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calcoloscientifico:userguide [27/09/2024 15:31] – [Table] federico.prostcalcoloscientifico:userguide [21/05/2025 17:34] (versione attuale) – [Table] fabio.spataro
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 <note>The first connection with SSH must be made after activating the VPN</note> <note>The first connection with SSH must be made after activating the VPN</note>
  
-NOTE: Please, in scientific publications add: +<note> Please, in scientific publications add: "This research benefits from the High Performance Computing facility of the University of Parma, Italy (HPC.unipr.it)".</note>
- "This research benefits from the High Performance Computing facility of the University of Parma, Italy (HPC.unipr.it)" .+
  
  
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 | wn48       | NVIDIA Corporation Device 2231 [RTX A5000 24GB] (rev a1)    | | wn48       | NVIDIA Corporation Device 2231 [RTX A5000 24GB] (rev a1)    |
 | wn49-wn50  | NVIDIA Corporation Device 26b9 [L40S 48GB] (rev a1)         | | wn49-wn50  | NVIDIA Corporation Device 26b9 [L40S 48GB] (rev a1)         |
 +| wn51       | NVIDIA Corporation Device 2321 [H100 NVL 96GB] (rev a1)     |
  
 **Peak Performance** **Peak Performance**
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 | cpu_guest       | cpu_guest       | wn[20-26]              |   440 core |   1-00:00:00 |           24 |         200 |          4 | Guest     | | cpu_guest       | cpu_guest       | wn[20-26]              |   440 core |   1-00:00:00 |           24 |         200 |          4 | Guest     |
 | gpu             | gpu             | wn[41-42,44-45]        |     24 gpu |   1-00:00:00 |            6 |        2000 |          4 | Public    | | gpu             | gpu             | wn[41-42,44-45]        |     24 gpu |   1-00:00:00 |            6 |        2000 |          4 | Public    |
-| gpu_vbd         | gpu_vbd         | wn[46,49]              |     12 gpu |  14-00:00:00 |            6 |        2000 |          2 | Private   |+| gpu_vbd         | gpu_vbd         | wn[46,49,51]           |     14 gpu |  14-00:00:00 |            6 |        2000 |          2 | Private   |
 | gpu_hylab       | gpu_hylab       | wn44                   |      4 gpu |   3-00:00:00 |            4 |        2000 |          1 | Private   | | gpu_hylab       | gpu_hylab       | wn44                   |      4 gpu |   3-00:00:00 |            4 |        2000 |          1 | Private   |
 +| gpu_fisstat     | gpu_fisstat     | wn50                   |      4 gpu |   7-00:00:00 |            4 |        2000 |          1 | Private   |
 | gpu_guest       | gpu_guest       | wn[44,46]              |      8 gpu |   1-00:00:00 |            6 |         200 |          2 | Guest     | | gpu_guest       | gpu_guest       | wn[44,46]              |      8 gpu |   1-00:00:00 |            6 |         200 |          2 | Guest     |
-| knl             | knl             | wn[51-54]              |  1088 core |  14-00:00:00 |           16 |        2000 |          4 | Public    | 
 | vrt             | vrt             | wn[61-64]              |     1 core |  10-00:00:00 |           24 |        2000 |          1 | Public    | | vrt             | vrt             | wn[61-64]              |     1 core |  10-00:00:00 |           24 |        2000 |          1 | Public    |
 | mngt            |                 | all                    |            | UNLIMITED    |              |             |            | Admin     | | mngt            |                 | all                    |            | UNLIMITED    |              |             |            | Admin     |
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 hpc-sinfo-cpu --partition=cpu hpc-sinfo-cpu --partition=cpu
 hpc-sinfo-cpu --partition=cpu_guest hpc-sinfo-cpu --partition=cpu_guest
-hpc-sinfo-cpu --partition=knl 
 hpc-sinfo-gpu --partition=gpu hpc-sinfo-gpu --partition=gpu
 hpc-sinfo-gpu --partition=gpu_guest hpc-sinfo-gpu --partition=gpu_guest
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 hpc-squeue --partition=cpu hpc-squeue --partition=cpu
 hpc-squeue --partition=cpu_guest hpc-squeue --partition=cpu_guest
-hpc-squeue --partition=knl 
 hpc-squeue --partition=gpu hpc-squeue --partition=gpu
 hpc-squeue --partition=gpu_guest hpc-squeue --partition=gpu_guest
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 <code> <code>
 srun --nodes=1 --nodelist=wn34 --pty bash srun --nodes=1 --nodelist=wn34 --pty bash
-</code> 
- 
-Reserve 1 chunk of 272 CPUs type KNL (a whole KNL node): 
-<code bash> 
-srun --nodes=1 --ntasks-per-node=272 --partition=knl --qos=knl --mem=8G --pty bash 
 </code> </code>
  
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 sbatch matrix-vector-product.sh sbatch matrix-vector-product.sh
 </code> </code>
- 
-=====  KNL jobs ===== 
- 
-The compiler to be used is Intel. 
- 
-The selection of the KNL cluster is done by specifying ''-p knl''. 
- 
-Each knl node includes 68  physical core and each physical core includes 4 virtual cores with hyperthreading technology. The maximum number of cores (ncpus) selectable per node is 272. 
- 
-MPI + OpenMP example on KNL: 
- 
-   cp /hpc/share/samples/mpi+omp/mpiomp_hello.c . 
- 
-<code c mpiomp_hello.c> 
-#include <stdio.h> 
-#include <mpi.h> 
-#include <omp.h> 
- 
-int main(int argc, char *argv[]) { 
-  int numprocs, rank, namelen; 
-  char processor_name[MPI_MAX_PROCESSOR_NAME]; 
-  int iam = 0, np = 1; 
- 
-  MPI_Init(&argc, &argv); 
-  MPI_Comm_size(MPI_COMM_WORLD, &numprocs); 
-  MPI_Comm_rank(MPI_COMM_WORLD, &rank); 
-  MPI_Get_processor_name(processor_name, &namelen); 
- 
-#pragma omp parallel default(shared) private(iam, np) 
-  { 
-    np = omp_get_num_threads(); 
-    iam = omp_get_thread_num(); 
-    printf("Hello from thread %3d out of %3d from process %3d out of %3d on %s\n", 
-           iam + 1, np, rank + 1, numprocs, processor_name); 
-  } 
- 
-  MPI_Finalize(); 
-} 
-</code> 
- 
-Sumbission script ''mpiomp_hello_knl.bash'' 
- 
-<code bash mpiomp_hello_knl.bash> 
-#!/bin/sh 
- 
-#< 2  nodes. Executes 1 MPI process per node and 68 threads per process 
- 
-#SBATCH --partition=knl 
-#SBATCH --qos=knl 
-#SBATCH --nodes=2 
-#SBATCH --ntasks=2 
-#SBATCH --cpus-per-task=68      #< Number of threads OpenMP for each process MPI 
-#SBATCH --time=0-00:30:00 
-#SBATCH --mem=4G 
- 
-## Uncomment the following line if you want to use an account other than your default account  
-##SBATCH --account=<account>  
-  
-export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK 
- 
-module load intel intelmpi 
-mpicc -qopenmp mpiomp_hello.c -o mpiomp_hello_knl 
-mpirun mpiomp_hello_knl 
-</code> 
- 
-===Submission=== 
- 
-  sbatch mpiomp_hello_knl.bash  
  
 ===== GPU jobs =====  ===== GPU jobs ===== 
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 ===== Applications ===== ===== Applications =====
 +
 +==== Alphafold ==== 
 +
 +[[calcoloscientifico:userguide:alphafold|{{:calcoloscientifico:userguide:alphafold.jpg?nolink&200|Alphafold}}]]
  
 ==== Mathematica ====  ==== Mathematica ==== 
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 [[calcoloscientifico:cluster:softwareapplicativo:fds|FDS]] [[calcoloscientifico:cluster:softwareapplicativo:fds|FDS]]
- 
  
 ==== SRA Toolkit ==== ==== SRA Toolkit ====
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 [[calcoloscientifico:userguide:castep|{{:calcoloscientifico:userguide:castep.jpg?nolink&200|castep}}]] [[calcoloscientifico:userguide:castep|{{:calcoloscientifico:userguide:castep.jpg?nolink&200|castep}}]]
 +
 +==== GAMESS ====
 +
 +[[calcoloscientifico:userguide:gamess|{{:calcoloscientifico:userguide:gamess.jpg?nolink&200|gamess}}]]
 +
 +==== Blender ====
 +
 +[[calcoloscientifico:userguide:blender|{{:calcoloscientifico:userguide:blender.jpg?nolink&200|blender}}]]
  
 ===== Libraries ==== ===== Libraries ====
calcoloscientifico/userguide.1727443904.txt.gz · Ultima modifica: da federico.prost
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