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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`
=> https://servicedesk.surf.nl/wiki/pages/viewpage.action?pageId=30660265#FAQSnellius/Lisa-systemfromabroad login from abroad
## 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
```sh
#!/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
```
|
