diff --git a/.bash_profile b/.bash_profile old mode 100755 new mode 100644 diff --git a/.bashrc b/.bashrc index ada0c5a..954d291 100644 --- a/.bashrc +++ b/.bashrc @@ -1,5 +1,23 @@ +# .bashrc + +# Source global definitions +if [ -f /etc/bashrc ]; then + . /etc/bashrc +fi + +# User specific aliases and functions +module load gcc +module load slurm + +#module add openmpi/gcc/64/1.6.5 +#module add openblas/sandybridge/0.2.6 +#module add lapack/gcc/64/3.4.2 +#module add fftw3/openmpi/gcc/64/3.3.3 +#module add intel-cluster-checker/2.1.1 +#module add intel-cluster-runtime/intel64/3.6 + # Export PATHs -export PATH=/software/common/bin:$PATH +export PATH=$HOME/bin:$PATH # Setup a fancy shell command prompt: prompt1="\[\e[0;33m\][\A]\[\e[0m\]" # Display the time in the bash prompt @@ -14,14 +32,6 @@ fi # Aliases alias ls="ls --color=auto" -# Setup the torque parallelization queue: -if [ $BASH ] && [[ $TERM == xterm* ]] -then - source /etc/profile.d/modules.sh - export LIBGL_ALWAYS_INDIRECT=yes - module add torque -fi - # Project specific environments source ~/.projects source ~/.custom_env diff --git a/.env/.omdev_environment b/.env/.omdev_environment new file mode 100644 index 0000000..3af4bde --- /dev/null +++ b/.env/.omdev_environment @@ -0,0 +1,39 @@ +#!/bin/bash + +# Source Nipype, FSL, Freesurfer +#source /software/python/setup-nipype-0.7.sh +module add openmind/fsl/5.0.7 +module add openmind/freesurfer/5.3.0 +module add openmind/git + +# add PATHs +#export ANTSPATH=/software/ANTS/versions/140107 +#export DTIPrepPATH=/software/DTIPrep/130630 +#export PATH=$DTIPrepPATH:$ANTSPATH:$PATH +#export PATH=/software/afni:$PATH + +module add openmind/miniconda/3.3.0 +export CONDA_ENVS_PATH=/om/user/satra/envs +source activate testenv + +# Freesurfer +# export SUBJECTS_DIR=/mindhive/xnat/surfaces/sad + +# Multithreading +export MKL_NUM_THREADS=4 +export OMP_NUM_THREADS=4 + +# Mindboggle +MINDBOGGLE_TOOLS=/om/user/satra/software_builds/mindboggle/mindboggle_tools/bin +export MINDBOGGLE_TOOLS +export PATH=$PATH:$MINDBOGGLE_TOOLS + +# Project name for prompt +export project_name="SDEV" +module add mit/matlab/2013a + +module add openmind/afni/2014.08.28 +module add openmind/c3d/1.0.0 +module add openmind/ants/2.1.0-1.c0c854 + + diff --git a/.env/.voice_environment b/.env/.voice_environment new file mode 100755 index 0000000..3122fab --- /dev/null +++ b/.env/.voice_environment @@ -0,0 +1,36 @@ +#!/bin/bash + + +module add mit/matlab/2015a +module add openmind/ants/2.1.0-1.c0c854 +module add openmind/freesurfer/5.3.0 +module add openmind/fsl/5.0.7 +module add openmind/git/1.9.3 +module add openmind/c3d/1.0.0 + +module add openmind/mricron/13.06.06 + + +#module add openmind/miniconda/3.7.0 +#export CONDA_ENVS_PATH=/om/project/voice/env/ +#source activate voice_env +module add openmind/miniconda/3.7.0 +export CONDA_ENVS_PATH=/om/user/gr21783/envs_python/ +source activate voice7 + +# Multithreading +export MKL_NUM_THREADS=4 +export OMP_NUM_THREADS=4 +export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 + +# Project name for prompt +export project_name="voice7" +#subjdir=/om/project/voice/mri/surfaces/ +subjdir=/om/project/voice/processedData/fsdata/ +export SUBJECTS_DIR=$subjdir + +#https://github.mit.edu/MGHPCC/OpenMind/wiki/Cookbook:-Getting-started#matlab +module add openmind/srun.x11/v1 +### This opens up an interactive node: srun.x11 -n1 -p om_interactive + +module add hdf5_18/1.8.12 \ No newline at end of file diff --git a/.projects b/.projects index c34a663..9d21b75 100644 --- a/.projects +++ b/.projects @@ -115,6 +115,17 @@ source ~/.env/.rtsz_environment } +function omdev_env() +{ + +source ~/.env/.omdev_environment +} + +function voice_env() +{ +source ~/.env/.voice_environment +} + function read_env() { @@ -135,7 +146,7 @@ function simba_env() source ~/.env/.simba_environment } -<<<<<<< HEAD + function cccbauer_env() {