAME} -nsteps -1 -v -maxh 1
- **Minimal performance 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 higher than 80% of the value obtained with our older aurum cluster.

## 2. Tests scaling in the bigmem nodes
### 1.2 Tests scaling in the bigmem nodes
- **Test name:**: scaling_test_mem
- **Nodes involved**: big memory cpu computational nodes
- **Number of tasks:** 2 x 5
@@ -119,7 +119,7 @@ The results for the same number of nodes with the number of cores per node restr
The results for the same number of nodes with the number of cores per node restricted to 36 should be at least higher than 80% of the value obtained with our older aurum cluster.


## 3. Tests scaling in the gpu nodes
## 1.3 Tests scaling in the gpu nodes
- **Test name:**: scaling_test_gpu
- **Nodes involved**: gpu computational nodes
- **Number of tasks:** 2 x 5
@@ -142,7 +142,7 @@ The results for the same number of nodes with the number of cores per node restr



## 4. Tests scaling in the biggpu nodes (CPU only)
## 1.4 Tests scaling in the biggpu nodes (CPU only)
- **Test name:**: scaling_test_biggpu
- **Nodes involved**: gpu computational nodes
- **Number of tasks:** 5 x 5
@@ -162,7 +162,7 @@ The results for the same number of nodes with the number of cores per node restr
The results for the same number of nodes with the number of cores per node restricted to 36 should be at least higher than 80% of the value obtained with our older aurum cluster.


## 5. Test endurance cluster - not internode calculations
## 2. Test endurance cluster - not internode calculations
- **Test name:**: endurance_test_all
- **Short description of the test:** Full occupation of all nodes (cpu, mem, gpu, and biggpu) using 1 job per node in cpu and mem nodes, and n jobs per nodes in the gpu and biggpunodes. It is a stress test where all the clusters should work under full load for at least 23h.
- **Number of tasks:** 1