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Merge pull request #12526 from milljm/hpc-instructions-12525

Fix mistakes with HPC and Manual instructions
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aeslaughter committed Nov 27, 2018
2 parents 5686e1d + 19ad2da commit b1536f0d1545194786c05cd8fa16ade89fb70cc5
@@ -2,6 +2,12 @@
These documentation pages are meant to be used by developers who are developing MOOSE-based applications.
[Syntax](syntax/index.md) - MOOSE syntax documentation
[Source Code](source/index.md) - MOOSE source documentation
[Doxygen](http://www.mooseframework.com/docs/doxygen/moose/classes.html) - MOOSE Doxygen
[Build System](/build_system.md) - How the hierarchical `make` system functions in MOOSE
[Test System](/test_system.md) - How to create/maintain tests for your application
@@ -24,8 +30,4 @@ These documentation pages are meant to be used by developers who are developing
[Moose-Wrapped Apps](/moose_wrapped_apps.md) - Coupling external codes to MOOSE
[Doxygen](http://www.mooseframework.com/docs/doxygen/moose/classes.html) - MOOSE Doxygen
[Syntax](syntax/index.md) - MOOSE syntax documentation
[Source Code](source/index.md) - MOOSE source documentation
@@ -80,6 +80,14 @@ a {
background-color: var(--inl-blue);
}
/*
Set a margin between <p> tags, if two or more paragraphs exist within an alert
*/
.card .card-content p + p
{
margin-top:10px;
}
.moose-exception {
color: red;
}
@@ -11,7 +11,7 @@ your operating system/platform and follow the instructions:
- [getting_started/installation/fedora.md]
- [getting_started/installation/centos.md]
- [getting_started/installation/windows10.md]
- [getting_started/installation/cluster.md]
- [getting_started/installation/hpc_install_moose.md]
- [getting_started/installation/manual_installation_gcc.md]
- [getting_started/installation/manual_installation_llvm.md]
@@ -1,4 +1,4 @@
# Getting Started with MOOSE on Cluster Machines
# HPC Cluster
The following instructions aims at setting up a baseline single-user environment for building MOOSE based applications in a job scheduling capable environment.
@@ -32,7 +32,7 @@ export PACKAGES_DIR=$HOME/moose-compilers
Use an editor to add the following contents to `$HOME/.moose_profile`
```bash
!package! code max-height=400
PACKAGES_DIR=$HOME/moose-compilers
export CC=mpicc
@@ -41,8 +41,8 @@ export F90=mpif90
export F77=mpif77
export FC=mpif90
export PETSC_DIR=$PACKAGES_DIR/petsc-3.8.3
```
export PETSC_DIR=$PACKAGES_DIR/petsc-__PETSC_DEFAULT__
!package-end!
## Source the MOOSE Profile
@@ -57,8 +57,4 @@ You will need to perform the above (`source $HOME/.moose_profile`) for every new
!include manual_cleanup.md
## Compiler Stack Finished
With the compiler stack ready, you can proceed to [Obtaining and Building MOOSE](getting_started/installation/install_moose.md).
!include getting_started/installation/post_moose_install.md
Head back over to the [getting_started/index.md] page to continue your tour of MOOSE.

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@@ -62,4 +62,3 @@ command in your ~/.bash_profile (or ~/.bashrc which ever your system uses).
With the compiler stack ready, you can proceed to [Obtaining and Building MOOSE](getting_started/installation/install_moose.md).
!include getting_started/installation/post_moose_install.md
@@ -1,5 +1,11 @@
# Manual Installation LLVM/MPICH
!alert! note title=Are you sure?
Getting a proper LLVM/MPICH compiler built is substantially more difficult than our [GCC/MPICH](getting_started/installation/manual_installation_gcc.md) combination. We need to build LLVM using a *modern* GCC compiler (not just a minimal C++11 compliant GCC compiler). Also, the higher the version of GCC, does not always guarantee success.
Furthermore, your millage will vary depending on the operating system. Building LLVM is a finicky process. If you are unsure as to why you are building an LLVM compiler, it might be best to build the [GCC/MPICH](getting_started/installation/manual_installation_gcc.md) compiler stack instead.
!alert-end!
!include getting_started/minimum_requirements.md
## Prerequisites
@@ -77,4 +83,3 @@ command in your ~/.bash_profile (or ~/.bashrc which ever your system uses).
With the compiler stack ready, you can proceed to [Obtaining and Building MOOSE](getting_started/installation/install_moose.md).
!include getting_started/installation/post_moose_install.md
@@ -1,5 +1,13 @@
## MPICH
Check and see if you already have an MPI wrapper available on your machine. One simple way of doing so, is to perform a `which` on the three necessary MPI wrapper binaries:
```bash
which mpicc mpicxx mpif90 | wc -l
```
If the above command returns '3', then you may skip the MPICH section. +However+, if you ended up building your own GCC compiler above, you will want to *NOT* skip this step. With the reason being, it is generally best to build an MPI wrapper based on the compiler you plan to use.
Download MPICH !!package mpich!!
!package! code
@@ -1,7 +1,7 @@
# MooseDocs Setup
Any MOOSE-based application can use the MooseDocs system to create custom websites. If a current
[MOOSE package](getting_started/installation/index.md) is installed then the necessary dependencies
[MOOSE package](getting_started/index.md) is installed then the necessary dependencies
exist. Also, if you have recently created an application with stork (after Aug. 15,
2018) then your application will have the files for a simple website created. The sections below will
aid in setting up your application if you do not have the dependencies or the necessary documentation
@@ -31,7 +31,7 @@ work well for phase field problems. They are summarized below:
This uses LU decomposition to directly apply the inverse of the Jacobian matrix. It is typically the
most accurate approach, but is expensive and does not scale well beyond tens of processors. Parallelization requires
_SUPERLU_ to be compiled into PETSc (as provided by the [MOOSE redistributable environment package](getting_started/installation/index.md)).
_SUPERLU_ to be compiled into PETSc (as provided by the [MOOSE redistributable environment package](getting_started/index.md)).
It is often a good debugging tool. Typical options in the block are
```

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