TysonRayJones · October 15, 2024 11:43 · May 7, 2022 · Apr 3, 2019 · Feb 20, 2019 · Jul 11, 2018
diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -1,3 +1,4 @@
+*this guide may be outdated for MacOS versions beyond 10.14 Mojave (and implied Xcode versions)*
 
 GSL
 ===

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -78,7 +78,14 @@ then open the new folder e.g.
 cd gsl-2.4
 ```
 
-To install without admin permissions, we'll keep the GSL files in a folder called `gsl` . Replace `YOURUSERNAME` below with your ARCUS-B username (e.g. `abcd1234`) and run
+To install without admin permissions, we'll keep the GSL files in a folder called `gsl` . 
+
+Note some newer versions off gcc (e.g. 8) seem incompatible. Use an older version (e.g. `gcc/5.3.0`) and first call
+```bash
+module load binutils libtool
+```
+
+Replace `YOURUSERNAME` below with your ARCUS-B username (e.g. `abcd1234`) and run
 ```
 export gsdir=/data/oums-quantopo/YOURUSERNAME/gsl
 

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -5,9 +5,11 @@ GSL
 **Table of Contents**
 - [Installation](#installation)
   - [OSX](#osx)
+  - [Ubuntu](#ubuntu)
   - [ARCUS-B](#arcus-b)
 - [Compilation](#compilation)
   - [OSX](#osx)
+  - [Ubuntu](#ubuntu)
   - [ARCUS-B](#arcus-b)
 - [Usage](#usage)
   - [import](#import)
@@ -46,6 +48,14 @@ make install
 
 You'll now be able to include GSL into your code from anywhere.
 
+## Ubuntu
+
+```bash
+sudo apt-get install libgsl-dev
+```
+
+You'll now be able to include GSL into your code from anywhere.
+
 ## ARCUS-B
 
 > Oh wait, explore the use of...
@@ -93,6 +103,10 @@ For example, we'd adapt the [QuEST makefile](https://github.com/aniabrown/QuEST/
 LIBS = -lm -lgsl -lgslcblas
 ```
 
+### Ubuntu
+
+Exactly as above for OSX.
+
 ## ARCUS-B
 
 Before compiling on ARCUS-B, we must extend `LD_LIBRARY` to include our gsl folder (replace `YOURUSERNAME` below)

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -48,6 +48,13 @@ You'll now be able to include GSL into your code from anywhere.
 
 ## ARCUS-B
 
+> Oh wait, explore the use of...
+> ```bash
+> module load gsl/1.15
+> module load gsl/1.16
+> module load gsl/2.1
+> ```
+
 In the ARCUS terminal, download GSL anywhere
 ```bash
 wget "ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz"

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -22,7 +22,7 @@ The GNU Scientific library ([GSL](https://www.gnu.org/software/gsl/)) is a power
 
 # Installation
 
-This guide assumes you already have a working `C`/`C++` compiler.
+This guide assumes you already have a working `C`/`C++` compiler - check by entering `gcc --version` in Terminal. OSX's default `Clang` compiler is fine, otherwise [this page](https://quest.qtechtheory.org/download/) describes how to install `gcc 4.9`.
 
 ## OSX
 

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -18,10 +18,12 @@ GSL
     - [numerical errors](#numerical-errors)
 
 
-The GNU Scientific library ([GSL](https://www.gnu.org/software/gsl/)) is a powerful C/C++ numerical library.
+The GNU Scientific library ([GSL](https://www.gnu.org/software/gsl/)) is a powerful `C`/`C++` numerical library.
 
 # Installation
 
+This guide assumes you already have a working `C`/`C++` compiler.
+
 ## OSX
 
 Apparently GSL can be installed through [Homebrew](https://brew.sh/) via 

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -34,6 +34,14 @@ though installing it manually is just as simple, which we now describe.
 - Open the unzipped `gsl` folder in Terminal (e.g. `cd ~/Downloads/gsl-2.4`
 - Run `sudo ./configure && make && make install`
 
+If the above gives a "permission denied" error, instead try
+```bash
+sudo make clean
+sudo chown -R $USER .
+./configure && make
+make install
+```
+
 You'll now be able to include GSL into your code from anywhere.
 
 ## ARCUS-B

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -146,7 +146,7 @@ Sometimes GSL is so powerful, it's confusing to figure out how to do some simple
 
 ### construct matrices and vectors
 
-Matrices are dynamic objects, indexed from 0.
+Matrices are dynamic objects, indexed from 0, which must be allocated before, and freed after, their use.
 
 ```C
 #include <gsl/gsl_matrix.h>
@@ -160,6 +160,8 @@ for (int i=0; i < 10; i++)
     for (int j=0; j < 20; j++)
         gsl_matrix_set(myMatr, i, j, 8);
 
+int elem = gsl_matrix_get(myMatr, 3, 4);
+
 gsl_matrix_free(myMatr);
 ```
 

diff --git a/gsl_on_osx_and_arcus_guide.md b/gsl_on_osx_and_arcus_guide.md
@@ -53,7 +53,7 @@ cd gsl-2.4
 
 To install without admin permissions, we'll keep the GSL files in a folder called `gsl` . Replace `YOURUSERNAME` below with your ARCUS-B username (e.g. `abcd1234`) and run
 ```
-export gsdir=data/oums-quantopo/YOURUSERNAME/gsl
+export gsdir=/data/oums-quantopo/YOURUSERNAME/gsl
 
 mkdir $gsdir
 

diff --git a/gsl_on_mac_and_arcus_guide.md → gsl_on_osx_and_arcus_guide.md b/gsl_on_mac_and_arcus_guide.md → gsl_on_osx_and_arcus_guide.md
diff --git a/gsl_on_mac_and_arcus_guide.md b/gsl_on_mac_and_arcus_guide.md
@@ -2,6 +2,22 @@
 GSL
 ===
 
+**Table of Contents**
+- [Installation](#installation)
+  - [OSX](#osx)
+  - [ARCUS-B](#arcus-b)
+- [Compilation](#compilation)
+  - [OSX](#osx)
+  - [ARCUS-B](#arcus-b)
+- [Usage](#usage)
+  - [import](#import)
+  - [functions](#functions)
+    - [construct matrices and vectors](#construct-matrices-and-vectors)
+    - [multiply matrices and vectors](#multiply-matrices-and-vectors)
+    - [solve linear equations](#solve-linear-equations)
+    - [numerical errors](#numerical-errors)
+
+
 The GNU Scientific library ([GSL](https://www.gnu.org/software/gsl/)) is a powerful C/C++ numerical library.
 
 # Installation

diff --git a/gsl_on_mac_and_arcus_guide.md b/gsl_on_mac_and_arcus_guide.md
@@ -113,4 +113,88 @@ See a complete example of my QuEST & gsl makefile [here](https://github.com/Tyso
 
 ## import
 
-## use
+The many different GSL functions are available in different source files. 
+
+For example, to use the matrix, linear equation solver, and matrix multiplication functionalities, respectively include
+```C
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_blas.h>
+```
+
+View available functions and their necessary header files can be found [here](https://www.gnu.org/software/gsl/doc/html/intro.html).
+
+## functions
+
+Sometimes GSL is so powerful, it's confusing to figure out how to do some simple things. So here are some examples
+
+### construct matrices and vectors
+
+Matrices are dynamic objects, indexed from 0.
+
+```C
+#include <gsl/gsl_matrix.h>
+```
+
+```C
+gsl_matrix* myMatr = gsl_matrix_alloc(10,20);
+
+// matrix of 8s
+for (int i=0; i < 10; i++)
+    for (int j=0; j < 20; j++)
+        gsl_matrix_set(myMatr, i, j, 8);
+
+gsl_matrix_free(myMatr);
+```
+
+For a vector, replace `matrix` above with `vector`.
+
+### multiply matrices and vectors
+
+GSL's matrix operations come under 'Basic Linear Algebra Subprograms' (BLAS), listed [here](https://www.gnu.org/software/gsl/doc/html/blas.html)
+
+```C
+#include <gsl/gsl_blas.h>
+```
+
+To multiply matrices `matrA` and `matrB` and store the result in `matrC` (all of which must be previously allocated by `gsl_matrix_alloc`), call:
+```C
+gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, matrA, matrB, 0.0, matrC); 
+```
+In the name `gsl_blas_dgemm`, the `d` refers to double-precision matrices, and the final `m` refers to matrix. The other arguments are explained [here](https://www.gnu.org/software/gsl/doc/html/blas.html#c.gsl_blas_dgemm).
+
+To multiply a matrix `matrA` and a vector `vecB` and store the result in `vecC` (previously allocated by `gsl_matrix_alloc` and `gsl_vector_alloc`), call:
+```C
+gsl_blas_dgemv(CblasNoTrans, 1.0, matrA, vecB, 0.0, vecC);
+```
+
+### solve linear equations
+
+[Linear algebra operations](https://www.gnu.org/software/gsl/doc/html/linalg.html) are provided by
+```C
+#include <gsl/gsl_linalg.h>
+```
+
+Here's how to solve **A x = b** (or *matrA vecX = vecB*) for **x** by LU decomposition, which involves creating an intermediate `permutation` structure
+```C
+gsl_permutation* perm = gsl_permutation_alloc(vecB->size);
+
+int swaps;
+gsl_linalg_LU_decomp(matrA, perm, &swaps);
+gsl_linalg_LU_solve(matrA, perm, vecB, vecX);
+
+gsl_permutation_free(perm);
+```
+
+### numerical errors
+
+By default, a numerical error (e.g. attempting to invert a non-invertible matrix) will cause an error message and execution to stop.
+To instead detect and handle numerical errors, include
+```C
+#include <gsl/gsl_errno.h>
+```
+and call
+```C
+gsl_set_error_handler_off();
+```
+before calling any numerical functions. Then functions (e.g. `gsl_linalg_LU_solve`) will return an integer `0` for success, otherwise an errorcode of those listed [here](https://www.gnu.org/software/gsl/doc/html/err.html) (e.g. `GSL_ERANGE`, `GSL_EIVANL`).
diff --git a/gistfile1.txt → gsl_on_mac_and_arcus_guide.md b/gistfile1.txt → gsl_on_mac_and_arcus_guide.md
diff --git a/gistfile1.txt b/gistfile1.txt
@@ -0,0 +1,116 @@
+
+GSL
+===
+
+The GNU Scientific library ([GSL](https://www.gnu.org/software/gsl/)) is a powerful C/C++ numerical library.
+
+# Installation
+
+## OSX
+
+Apparently GSL can be installed through [Homebrew](https://brew.sh/) via 
+```bash
+brew install gsl
+```
+though installing it manually is just as simple, which we now describe.
+
+- Download [gsl-latest.tar.gz](ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz) from the [GSL ftp site](ftp://ftp.gnu.org/gnu/gsl/) and unzip it anywhere (e.g. /Downloads)
+- Open the unzipped `gsl` folder in Terminal (e.g. `cd ~/Downloads/gsl-2.4`
+- Run `sudo ./configure && make && make install`
+
+You'll now be able to include GSL into your code from anywhere.
+
+## ARCUS-B
+
+In the ARCUS terminal, download GSL anywhere
+```bash
+wget "ftp://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz"
+```
+and unzip it
+```bash
+tar -xf gsl-latest.tar.gz
+```
+then open the new folder e.g.
+```bash
+cd gsl-2.4
+```
+
+To install without admin permissions, we'll keep the GSL files in a folder called `gsl` . Replace `YOURUSERNAME` below with your ARCUS-B username (e.g. `abcd1234`) and run
+```
+export gsdir=data/oums-quantopo/YOURUSERNAME/gsl
+
+mkdir $gsdir
+
+./configure --prefix=$gsdir && make && make install
+```
+
+We'll need to remember this location when compiling
+
+# Compilation
+
+## OSX
+
+Compiling GSL with our code is easy; we simply add library flags `-lm -lgsl -lgslcblas` to our calls to `gcc`.
+
+For example, we'd adapt the [QuEST makefile](https://github.com/aniabrown/QuEST/blob/master/examples/makefile) to include
+```bash
+#
+# --- libraries
+#
+LIBS = -lm -lgsl -lgslcblas
+```
+
+## ARCUS-B
+
+Before compiling on ARCUS-B, we must extend `LD_LIBRARY` to include our gsl folder (replace `YOURUSERNAME` below)
+```
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/data/oums-quantopo/YOURUSERNAME/gsl/lib
+```
+This need only be done once each time we SSH into ARCUS. 
+
+Our compilation must additionally include the ` -lm -lgsl -lgslcblas` libraries and flags `-I/data/oums-quantopo/YOURUSERNAME/gsl/include` and `-L/data/oums-quantopo/YOURUSERNAME/gsl/lib`.
+
+For example, we'd modify the [QuEST makefile](https://github.com/aniabrown/QuEST/blob/master/examples/makefile) to include
+```bash
+#
+# --- libraries
+#
+LIBS = -lm -lgsl -lgslcblas
+```
+and just after that, insert
+```
+#
+# --- GSL link
+#
+GSL_INCLUDE = -I/data/oums-quantopo/YOURUSERNAME/gsl/include
+GSL_LINK = -L/data/oums-quantopo/YOURUSERNAME/gsl/lib
+```
+and modify the rules list
+```
+#
+# --- rules
+#
+%.o: %.c
+	$(CC) $(CFLAGS) $(CFLAGS_OMP) $(GSL_INCLUDE) -c $<
+
+%.o: $(QUEST_DIR)/%.c
+	$(CC) $(CFLAGS) $(CFLAGS_OMP) $(GSL_INCLUDE) -c $<
+```
+and finally the build commands
+```
+#
+# --- build
+#
+default:	$(EXE)
+
+$(EXE):		$(OBJ)
+		$(CC) $(CFLAGS) $(CFLAGS_OMP) $(GSL_INCLUDE) -o $(EXE) $(OBJ) $(LIBS) $(GSL_LINK)
+```
+
+See a complete example of my QuEST & gsl makefile [here](https://github.com/TysonRayJones/CTools/blob/master/gslquest/makefile).
+
+# Usage
+
+## import
+
+## use
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