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Snellius

Login to head node

After adding your ssh key to

https://portal.cua.surf.nl/

Use `ssh user@doornode.surfsara.nl`

Stats

sinfo -s
PARTITION AVAIL  TIMELIMIT   NODES(A/I/O/T) NODELIST
thin*        up 5-00:00:00     483/27/8/518 tcn[5-522]
course       up 5-00:00:00          0/1/1/2 tcn[1,4]
fat          up 5-00:00:00        68/4/0/72 fcn[1-72]
gpu          up 5-00:00:00       53/14/2/69 gcn[4-72]
gpu_vis      up 1-00:00:00       53/14/2/69 gcn[4-72]
himem_4tb    up 5-00:00:00          0/2/0/2 hcn[1-2]
himem_8tb    up 5-00:00:00          0/2/0/2 hcn[3-4]
staging      up 5-00:00:00          3/4/0/7 srv[1-7]
cbuild       up 5-00:00:00          0/2/0/2 srv[1-2]

Test build

git clone https://github.com/smarco/WFA2-lib.git
cd WFA2-lib/
mkdir build
cd build
cmake ..
make
make test
Running tests...
Test project /home/prins/WFA2-lib/build
    Start 1: wfa2lib
1/1 Test #1: wfa2lib ..........................   Passed    0.16 sec

100% tests passed, 0 tests failed out of 1

using gcc version 8.5.0 20210514.

Run a test script

Write a batch script using the hints from

https://servicedesk.surf.nl/wiki/display/WIKI/SLURM+batch+system

#!/bin/bash
#SBATCH -t 00:01:00
#SBATCH -N 1
pwd
ls -l

submit the job with

sbatch my_job.sh
Submitted batch job 2328193

and

[prins@int5 build]$ cat slurm-2328193.out
/gpfs/home4/prins/WFA2-lib/build
total 622
-rw-r--r-- 1 prins prins  17487 Feb 28 10:41 CMakeCache.txt
drwxr-xr-x 8 prins prins   4096 Feb 28 10:42 CMakeFiles
-rw-r--r-- 1 prins prins    545 Feb 28 10:41 CTestTestfile.cmake
-rw-r--r-- 1 prins prins  64644 Feb 28 10:41 Makefile
drwxr-xr-x 3 prins prins   4096 Feb 28 10:42 Testing
-rw-r--r-- 1 prins prins   9065 Feb 28 10:41 cmake_install.cmake
-rw-r--r-- 1 prins prins 274742 Feb 28 10:42 libwfa2.a
lrwxrwxrwx 1 prins prins     12 Feb 28 10:42 libwfa2.so -> libwfa2.so.0
-rwxr-xr-x 1 prins prins 185672 Feb 28 10:42 libwfa2.so.0
-rw-r--r-- 1 prins prins  18322 Feb 28 10:42 libwfa2cpp.a
lrwxrwxrwx 1 prins prins     15 Feb 28 10:42 libwfa2cpp.so -> libwfa2cpp.so.0
-rwxr-xr-x 1 prins prins  27032 Feb 28 10:42 libwfa2cpp.so.0
-rw-r--r-- 1 prins prins     55 Feb 28 10:51 my_job.sh
-rw-r--r-- 1 prins prins     33 Feb 28 10:52 slurm-2328193.out
JOB STATISTICS
==============
Job ID: 2328193
Cluster: snellius
User/Group: prins/prins
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 32
CPU Utilized: 00:00:00
CPU Efficiency: 0.00% of 00:04:16 core-walltime
Job Wall-clock time: 00:00:08
Memory Utilized: 1.62 MB
Memory Efficiency: 0.00% of 56.00 GB