diff options
| -rw-r--r-- | topics/hpc/surfsara/snellius.gmi | 103 | ||||
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 7 |
2 files changed, 110 insertions, 0 deletions
diff --git a/topics/hpc/surfsara/snellius.gmi b/topics/hpc/surfsara/snellius.gmi new file mode 100644 index 0000000..ef43853 --- /dev/null +++ b/topics/hpc/surfsara/snellius.gmi @@ -0,0 +1,103 @@ +# 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 +``` diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi new file mode 100644 index 0000000..7ac7eeb --- /dev/null +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -0,0 +1,7 @@ +# Precompute mapping input data + +The original reaper precompute lives in + +=> https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/QTL_Reaper_v6.py + +This script first fetches |