Commit 91c3144b authored by Lukáš Krupčík's avatar Lukáš Krupčík
Browse files

fix

parent 3d4c1886
# Singularity on IT4Innovations
On clusters we have different versions of operating systems singularity images. Below you see the available operating systems singularity images.
Our images bootstrap, wrappers, features are [here](https://code.it4i.cz/sccs/it4i-singularity).
```console
Salomon Anselm
......@@ -44,7 +45,7 @@ Open image and run command into image.
```console
$ ml CentOS/7.3
Your image of CentOS/7.3 is at location: /home/kru0052/.singularity/images/CentOS-7.3_20180220104046.img
Your image of CentOS/7.3 is at location: /home/login/.singularity/images/CentOS-7.3_20180220104046.img
image-exec cat /etc/centos-release
CentOS Linux release 7.3.1708 (Core)
```
......@@ -103,7 +104,7 @@ Your image of CentOS/6.9 is at location: /home/login/.singularity/images/CentOS-
!!! note
First usage image copy image from /apps/all/OS/... to your /home (.singularity/images)
For GPU and MIC image
For GPU and MIC images
```console
$ ml CentOS/6.9-GPU
......@@ -116,6 +117,94 @@ $ ml CentOS/6.9-MIC
!!! note
For the GPU image, you must allocate node with GPU card and for the MIC image, you must allocate node with the Intel Xeon Phi cards.
### Intel Xeon Phi Cards - MIC
For example submit job `qsub -A PROJECT -q qprod -l select=1:mpiprocs=24:accelerator=true -I`
!!! info
MIC image was prepared for only Salomon cluster
**Code for testing offload**
```c
#include <stdio.h>
#include <thread>
#include <stdlib.h>
#include <unistd.h>
int main() {
char hostname[1024];
gethostname(hostname, 1024);
unsigned int nthreads = std::thread::hardware_concurrency();
printf("Hello world, #of cores: %d\n",nthreads);
#pragma offload target(mic)
{
nthreads = std::thread::hardware_concurrency();
printf("Hello world from MIC, #of cores: %d\n",nthreads);
}
}
```
**Compile and run**
```console
[login@r38u03n975 ~]$ ml CentOS/6.9-MIC
Your image of CentOS/6.9-MIC is at location: /home/login/.singularity/images/CentOS-6.9-MIC_20180220112004.img
[login@r38u03n975 ~]$ image-shell
Singularity: Invoking an interactive shell within container...
Singularity CentOS-6.9-MIC_20180220112004.img:~> ml intel/2017b
Singularity CentOS-6.9-MIC_20180220112004.img:~> ml
Currently Loaded Modules:
1) GCCcore/6.3.0 3) icc/2017.1.132-GCC-6.3.0-2.27 5) iccifort/2017.1.132-GCC-6.3.0-2.27 7) iimpi/2017a 9) intel/2017a
2) binutils/2.27-GCCcore-6.3.0 4) ifort/2017.1.132-GCC-6.3.0-2.27 6) impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27 8) imkl/2017.1.132-iimpi-2017a
Singularity CentOS-6.9-MIC_20180220112004.img:~> icpc -std=gnu++11 -qoffload=optional hello.c -o hello-host
Singularity CentOS-6.9-MIC_20180220112004.img:~> ./hello-host
Hello world, #of cores: 24
Hello world from MIC, #of cores: 244
```
### GPU image
For example submit job `qsub -A PROJECT -q qnvidia -l select=1:ncpus=16:mpiprocs=16 -l walltime=01:00:00 -I`
!!! info
GPU image was prepared for only Anselm cluster
**Checking nvidia driver inside image**
```console
[login@cn187.anselm ~]$ ml CentOS/6.9-GPU
Your image of CentOS/6.9-GPU is at location: /home/login/.singularity/images/CentOS-6.9-GPU_20171024164243.img
[login@cn187.anselm ~]$ image-shell
Singularity: Invoking an interactive shell within container...
Singularity CentOS-6.9-GPU_20171024164243.img:~> nvidia-smi
Wed Mar 7 14:35:40 2018
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 384.111 Driver Version: 384.111 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 Tesla K20m Off | 00000000:02:00.0 Off | 0 |
| N/A 37C P0 54W / 225W | 0MiB / 4742MiB | 87% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
```
### MPI
For example submit job `qsub -A PROJECT -q qprod -l select=2:mpiprocs=24 -l walltime=00:30:00 -I`
......@@ -151,7 +240,7 @@ Singularity CentOS-6.9_20180220092823.img:~> mpirun hostname | wc -l
```console
$ ml CentOS/6.9
Your image of CentOS/6.9 is at location: /home/kru0052/.singularity/images/CentOS-6.9_20180220092823.img
Your image of CentOS/6.9 is at location: /home/login/.singularity/images/CentOS-6.9_20180220092823.img
$ image-mpi hostname | wc -l
48
```
......
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