From 077dc48c8f4542a79e1499120a7508be1e5d19d4 Mon Sep 17 00:00:00 2001
From: Jan Siwiec <jan.siwiec@vsb.cz>
Date: Fri, 11 Feb 2022 08:44:10 +0100
Subject: [PATCH] Delete mic_environment.md
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-# Intel Xeon Phi Environment
-
-The Intel Xeon Phi (so-called MIC) accelerator can be used in several modes ([Offload][1] and [Native][2]). The default mode on the cluster is the offload mode, but all modes described in this document are supported.
-
-For more details, see the sections below.
-
-## Intel Utilities for Xeon Phi
-
-Continue [here][3].
-
-## GCC With KNC Support
-
-On Salomon, we have the `GCC/5.1.1-knc` module with cross-compiled (offload) support for [KNC][a]. (gcc, g++ and gfortran)
-
-!!! warning
- Available on Salomon only.
-
-To compile a code using GCC compiler, run the following commands:
-
-* Create `reduce_mul.c`:
-
-```console
-$ vim reduce_mul.c
-```
-
-```c
-#include <immintrin.h>
-
-double reduce(double* values)
-{
- __m512d val = _mm512_load_pd(values);
- return _mm512_reduce_mul_pd(val);
-}
-```
-
-* Create `main.c`:
-
-```console
-vim main.c
-```
-
-```c
-#include <immintrin.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-double reduce(double* values);
-
-int main(int argc, char* argv[])
-{
- // Generate random input vector of [-1, 1] values.
- double values[8] __attribute__((aligned(64)));
- for (int i = 0; i < 8; i++)
- values[i] = 2 * (0.5 - rand() / (double)RAND_MAX);
-
- double vector = reduce(values);
- double scalar = values[0];
- for (int i = 1; i < 8; i++)
- scalar *= values[i];
-
- printf("%f vs %f\n", vector, scalar);
-
- fflush(stdout);
-
- return 0;
-}
-```
-
-* Compile:
-
-```console
-$ ml GCC/5.1.1-knc
-$ gcc -mavx512f -O3 -c reduce_mul.c -o reduce_mul.s -S
-$ gcc -O3 -c reduce_mul.s -o reduce_mul.o
-$ gcc -std=c99 -O3 -c main.c -o main_gcc.o
-$ gcc -O3 reduce_mul.o main_gcc.o -o reduce_mul
-```
-
-* To execute the code, run the following command on the host:
-
-```console
-$ micnativeloadex ./reduce_mul
--0.004276 vs -0.004276
-```
-
-## Native Mode
-
-In the native mode, a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.
-
-To compile code, the user has to be connected to a compute node with MIC and load the Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module, use following commands:
-
-```console
-$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True -A NONE-0-0
-$ ml intel/2017b
-```
-
-To produce a binary compatible with the Intel Xeon Phi architecture, the user has to specify the `-mmic` compiler flag. Two compilation examples are shown below. The first example shows how to compile the OpenMP parallel code `vect-add.c` for host only:
-
-```c
-#include <stdio.h>
-
-typedef int T;
-
-#define SIZE 1000
-
-#pragma offload_attribute(push, target(mic))
-T in1[SIZE];
-T in2[SIZE];
-T res[SIZE];
-#pragma offload_attribute(pop)
-
-// MIC function to add two vectors
-__attribute__((target(mic))) add_mic(T *a, T *b, T *c, int size) {
- int i = 0;
- #pragma omp parallel for
- for (i = 0; i < size; i++)
- c[i] = a[i] + b[i];
-}
-
-// CPU function to add two vectors
-void add_cpu (T *a, T *b, T *c, int size) {
- int i;
- for (i = 0; i < size; i++)
- c[i] = a[i] + b[i];
-}
-
-// CPU function to generate a vector of random numbers
-void random_T (T *a, int size) {
- int i;
- for (i = 0; i < size; i++)
- a[i] = rand() % 10000; // random number between 0 and 9999
-}
-
-// CPU function to compare two vectors
-int compare(T *a, T *b, T size ){
- int pass = 0;
- int i;
- for (i = 0; i < size; i++){
- if (a[i] != b[i]) {
- printf("Value mismatch at location %d, values %d and %dn",i, a[i], b[i]);
- pass = 1;
- }
- }
- if (pass == 0) printf ("Test passedn"); else printf ("Test Failedn");
- return pass;
-}
-
-int main()
-{
- int i;
- random_T(in1, SIZE);
- random_T(in2, SIZE);
-
- #pragma offload target(mic) in(in1,in2) inout(res)
- {
-
- // Parallel loop from main function
- #pragma omp parallel for
- for (i=0; i<SIZE; i++)
- res[i] = in1[i] + in2[i];
-
- // or parallel loop is called inside the function
- add_mic(in1, in2, res, SIZE);
-
- }
-
- //Check the results with CPU implementation
- T res_cpu[SIZE];
- add_cpu(in1, in2, res_cpu, SIZE);
- compare(res, res_cpu, SIZE);
-
-}
-```
-
-```console
-$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host
-```
-
-* To run this code on host, use:
-
-```console
-$ ./vect-add-host
-Test passed
-```
-
-* The second example shows how to compile the same code for Intel Xeon Phi:
-
-```console
-$ icc -mmic -fopenmp vect-add.c -o vect-add-mic
-```
-
-* Execution of the Program in Native Mode on Intel Xeon Phi:
-
-The user access to the Intel Xeon Phi is through the SSH. Since user home directories are mounted using NFS on the accelerator, users do not have to copy binary files or libraries between the host and accelerator. Get the PATH of MIC enabled libraries for currently used Intel Compiler.
-
-* To run this code on Intel Xeon Phi:
-
-```console
-$ ssh mic0
-$ ./vect-add-mic
-./vect-add-mic: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
-$ export LD_LIBRARY_PATH=LD_LIBRARY_PATH:/apps/all/icc/2017.4.196-GCC-6.4.0-2.28/compilers_and_libraries/linux/lib/mic
-$ ./vect-add-mic
-Test passed
-```
-
-!!! tip
- Alternatively, use the procedure from the [Devel Environment][4] chapter.
-
-## Only Intel Xeon Phi Cards
-
-Execute a native job:
-
-```console
-$ qsub -A NONE-0-0 -q qmic -l select=1 -l walltime=10:00:00 -I
-r21u01n577-mic1:~$
-```
-
-## Devel Environment
-
-To get an overview of the currently loaded modules, use `module list` or `ml` (without specifying extra arguments):
-
-```console
-r21u02n578-mic0:~$ ml
-No modules loaded
-```
-
-To get an overview of all available modules, you can use `ml avail` or simply `ml av`:
-
-```console
-r21u02n578-mic0:~$ ml av
-
--------------- /apps/phi/system/devel --------------------------
- devel_environment/1.0 (S)
-
- Where:
- S: Module is Sticky, requires --force to unload or purge
-
-```
-
-Activate devel environment:
-
-```console
-r21u02n578-mic0:~$ ml devel_environment
-```
-
-And again to get an overview of all available modules, you can use `ml avail` or simply `ml av`:
-
-```console
-r21u02n578-mic0:~$ ml av
-
--------------- /apps/phi/modules/compiler --------------------------
- icc/2017.4.196-GCC-6.4.0-2.28
-
--------------- /apps/phi/modules/devel --------------------------
- M4/1.4.18 devel_environment/1.0 (S) ncurses/6.0
-
--------------- /apps/phi/modules/lang --------------------------
- Bison/3.0.4 Tcl/8.6.6 flex/2.6.4
-
--------------- /apps/phi/modules/lib --------------------------
- libreadline/7.0 zlib/1.2.11
-
--------------- /apps/phi/modules/math --------------------------
- Octave/3.8.2
-
--------------- /apps/phi/modules/mpi --------------------------
- impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28
-
--------------- /apps/phi/modules/toolchain --------------------------
- iccifort/2017.4.196-GCC-6.4.0-2.28 ifort/2017.4.196-GCC-6.4.0-2.28
-
--------------- /apps/phi/modules/tools --------------------------
- bzip2/1.0.6 cURL/7.53.1 expat/2.2.5
-
--------------- /apps/phi/modules/vis --------------------------
- gettext/0.19.8
-
- Where:
- S: Module is Sticky, requires --force to unload or purge
-
-```
-
-After loading the `devel_environment` module, modules for the k1om-mpss-linux architecture become available and system software (GCC, CMake, Make, Git, htop, Vim...) can be used.
-
-* Example
-
-```console
-r21u02n578-mic0:~$ gcc --version
-gcc (GCC) 5.1.1
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions. There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
-@r21u02n578-mic0:~$ cmake --version
-cmake version 2.8.7
-
-r21u02n578-mic0:~$ git --version
-git version 1.7.7
-
-r21u02n578-mic0:~$ make --version
-GNU Make 3.82
-Built for k1om-mpss-linux-gnu
-Copyright (C) 2010 Free Software Foundation, Inc.
-License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
-This is free software: you are free to change and redistribute it.
-There is NO WARRANTY, to the extent permitted by law.
-
-r21u02n578-mic0:~$ perl --version
-
-This is perl 5, version 14, subversion 2 (v5.14.2) built for k1om-linux
-
-Copyright 1987-2011, Larry Wall
-
-Perl may be copied only under the terms of either the Artistic License or the
-GNU General Public License, which may be found in the Perl 5 source kit.
-
-Complete documentation for Perl, including FAQ lists, should be found on
-this system using "man perl" or "perldoc perl". If you have access to the
-Internet, point your browser at http://www.perl.org/, the Perl Home Page.
-
-...
-```
-
-* Execute previous cross-compiled code `vect-add-mic`
-
-```console
-r21u01n577-mic1:~$ ml devel_environment
-r21u01n577-mic1:~$ ml icc
-r21u01n577-mic1:~$ ./vect-add-mic
-Test passed
-```
-
-!!! tip
- PATH of MIC libraries for Intel Compiler is set automatically.
-
-## Modules
-
-Examples for modules.
-
-### MPI
-
-Load the `devel_environment` and the `impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28` (`intel/2017b`) modules.
-
-Execute the test:
-
-```console
-$ qsub -A SERVICE -q qmic -l select=4 -l walltime=01:00:00 -I
-r21u01n577-mic0:~$ ml devel_environment
-r21u01n577-mic0:~$ ml impi
-r21u01n577-mic0:~$ ml
-
-Currently Loaded Modules:
- 1) devel_environment/1.0 (S) 3) ifort/2017.4.196-GCC-6.4.0-2.28 5) impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28
- 2) icc/2017.4.196-GCC-6.4.0-2.28 4) iccifort/2017.4.196-GCC-6.4.0-2.28
-
- Where:
- S: Module is Sticky, requires --force to unload or purge
-r21u01n577-mic0:~$ mpirun -n 244 hostname | sort | uniq -c | sort -n
- 61 r21u01n577-mic0
- 61 r21u01n577-mic1
- 61 r21u02n578-mic0
- 61 r21u02n578-mic1
-r21u01n577-mic0:~$ mpirun -n 976 hostname | sort | uniq -c | sort -n
- 244 r21u01n577-mic0
- 244 r21u01n577-mic1
- 244 r21u02n578-mic0
- 244 r21u02n578-mic1
-r21u01n577-mic0:~$ mpirun hostname | sort | uniq -c | sort -n
- 1 r21u01n577-mic0
- 1 r21u01n577-mic1
- 1 r21u02n578-mic0
- 1 r21u02n578-mic1
-```
-
-!!! warning
- Modules `icc`, `ifort`, and `iccifort` are only libraries and headers, not compilers. To compile, use the procedure from the [Native Mode](#native-mode) chapter.
-
-### Octave/3.8.2
-
-Load the `devel_environment` and the `Octave/3.8.2` modules and run the test:
-
-```console
-r21u01n577-mic0:~$ ml devel_environment
-r21u01n577-mic0:~$ ml Octave/3.8.2
-r21u01n577-mic0:~$ octave -q /apps/phi/software/Octave/3.8.2/example/test0.m
-warning: docstring file '/apps/phi/software/Octave/3.8.2/share/octave/3.8.2/etc/built-in-docstrings' not found
-warning: readline is not linked, so history control is not available
-Use some basic operators ...
-Work with some small matrixes ...
-Save matrix to file ...
-Load matrix from file ...
-Display matrix ...
-m3 =
-
- 39.200 19.600 39.200
- 58.800 117.600 156.800
- 254.800 411.600 686.000
-
-Work with some big matrixes ...
-Sum ...
-Multiplication ...
-r21u01n577-mic0:~$ cat test.mat
-# Created by Octave 3.8.2, Thu Dec 07 11:11:09 2017 CET <kru0052@r21u01n577-mic0>
-# name: m3
-# type: matrix
-# rows: 3
-# columns: 3
- 39.2 19.6 39.2
- 58.8 117.6 156.8
- 254.8 411.6 686
-```
-
-## Native Build Software With Devel Environment
-
-Compiler
-
-* gcc (GCC) 5.1.1 **without** gfortran support
-
-Architecture (depends on the compiled software):
-
-* k1om-unknown-linux-gnu
-* k1om-mpss-linux-gnu
-* x86_64-k1om-linux
-* k1om-mpss-linux
-
-Configure step (for the `configure`,`make` and `make install` software).
-
-* specify architecture `--build=`
-
-```console
-./configure --prefix=/apps/phi/software/ncurses/6.0 --build=k1om-mpss-linux
-```
-
-Modulefile and Lmod
-
-* Read Lmod
-
-[1]: ../intel/intel-xeon-phi-salomon.md#offload-mode
-[2]: #native-mode
-[3]: ../intel/intel-xeon-phi-salomon.md
-[4]: #devel-environment
-
-[a]: https://en.wikipedia.org/wiki/Xeon_Phi
--
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