Updates to accessibility

.gitignore

@@ -1,5 +1,6 @@
-.DS_Store
-Thumbs.db
-public/
-.*.swp
-resources/
+.DS_Store
+Thumbs.db
+public/
+.*.swp
+resources/
+venv/

config/_default/params.toml

@@ -14,7 +14,8 @@
 theme = "rc-theme"
 
 # Enable users to switch between day and night mode?
-day_night = false
+#day_night = false
+day_night = true
 
 # Override the theme's font set (optional).
 #   Latest font sets (may require updating): https://sourcethemes.com/academic/themes/

content/authors/dat/_index.md

@@ -0,0 +1,27 @@
+---
+# Display name
+title: Deb Triant
+
+# Username (this should match the folder name)
+authors:
+- dat
+
+# Is this the primary user of the site?
+superuser: false
+
+# Role/position
+role: Research Computing Scientist
+
+# Organizations/Affiliations
+organizations:
+- name: University of Virginia Research Computing
+  url: "https://www.rc.virginia.edu"
+
+# Short bio (displayed in user profile at end of posts) - Optionally remove # to use
+#bio: 
+
+interests:
+- Bioinformatics
+- HPC
+- Research
+---

content/authors/det/_index.md

@@ -0,0 +1,26 @@
+---
+# Display name
+title: Deb Triant
+
+# Username (this should match the folder name)
+authors:
+- det
+
+# Is this the primary user of the site?
+superuser: false
+
+# Role/position
+role: Research Computing Scientist
+
+# Organizations/Affiliations
+organizations:
+- name: University of Virginia Research Computing
+  url: "https://www.rc.virginia.edu"
+
+
+interests:
+- Bioinformatics
+- HPC 
+- Research
+
+---

content/courses/fortran-introduction/advanced_file_io.md

@@ -40,6 +40,7 @@ The permitted values for `fmt` are 'FORMATTED' (the default, for a text file) or
 ACCESS=acc
 ```
 The access `acc` can be 'SEQUENTIAL' (the default), 'DIRECT', or 'STREAM'. Direct files must be unformatted.
+
 Unless access is 'STREAM', an unformatted file will have a header and footer that is specific to a compiler and platform and may not be portable.  This is a relic of magnetic tape drives and allowed them to backspace and skip forward in the tape.  For a binary-format file similar to that produced by C/C++ programs and interchangeable with them, use
 ```fortran
 OPEN(UNIT=iunit,FILE=fname,ACCESS=stream,FORM=unformatted)

content/courses/parallel-computing-introduction/codes/'

@@ -0,0 +1,204 @@
+#include <iostream>
+#include <cstring>
+#include <mpi.h>
+
+using namespace std;
+
+int main (int argc, char *argv[]) {
+
+    int i, j;
+    int N;
+
+    // Added for MPI
+    int nr, nrl, nc, ncl;
+    int rank, nprocs;
+    MPI_Status status;
+    int root=0, tag=0;
+    int up, down;
+
+     //Initialize MPI
+    MPI_Init(&argc, &argv);
+    MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
+    MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+
+   //Usually we would read in nr and nc; they represent the global grid RxC;
+   //For this case they are both N.
+    N=12;
+    nr=N;
+    nc=N;
+
+    //Use ncl for clarity
+    ncl=nc;
+
+    if (nr%nprocs!=0) {
+        MPI_Finalize();
+        cout<<"Not an even division of the arrays.\n";
+        return 0;
+    } 
+    else {
+    nrl=nr/nprocs;
+    }
+
+    //Find my neighbors
+    if (rank==0) {
+        up=MPI_PROC_NULL;
+    }
+    else {
+        up=rank-1;
+    }
+
+    if (rank==nprocs-1) {
+        down=MPI_PROC_NULL;
+    }
+    else {
+        down=rank+1;
+    }
+
+    cout<<"Topology "<<rank<<" "<<up<<" "<<down<<endl;
+
+    int nrows=nrl+2; int ncols=ncl+2; 
+    double **w=new double*[nrows];
+    double *wptr=new double[(nrows)*(ncols)];
+
+    for (int i=0;i<nrl+2;++i,wptr+=ncl+2) {
+       w[i] = wptr;
+    }
+
+    //Initialize 
+
+    for (int i=0; i<=nrl+1; ++i) {
+        for (int j=0; j<=ncl+1; ++j) {
+            w[i][j]=50.;
+        }
+    }
+
+    for ( int j=0; j<=ncl+1; ++j ) {
+        w[1][j]=(double)(rank+1)*2.;
+        w[nrl][j]=(double)(rank+1)*2.5;
+    }
+
+    double topBC=0.;
+    double bottomBC=200.;
+    double leftBC=100.;
+    double rightBC=100.;
+
+    for (int i=0;i<=nrl+1;++i){
+        w[i][0]=leftBC;
+        w[i][ncl+1]=rightBC;
+    }
+
+    if (rank==0) {
+       for (int i=0;i<=ncl+1;++i){
+          w[0][i]=topBC;
+       }
+    }
+    if (rank==nprocs-1) {
+        for (int i=0;i<+ncl+1;++i){
+            w[nrl+1][i]=bottomBC;
+       }
+    }
+
+    MPI_Barrier(MPI_COMM_WORLD);
+    if ( rank == 0 ) {
+        cout<<"---W Before for rank 0---"<<endl;
+        for (int i=0;i<nrl+2;i++) {
+            for (int j=0;j<ncl+2;j++) {
+                cout<<w[i][j]<<" ";
+            }
+            cout<<endl;
+        }
+        MPI_Finalize();
+        exit(1);
+
+    //starting
+    //This forces the output to show one rank at a time. It's not efficient.
+    int uwsize=(nrl+2)*(ncl+2);
+    double *u =  new double[uwsize];
+    memset(u,0.,uwsize);
+    int position;
+
+    MPI_Barrier(MPI_COMM_WORLD);
+    if ( rank == 0 ) {
+        cout<<"---W Before for rank 0---"<<endl;
+        for (int i=0;i<nrl+2;i++) {
+            for (int j=0;j<ncl+2;j++) {
+                cout<<w[i][j]<<" ";
+            }
+            cout<<endl;
+        }
+        for (int n=1;n<nprocs;++n) {
+
+            memset(u,0.,uwsize);
+            MPI_Recv(u,uwsize,MPI_DOUBLE,MPI_ANY_SOURCE,MPI_ANY_TAG,MPI_COMM_WORLD,&status);
+            cout<<"--Before for rank "<<status.MPI_SOURCE<<endl;
+            for (int i=0;i<=nrl+1;i++) {
+                for (int j=0;j<=ncl+1;j++) {
+                    cout<<u[i*(nrl+2)+j]<<" ";
+                }
+                cout<<endl;
+            }
+        }
+    }
+    else {
+
+        // Pack the 2D array into the buffer
+        position=0;
+        for (int i=0; i<=nrl+1; i++)
+            for (int j=0;j<=ncl+1; j++)
+                u[position++]=w[i][j];
+
+        MPI_Send(u,uwsize, MPI_DOUBLE, 0, rank, MPI_COMM_WORLD);
+
+    }
+
+    MPI_Barrier(MPI_COMM_WORLD);
+
+
+    MPI_Sendrecv(&w[1][0],ncl+2, MPI_DOUBLE,up,tag,&w[nrl+1][0],
+                          ncl+2, MPI_DOUBLE,down,tag,MPI_COMM_WORLD,&status);
+
+    MPI_Sendrecv(&w[nrl][0],ncl+2,MPI_DOUBLE,down,tag,&w[0][0],
+                             ncl+2,MPI_DOUBLE,up,tag,MPI_COMM_WORLD,&status);
+
+       //Print results
+
+    MPI_Barrier(MPI_COMM_WORLD);
+
+    if ( rank == 0 ) {
+        cout<<"---After for rank 0---"<<endl;
+        for (int i=0;i<nrl+2;i++) {
+            for (int j=0;j<ncl+2;j++) {
+                cout<<w[i][j]<<" ";
+            }
+            cout<<endl;
+        }
+        for (int n=1;n<nprocs;++n) {
+
+            memset(u,0.,uwsize);
+            MPI_Recv(u,uwsize,MPI_DOUBLE,MPI_ANY_SOURCE,MPI_ANY_TAG,MPI_COMM_WORLD,&status);
+            cout<<"--After for rank "<<status.MPI_SOURCE<<endl;
+            for (int i=0;i<=nrl+1;i++) {
+                for (int j=0;j<=ncl+1;j++) {
+                    cout<<u[i*(nrl+2)+j]<<" ";
+                }
+                cout<<endl;
+            }
+        }
+    }
+    else {
+
+        // Pack the 2D array into the buffer
+        position=0;
+        for (int i=0; i<=nrl+1; i++)
+            for (int j=0;j<=ncl+1; j++)
+                u[position++]=w[i][j];
+
+        MPI_Send(u,uwsize, MPI_DOUBLE, 0, rank, MPI_COMM_WORLD);
+
+    }
+    MPI_Barrier(MPI_COMM_WORLD);
+
+    MPI_Finalize();
+
+}
+

content/courses/parallel-computing-introduction/codes/bcast.cxx

@@ -12,9 +12,13 @@ int main(int argc, char *argv[]) {
     MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
     MPI_Comm_rank(MPI_COMM_WORLD,&rank);
 
-    char message[]="I have a secret";
+    //extra spece for null terminator
+    double message;
+    if (rank==0) {
+        message=42.;
+    }
 
-    MPI_Bcast(message,1,MPI_CHAR,0,MPI_COMM_WORLD);
+    MPI_Bcast(&message,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
 
     cout<<rank<<" "<<message<<endl;
 

content/courses/parallel-computing-introduction/codes/bcast.f90

@@ -3,16 +3,17 @@ program broadcaster
     implicit none
 
     integer           :: nprocs, rank, ierr
-    integer           :: sendcount
-    character(len=15) :: message
+    double precision  :: message
 
     call MPI_Init(ierr)
     call MPI_Comm_size(MPI_COMM_WORLD,nprocs,ierr)
     call MPI_Comm_rank(MPI_COMM_WORLD,rank,ierr)
 
-    message="I have a secret"
+    if (rank==0) then
+        message=42.
+    endif
 
-    call MPI_Bcast(message,1,MPI_CHAR,0,MPI_COMM_WORLD,ierr)
+    call MPI_Bcast(message,1,MPI_DOUBLE_PRECISION,0,MPI_COMM_WORLD,ierr)
 
     print*, rank, message
 

content/courses/parallel-computing-introduction/codes/bcast.py

@@ -6,8 +6,12 @@
 nprocs=comm.Get_size()
 rank=comm.Get_rank()
 
-message=np.array(["I have a secret"],dtype='str')
+# Make sure the types match
+if rank==0:
+    message=np.array([42.])
+else:
+    message=np.array([0.])
 
-comm.Bcast([message,MPI.CHAR])
+comm.Bcast([message,MPI.DOUBLE])
 
-print(rank,message)
+print(rank,message[0])

content/courses/parallel-computing-introduction/codes/bcast_ch.cxx

@@ -0,0 +1,31 @@
+#include <iostream>
+#include <iomanip>
+#include <cstring>
+#include "mpi.h"
+
+using namespace std;
+
+int main(int argc, char *argv[]) {
+
+    int nprocs,rank;
+
+    MPI_Init(&argc,&argv);
+    MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
+    MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+
+    //extra spece for null terminator
+    char message[16];
+    strcpy(message,"               ");
+    if (rank==0) {
+        strcpy(message,"I have a secret");
+    }
+
+    MPI_Bcast(message,strlen(message),MPI_CHAR,0,MPI_COMM_WORLD);
+
+    cout<<rank<<" "<<message<<endl;
+
+    MPI_Finalize();
+
+}
+
+