From 73bba477f607240e803491c96a58d6c1bf76d3ea Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Fri, 26 Sep 2014 16:42:02 -0400 Subject: [PATCH 1/7] openmind configuration --- .bash_profile | 0 .bashrc | 28 +++++++++++++++++++--------- .env/.omdev_environment | 39 +++++++++++++++++++++++++++++++++++++++ .projects | 5 +++++ 4 files changed, 63 insertions(+), 9 deletions(-) mode change 100755 => 100644 .bash_profile create mode 100644 .env/.omdev_environment 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:$MINDBOGGLE_TOOLS + +# Project name for prompt +export project_name="SDEV" +module add mit/matlab/2013a + +module add openmind/afni/2014.08.28 +module add openmind/c3d/1.0.0 +module add openmind/ants/2.1.0-1.c0c854 + + diff --git a/.projects b/.projects index b7ac9c3..7ccbe60 100644 --- a/.projects +++ b/.projects @@ -95,3 +95,8 @@ source ~/.env/.rtsz_environment } +function omdev_env() +{ + +source ~/.env/.omdev_environment +} From 68e9e010e83658af694524f012d323d3ce24f23c Mon Sep 17 00:00:00 2001 From: cdla Date: Fri, 3 Oct 2014 11:15:49 -0400 Subject: [PATCH 2/7] added voice environment for openmind --- .projects | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.projects b/.projects index 61e614a..e0d07c5 100644 --- a/.projects +++ b/.projects @@ -120,3 +120,8 @@ function omdev_env() source ~/.env/.omdev_environment } + +function voice_env() +{ +source ~/.env/.voice_environment +} From 8bb07be4c87e786a55f26b3b5944ce0bf1fc7948 Mon Sep 17 00:00:00 2001 From: cdla Date: Fri, 3 Oct 2014 11:17:35 -0400 Subject: [PATCH 3/7] added voice environment for openmind --- .env/.voice_environment | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .env/.voice_environment diff --git a/.env/.voice_environment b/.env/.voice_environment new file mode 100644 index 0000000..5e9270d --- /dev/null +++ b/.env/.voice_environment @@ -0,0 +1,22 @@ +#!/bin/bash + + +module add mit/matlab/2013a +module add openmind/ants/2.1.0-1.c0c854 +module add openmind/freesurfer/5.3.0 +module add openmind/fsl/5.0.7 +module add openmind/git/1.9.3 + +module add openmind/miniconda/3.5.2 +export CONDA_ENVS_PATH=/om/project/voice/env/ +source activate voice_env + +# Multithreading +export MKL_NUM_THREADS=4 +export OMP_NUM_THREADS=4 + +# Project name for prompt +export project_name="voice_env" +subjdir=/om/project/voice/mri/surfaces/ +export SUBJECTS_DIR=$subjdir + From 3f72a55f822c46b1a9b46aa0ff50aec63246a0b2 Mon Sep 17 00:00:00 2001 From: cdla Date: Mon, 6 Oct 2014 17:12:13 -0400 Subject: [PATCH 4/7] updated voice environment --- .env/.voice_environment | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.env/.voice_environment b/.env/.voice_environment index 5e9270d..4b4f369 100644 --- a/.env/.voice_environment +++ b/.env/.voice_environment @@ -6,8 +6,9 @@ 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/miniconda/3.5.2 +module add openmind/miniconda/3.7.0 export CONDA_ENVS_PATH=/om/project/voice/env/ source activate voice_env From cc08a5405a69e004ab0f640827fbc2b202851515 Mon Sep 17 00:00:00 2001 From: cdla Date: Wed, 8 Oct 2014 11:52:46 -0400 Subject: [PATCH 5/7] voice_env updated ITK_num_threads variable --- .env/.voice_environment | 1 + 1 file changed, 1 insertion(+) diff --git a/.env/.voice_environment b/.env/.voice_environment index 4b4f369..998c4fc 100644 --- a/.env/.voice_environment +++ b/.env/.voice_environment @@ -15,6 +15,7 @@ source activate voice_env # 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="voice_env" From 1b220fc8acb66378f999a0a3b9065c93aed7f7c8 Mon Sep 17 00:00:00 2001 From: gr21783 Date: Thu, 27 Aug 2015 21:28:12 -0400 Subject: [PATCH 6/7] voice env updated --- .env/.voice_environment | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) mode change 100644 => 100755 .env/.voice_environment diff --git a/.env/.voice_environment b/.env/.voice_environment old mode 100644 new mode 100755 index 998c4fc..68b5c58 --- a/.env/.voice_environment +++ b/.env/.voice_environment @@ -8,9 +8,15 @@ 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/project/voice/env/ -source activate voice_env +export CONDA_ENVS_PATH=/om/user/gr21783/envs_python/ +source activate voice7 # Multithreading export MKL_NUM_THREADS=4 @@ -18,7 +24,13 @@ export OMP_NUM_THREADS=4 export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 # Project name for prompt -export project_name="voice_env" -subjdir=/om/project/voice/mri/surfaces/ +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 From dcb2f1dff75a4f4c8d2961374b801e9fbf2e903e Mon Sep 17 00:00:00 2001 From: gr21783 Date: Fri, 6 Nov 2015 09:50:01 -0500 Subject: [PATCH 7/7] upgraded matlab from 2013a to 2015a --- .env/.voice_environment | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.env/.voice_environment b/.env/.voice_environment index 68b5c58..3122fab 100755 --- a/.env/.voice_environment +++ b/.env/.voice_environment @@ -1,7 +1,7 @@ #!/bin/bash -module add mit/matlab/2013a +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