From 63994f956e008a0c35886197a34039e4f0b3c40c Mon Sep 17 00:00:00 2001
From: Carrie A Brown <cbrown58@unl.edu>
Date: Thu, 20 Dec 2018 17:17:42 -0600
Subject: [PATCH] Moved extra docs out of quickstarts
---
.../using_nus_gitlab_instance/_index.md | 0
.../setting_up_gitlab_on_hcc_clusters.md | 0
.../running_applications}/fortran_c_on_hcc.md | 0
.../submitting_jobs}/condor_jobs_on_hcc.md | 0
.../how_to_setup_x11_forwarding.md | 59 ----
content/quickstarts/mpi_jobs_on_hcc.md | 322 ------------------
6 files changed, 381 deletions(-)
rename content/{quickstarts => guides/handling_data}/using_nus_gitlab_instance/_index.md (100%)
rename content/{quickstarts => guides/handling_data}/using_nus_gitlab_instance/setting_up_gitlab_on_hcc_clusters.md (100%)
rename content/{quickstarts => guides/running_applications}/fortran_c_on_hcc.md (100%)
rename content/{quickstarts => guides/submitting_jobs}/condor_jobs_on_hcc.md (100%)
delete mode 100644 content/quickstarts/how_to_setup_x11_forwarding.md
delete mode 100644 content/quickstarts/mpi_jobs_on_hcc.md
diff --git a/content/quickstarts/using_nus_gitlab_instance/_index.md b/content/guides/handling_data/using_nus_gitlab_instance/_index.md
similarity index 100%
rename from content/quickstarts/using_nus_gitlab_instance/_index.md
rename to content/guides/handling_data/using_nus_gitlab_instance/_index.md
diff --git a/content/quickstarts/using_nus_gitlab_instance/setting_up_gitlab_on_hcc_clusters.md b/content/guides/handling_data/using_nus_gitlab_instance/setting_up_gitlab_on_hcc_clusters.md
similarity index 100%
rename from content/quickstarts/using_nus_gitlab_instance/setting_up_gitlab_on_hcc_clusters.md
rename to content/guides/handling_data/using_nus_gitlab_instance/setting_up_gitlab_on_hcc_clusters.md
diff --git a/content/quickstarts/fortran_c_on_hcc.md b/content/guides/running_applications/fortran_c_on_hcc.md
similarity index 100%
rename from content/quickstarts/fortran_c_on_hcc.md
rename to content/guides/running_applications/fortran_c_on_hcc.md
diff --git a/content/quickstarts/condor_jobs_on_hcc.md b/content/guides/submitting_jobs/condor_jobs_on_hcc.md
similarity index 100%
rename from content/quickstarts/condor_jobs_on_hcc.md
rename to content/guides/submitting_jobs/condor_jobs_on_hcc.md
diff --git a/content/quickstarts/how_to_setup_x11_forwarding.md b/content/quickstarts/how_to_setup_x11_forwarding.md
deleted file mode 100644
index 4380eb2e..00000000
--- a/content/quickstarts/how_to_setup_x11_forwarding.md
+++ /dev/null
@@ -1,59 +0,0 @@
-+++
-title = "How to setup X11 forwarding"
-description = "Use X11 forwarding to view GUI programs remotely"
-weight = "35"
-+++
-
-##### If you are connecting to HCC clusters via a PC running Windows, please take the following steps to setup X11 forwarding.
-
-1. Download Xming to your local PC and install. Download
- link: https://downloads.sourceforge.net/project/xming/Xming/6.9.0.31/Xming-6-9-0-31-setup.exe
-2. Download PuTTY to your local PC and install. Download link: http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe
-3. Open Xming and keep it running in the background.
-4. Configure PuTTY as below:
- {{< figure src="/images/11637370.png" height="400" >}}
- {{< figure src="/images/11637371.jpg" height="400" >}}
-
-5. To test your X11 setup, after login, type command `xeyes` and press
- enter.
- {{< figure src="/images/11637372.png" height="400" >}}
-
-6. Close the xeyes application by "Ctrl + c" from the terminal or click
- the close button on the up-right corner of the graphical window.
-
-
-
-##### If you are connecting to HCC clusters via a Macintosh, please take the following steps to setup X11 forwarding.
-
-- Check the OS version on your Mac, if it's below 10.8., you can simply type `ssh -Y username@hostname` in your terminal to login.
-
-- If your OS version is newer than 10.8, please do the following:
- 1. Download and install XQuartz.
- Download link: https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg
- 2. Type `ssh -Y username@hostname` in your terminal to login.
- 3. To test your X11 setup, after login, type command "xeyes" and press
- enter.
-
- {{< figure src="/images/11637374.png" height="400" >}}
- 4. Close the xeyes application by "Control + c" from the terminal or
- click the close button on the up-left corner of the graphical
- window.
-
-##### If you are connecting to HCC clusters via a Linux laptop, please take the following steps to setup X11 forwarding.
-
-1. Open the remote client terminal.
-2. Type `ssh -Y username@hostname`" in your terminal to login.
-3. To test your X11 setup, after login, type command "xeyes" and press
- enter.
-4. Close the xeyes application by "Ctrl + c" from the terminal or click
- the close button on the up-right corner of the graphical window.
-
-
-
-#### Related articles
-
-[X11 on Windows](http://www.straightrunning.com/XmingNotes)
-
-[X11 on Mac](https://en.wikipedia.org/wiki/XQuartz)
-
-[X11 on Linux](http://www.wikihow.com/Configure-X11-in-Linux)
diff --git a/content/quickstarts/mpi_jobs_on_hcc.md b/content/quickstarts/mpi_jobs_on_hcc.md
deleted file mode 100644
index 7bc5c9ec..00000000
--- a/content/quickstarts/mpi_jobs_on_hcc.md
+++ /dev/null
@@ -1,322 +0,0 @@
-+++
-title = "MPI Jobs on HCC"
-description = "How to compile and run MPI programs on HCC machines"
-weight = "52"
-+++
-
-This quick start demonstrates how to implement a parallel (MPI)
-Fortran/C program on HCC supercomputers. The sample codes and submit
-scripts can be downloaded from [mpi_dir.zip](/attachments/mpi_dir.zip).
-
-#### Login to a HCC Cluster
-
-Log in to a HCC cluster through PuTTY ([For Windows Users]({{< relref "/quickstarts/for_windows_users">}})) or Terminal ([For Mac/Linux
-Users]({{< relref "/quickstarts/for_maclinux_users">}})) and make a subdirectory called `mpi_dir` under the `$WORK` directory.
-
-{{< highlight bash >}}
-$ cd $WORK
-$ mkdir mpi_dir
-{{< /highlight >}}
-
-In the subdirectory `mpi_dir`, save all the relevant codes. Here we
-include two demo programs, `demo_f_mpi.f90` and `demo_c_mpi.c`, that
-compute the sum from 1 to 20 through parallel processes. A
-straightforward parallelization scheme is used for demonstration
-purpose. First, the master core (i.e. `myid=0`) distributes equal
-computation workload to a certain number of cores (as specified by
-`--ntasks `in the submit script). Then, each worker core computes a
-partial summation as output. Finally, the master core collects the
-outputs from all worker cores and perform an overall summation. For easy
-comparison with the serial code ([Fortran/C on HCC]({{< relref "fortran_c_on_hcc">}})), the
-added lines in the parallel code (MPI) are marked with "!=" or "//=".
-
-{{%expand "demo_f_mpi.f90" %}}
-{{< highlight fortran >}}
-Program demo_f_mpi
-!====== MPI =====
- use mpi
-!================
- implicit none
- integer, parameter :: N = 20
- real*8 w
- integer i
- common/sol/ x
- real*8 x
- real*8, dimension(N) :: y
-!============================== MPI =================================
- integer ind
- real*8, dimension(:), allocatable :: y_local
- integer numnodes,myid,rc,ierr,start_local,end_local,N_local
- real*8 allsum
-!====================================================================
-
-!============================== MPI =================================
- call mpi_init( ierr )
- call mpi_comm_rank ( mpi_comm_world, myid, ierr )
- call mpi_comm_size ( mpi_comm_world, numnodes, ierr )
- !
- N_local = N/numnodes
- allocate ( y_local(N_local) )
- start_local = N_local*myid + 1
- end_local = N_local*myid + N_local
-!====================================================================
- do i = start_local, end_local
- w = i*1d0
- call proc(w)
- ind = i - N_local*myid
- y_local(ind) = x
-! y(i) = x
-! write(6,*) 'i, y(i)', i, y(i)
- enddo
-! write(6,*) 'sum(y) =',sum(y)
-!============================================== MPI =====================================================
- call mpi_reduce( sum(y_local), allsum, 1, mpi_real8, mpi_sum, 0, mpi_comm_world, ierr )
- call mpi_gather ( y_local, N_local, mpi_real8, y, N_local, mpi_real8, 0, mpi_comm_world, ierr )
-
- if (myid == 0) then
- write(6,*) '-----------------------------------------'
- write(6,*) '*Final output from... myid=', myid
- write(6,*) 'numnodes =', numnodes
- write(6,*) 'mpi_sum =', allsum
- write(6,*) 'y=...'
- do i = 1, N
- write(6,*) y(i)
- enddo
- write(6,*) 'sum(y)=', sum(y)
- endif
-
- deallocate( y_local )
- call mpi_finalize(rc)
-!========================================================================================================
-
-Stop
-End Program
-Subroutine proc(w)
- real*8, intent(in) :: w
- common/sol/ x
- real*8 x
-
- x = w
-
-Return
-End Subroutine
-{{< /highlight >}}
-{{% /expand %}}
-
-{{%expand "demo_c_mpi.c" %}}
-{{< highlight c >}}
-//demo_c_mpi
-#include <stdio.h>
-//======= MPI ========
-#include "mpi.h"
-#include <stdlib.h>
-//====================
-
-double proc(double w){
- double x;
- x = w;
- return x;
-}
-
-int main(int argc, char* argv[]){
- int N=20;
- double w;
- int i;
- double x;
- double y[N];
- double sum;
-//=============================== MPI ============================
- int ind;
- double *y_local;
- int numnodes,myid,rc,ierr,start_local,end_local,N_local;
- double allsum;
-//================================================================
-//=============================== MPI ============================
- MPI_Init(&argc, &argv);
- MPI_Comm_rank( MPI_COMM_WORLD, &myid );
- MPI_Comm_size ( MPI_COMM_WORLD, &numnodes );
- N_local = N/numnodes;
- y_local=(double *) malloc(N_local*sizeof(double));
- start_local = N_local*myid + 1;
- end_local = N_local*myid + N_local;
-//================================================================
-
- for (i = start_local; i <= end_local; i++){
- w = i*1e0;
- x = proc(w);
- ind = i - N_local*myid;
- y_local[ind-1] = x;
-// y[i-1] = x;
-// printf("i,x= %d %lf\n", i, y[i-1]) ;
- }
- sum = 0e0;
- for (i = 1; i<= N_local; i++){
- sum = sum + y_local[i-1];
- }
-// printf("sum(y)= %lf\n", sum);
-//====================================== MPI ===========================================
- MPI_Reduce( &sum, &allsum, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD );
- MPI_Gather( &y_local[0], N_local, MPI_DOUBLE, &y[0], N_local, MPI_DOUBLE, 0, MPI_COMM_WORLD );
-
- if (myid == 0){
- printf("-----------------------------------\n");
- printf("*Final output from... myid= %d\n", myid);
- printf("numnodes = %d\n", numnodes);
- printf("mpi_sum = %lf\n", allsum);
- printf("y=...\n");
- for (i = 1; i <= N; i++){
- printf("%lf\n", y[i-1]);
- }
- sum = 0e0;
- for (i = 1; i<= N; i++){
- sum = sum + y[i-1];
- }
-
- printf("sum(y) = %lf\n", sum);
-
- }
-
- free( y_local );
- MPI_Finalize ();
-//======================================================================================
-
-return 0;
-}
-{{< /highlight >}}
-{{% /expand %}}
-
----
-
-#### Compiling the Code
-
-The compiling of a MPI code requires first loading a compiler "engine"
-such as `gcc`, `intel`, or `pgi` and then loading a MPI wrapper
-`openmpi`. Here we will use the GNU Complier Collection, `gcc`, for
-demonstration.
-
-{{< highlight bash >}}
-$ module load compiler/gcc/6.1 openmpi/2.1
-$ mpif90 demo_f_mpi.f90 -o demo_f_mpi.x
-$ mpicc demo_c_mpi.c -o demo_c_mpi.x
-{{< /highlight >}}
-
-The above commends load the `gcc` complier with the `openmpi` wrapper.
-The compiling commands `mpif90` or `mpicc` are used to compile the codes
-to`.x` files (executables).
-
-### Creating a Submit Script
-
-Create a submit script to request 5 cores (with `--ntasks`). A parallel
-execution command `mpirun ./` needs to enter to last line before the
-main program name.
-
-{{% panel header="`submit_f.mpi`"%}}
-{{< highlight bash >}}
-#!/bin/sh
-#SBATCH --ntasks=5
-#SBATCH --mem-per-cpu=1024
-#SBATCH --time=00:01:00
-#SBATCH --job-name=Fortran
-#SBATCH --error=Fortran.%J.err
-#SBATCH --output=Fortran.%J.out
-
-mpirun ./demo_f_mpi.x
-{{< /highlight >}}
-{{% /panel %}}
-
-{{% panel header="`submit_c.mpi`"%}}
-{{< highlight bash >}}
-#!/bin/sh
-#SBATCH --ntasks=5
-#SBATCH --mem-per-cpu=1024
-#SBATCH --time=00:01:00
-#SBATCH --job-name=C
-#SBATCH --error=C.%J.err
-#SBATCH --output=C.%J.out
-
-mpirun ./demo_c_mpi.x
-{{< /highlight >}}
-{{% /panel %}}
-
-#### Submit the Job
-
-The job can be submitted through the command `sbatch`. The job status
-can be monitored by entering `squeue` with the `-u` option.
-
-{{< highlight bash >}}
-$ sbatch submit_f.mpi
-$ sbatch submit_c.mpi
-$ squeue -u <username>
-{{< /highlight >}}
-
-Replace `<username>` with your HCC username.
-
-Sample Output
--------------
-
-The sum from 1 to 20 is computed and printed to the `.out` file (see
-below). The outputs from the 5 cores are collected and processed by the
-master core (i.e. `myid=0`).
-
-{{%expand "Fortran.out" %}}
-{{< highlight batchfile>}}
- -----------------------------------------
- *Final output from... myid= 0
- numnodes = 5
- mpi_sum = 210.00000000000000
- y=...
- 1.0000000000000000
- 2.0000000000000000
- 3.0000000000000000
- 4.0000000000000000
- 5.0000000000000000
- 6.0000000000000000
- 7.0000000000000000
- 8.0000000000000000
- 9.0000000000000000
- 10.000000000000000
- 11.000000000000000
- 12.000000000000000
- 13.000000000000000
- 14.000000000000000
- 15.000000000000000
- 16.000000000000000
- 17.000000000000000
- 18.000000000000000
- 19.000000000000000
- 20.000000000000000
- sum(y)= 210.00000000000000
-{{< /highlight >}}
-{{% /expand %}}
-
-{{%expand "C.out" %}}
-{{< highlight batchfile>}}
------------------------------------
-*Final output from... myid= 0
-numnodes = 5
-mpi_sum = 210.000000
-y=...
-1.000000
-2.000000
-3.000000
-4.000000
-5.000000
-6.000000
-7.000000
-8.000000
-9.000000
-10.000000
-11.000000
-12.000000
-13.000000
-14.000000
-15.000000
-16.000000
-17.000000
-18.000000
-19.000000
-20.000000
-sum(y) = 210.000000
-{{< /highlight >}}
-{{% /expand %}}
-
--
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