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Commit e3049f2b authored by Caughlin Bohn's avatar Caughlin Bohn
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Replaced dropdowns with links.

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content/applications/app_specific/fortran_c_on_hcc.md
+ 7
− 145
View file @ e3049f2b
...@@ -21,72 +21,9 @@ $ mkdir serial_dir ...@@ -21,72 +21,9 @@ $ mkdir serial_dir
In the subdirectory `serial_dir`, save all the relevant Fortran/C codes. Here we include two demo In the subdirectory `serial_dir`, save all the relevant Fortran/C codes. Here we include two demo
programs, `demo_f_serial.f90` and `demo_c_serial.c`, that compute the sum from 1 to 20. programs, `demo_f_serial.f90` and `demo_c_serial.c`, that compute the sum from 1 to 20.
{{%expand "demo_f_serial.f90" %}} [demo_c_serial.c](https://raw.githubusercontent.com/unlhcc/job-examples/master/C/demo_c_serial.c)
{{< highlight bash >}}
Program demo_f_serial [demo_f_serial.f90](https://raw.githubusercontent.com/unlhcc/job-examples/master/fortran/demo_f_serial.f90)
implicit none
integer, parameter :: N = 20
real*8 w
integer i
common/sol/ x
real*8 x
real*8, dimension(N) :: y
do i = 1,N
w = i*1d0
call proc(w)
y(i) = x
write(6,*) 'i,x = ', i, y(i)
enddo
write(6,*) 'sum(y) =',sum(y)
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_serial.c" %}}
{{< highlight c >}}
//demo_c_serial
#include <stdio.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;
for (i = 1; i <= N; i++){
w = i*1e0;
x = proc(w);
y[i-1] = x;
printf("i,x= %d %lf\n", i, y[i-1]) ;
}
sum = 0e0;
for (i = 1; i<= N; i++){
sum = sum + y[i-1];
}
printf("sum(y)= %lf\n", sum);
return 0;
}
{{< /highlight >}}
{{% /expand %}}
--- ---
...@@ -121,33 +58,10 @@ Create a submit script to request one core (default) and 1-min run time ...@@ -121,33 +58,10 @@ Create a submit script to request one core (default) and 1-min run time
on the supercomputer. The name of the main program enters at the last on the supercomputer. The name of the main program enters at the last
line. line.
{{% panel header="`submit_f.serial`"%}} [submit_f.serial](https://raw.githubusercontent.com/unlhcc/job-examples/master/fortran/submit_f.serial)
{{< highlight bash >}}
#!/bin/sh [submit_c.serial](https://raw.githubusercontent.com/unlhcc/job-examples/master/C/submit_c.serial)
#SBATCH --mem-per-cpu=1024
#SBATCH --time=00:01:00
#SBATCH --job-name=Fortran
#SBATCH --error=Fortran.%J.err
#SBATCH --output=Fortran.%J.out
module load compiler/gcc/4.9
./demo_f_serial.x
{{< /highlight >}}
{{% /panel %}}
{{% panel header="`submit_c.serial`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --mem-per-cpu=1024
#SBATCH --time=00:01:00
#SBATCH --job-name=C
#SBATCH --error=C.%J.err
#SBATCH --output=C.%J.out
module load compiler/gcc/4.9
./demo_c_serial.x
{{< /highlight >}}
{{% /panel %}}
#### Submit the Job #### Submit the Job
...@@ -164,56 +78,4 @@ Replace `<username>` with your HCC username. ...@@ -164,56 +78,4 @@ Replace `<username>` with your HCC username.
#### Sample Output #### Sample Output
The sum from 1 to 20 is computed and printed to the `.out` file (see The sum from 1 to 20 is computed and printed to the `.out` files.
below).
{{%expand "Fortran.out" %}}
{{< highlight batchfile>}}
i,x = 1 1.0000000000000000
i,x = 2 2.0000000000000000
i,x = 3 3.0000000000000000
i,x = 4 4.0000000000000000
i,x = 5 5.0000000000000000
i,x = 6 6.0000000000000000
i,x = 7 7.0000000000000000
i,x = 8 8.0000000000000000
i,x = 9 9.0000000000000000
i,x = 10 10.000000000000000
i,x = 11 11.000000000000000
i,x = 12 12.000000000000000
i,x = 13 13.000000000000000
i,x = 14 14.000000000000000
i,x = 15 15.000000000000000
i,x = 16 16.000000000000000
i,x = 17 17.000000000000000
i,x = 18 18.000000000000000
i,x = 19 19.000000000000000
i,x = 20 20.000000000000000
sum(y) = 210.00000000000000
{{< /highlight >}}
{{% /expand %}}
{{%expand "C.out" %}}
{{< highlight batchfile>}}
i,x= 1 1.000000
i,x= 2 2.000000
i,x= 3 3.000000
i,x= 4 4.000000
i,x= 5 5.000000
i,x= 6 6.000000
i,x= 7 7.000000
i,x= 8 8.000000
i,x= 9 9.000000
i,x= 10 10.000000
i,x= 11 11.000000
i,x= 12 12.000000
i,x= 13 13.000000
i,x= 14 14.000000
i,x= 15 15.000000
i,x= 16 16.000000
i,x= 17 17.000000
i,x= 18 18.000000
i,x= 19 19.000000
i,x= 20 20.000000
sum(y)= 210.000000
{{< /highlight >}}
{{% /expand %}}
content/applications/app_specific/mpi_jobs_on_hcc.md
+ 5
− 242
View file @ e3049f2b
...@@ -30,160 +30,9 @@ outputs from all worker cores and perform an overall summation. For easy ...@@ -30,160 +30,9 @@ 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 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 "//=". added lines in the parallel code (MPI) are marked with "!=" or "//=".
{{%expand "demo_f_mpi.f90" %}} [demo_f_mpi.f90](https://raw.githubusercontent.com/unlhcc/job-examples/master/fortran/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 ================================= [demo_c_mpi.c](https://raw.githubusercontent.com/unlhcc/job-examples/master/C/demo_c_mpi.c)
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 %}}
--- ---
...@@ -210,33 +59,10 @@ Create a submit script to request 5 cores (with `--ntasks`). A parallel ...@@ -210,33 +59,10 @@ Create a submit script to request 5 cores (with `--ntasks`). A parallel
execution command `mpirun ./` needs to enter to last line before the execution command `mpirun ./` needs to enter to last line before the
main program name. main program name.
{{% panel header="`submit_f.mpi`"%}} [submit_f.mpi](https://raw.githubusercontent.com/unlhcc/job-examples/master/fortran/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`"%}} [submit_c.mpi](https://raw.githubusercontent.com/unlhcc/job-examples/master/C/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 #### Submit the Job
...@@ -254,69 +80,6 @@ Replace `<username>` with your HCC username. ...@@ -254,69 +80,6 @@ Replace `<username>` with your HCC username.
Sample Output Sample Output
------------- -------------
The sum from 1 to 20 is computed and printed to the `.out` file (see The sum from 1 to 20 is computed and printed to the `.out` files. The outputs from the 5 cores are collected and processed by the
below). The outputs from the 5 cores are collected and processed by the
master core (i.e. `myid=0`). 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 %}}
content/applications/app_specific/running_sas.md
+ 2
− 49
View file @ e3049f2b
...@@ -20,39 +20,7 @@ called `sas_demo` under your `$WORK` directory.  ...@@ -20,39 +20,7 @@ called `sas_demo` under your `$WORK` directory. 
In the subdirectory `sas_demo`, save the sas code. Here we include a single demo In the subdirectory `sas_demo`, save the sas code. Here we include a single demo
programs, `t_test.sas`, to perform a t test analysis on a small data set. programs, `t_test.sas`, to perform a t test analysis on a small data set.
{{%expand "t-test.sas" %}} [t_test.sas](https://raw.githubusercontent.com/unlhcc/job-examples/master/sas/t-test.sas)
{{< highlight sas >}}
* load the dataset;
data pulse;
input pre post;
datalines;
62 61
63 62
58 59
64 61
64 63
61 58
68 61
66 64
65 62
67 68
69 65
61 67
64 65
61 63
63 62
;
* it is always a good idea to print out the dataset;
proc print;
run;
* perform the analysis using PROC TTEST;
proc ttest;
paired pre*post; * tells sas to compute the test for the paired differences;
run;
{{< /highlight >}}
{{% /expand %}}
...@@ -64,22 +32,7 @@ Create a submit script to request one core (default) and 10-min run time ...@@ -64,22 +32,7 @@ Create a submit script to request one core (default) and 10-min run time
on the supercomputer. The name of the main program enters at the last on the supercomputer. The name of the main program enters at the last
line. line.
{{% panel header="`sas.submit`"%}} [sas.submit](https://raw.githubusercontent.com/unlhcc/job-examples/master/sas/sas.submit)
{{< highlight bash >}}
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=1gb
#SBATCH --time=00:10:00
#SBATCH --job-name=sas_example
#SBATCH --error=sas_example.%J.err
#SBATCH --output=sas_example.%J.out
module load sas/9.4
sas t-test.sas
{{< /highlight >}}
{{% /panel %}}
#### Submit the Job #### Submit the Job
......
content/submitting_jobs/job_dependencies.md
+ 8
− 9
View file @ e3049f2b
...@@ -31,8 +31,7 @@ depends on Jobs B and C completing. ...@@ -31,8 +31,7 @@ depends on Jobs B and C completing.
{{< figure src="/images/4980738.png" width="400" >}} {{< figure src="/images/4980738.png" width="400" >}}
The SLURM submit files for each step are below. The SLURM submit files for each step are below.
{{% panel theme="info" header="JobA.submit" %}}
{{%expand "JobA.submit" %}}
{{< highlight batch >}} {{< highlight batch >}}
#!/bin/sh #!/bin/sh
#SBATCH --job-name=JobA #SBATCH --job-name=JobA
...@@ -44,10 +43,10 @@ echo "I'm job A" ...@@ -44,10 +43,10 @@ echo "I'm job A"
echo "Sample job A output" > jobA.out echo "Sample job A output" > jobA.out
sleep 120 sleep 120
{{< /highlight >}} {{< /highlight >}}
{{% /expand %}} {{% /panel %}}
{{%expand "JobB.submit" %}} {{% panel theme="info" header="JobB.submit" %}}
{{< highlight batch >}} {{< highlight batch >}}
#!/bin/sh #!/bin/sh
#SBATCH --job-name=JobB #SBATCH --job-name=JobB
...@@ -62,9 +61,9 @@ echo "" >> jobB.out ...@@ -62,9 +61,9 @@ echo "" >> jobB.out
echo "Sample job B output" >> jobB.out echo "Sample job B output" >> jobB.out
sleep 120 sleep 120
{{< /highlight >}} {{< /highlight >}}
{{% /expand %}} {{% /panel %}}
{{%expand "JobC.submit" %}} {{% panel theme="info" header="JobC.submit" %}}
{{< highlight batch >}} {{< highlight batch >}}
#!/bin/sh #!/bin/sh
#SBATCH --job-name=JobC #SBATCH --job-name=JobC
...@@ -79,9 +78,9 @@ echo "" >> jobC.out ...@@ -79,9 +78,9 @@ echo "" >> jobC.out
echo "Sample job C output" >> jobC.out echo "Sample job C output" >> jobC.out
sleep 120 sleep 120
{{< /highlight >}} {{< /highlight >}}
{{% /expand %}} {{% /panel %}}
{{%expand "JobC.submit" %}} {{% panel theme="info" header="JobD.submit" %}}
{{< highlight batch >}} {{< highlight batch >}}
#!/bin/sh #!/bin/sh
#SBATCH --job-name=JobD #SBATCH --job-name=JobD
...@@ -98,7 +97,7 @@ echo "" >> jobD.out ...@@ -98,7 +97,7 @@ echo "" >> jobD.out
echo "Sample job D output" >> jobD.out echo "Sample job D output" >> jobD.out
sleep 120 sleep 120
{{< /highlight >}} {{< /highlight >}}
{{% /expand %}} {{% /panel %}}
To start the workflow, submit Job A first: To start the workflow, submit Job A first:
......
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